Starting phenix.real_space_refine
on Thu May 22 08:45:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fm6_50549/05_2025/9fm6_50549.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fm6_50549/05_2025/9fm6_50549.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fm6_50549/05_2025/9fm6_50549.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fm6_50549/05_2025/9fm6_50549.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fm6_50549/05_2025/9fm6_50549.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fm6_50549/05_2025/9fm6_50549.cif"
  }
  resolution = 2.2
  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=  -0.000 sd=   0.068
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      56      5.16       5
     C   14399      2.51       5
     N    3899      2.21       5
     O    4389      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 22743
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 412, 3249
          Classifications: {'peptide': 412}
          Link IDs: {'PTRANS': 24, 'TRANS': 387}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, G, F
  Time building chain proxies: 8.82, per 1000 atoms: 0.39
  Number of scatterers: 22743
  At special positions: 0
  Unit cell: (175.13, 176.79, 116.2, 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      56     16.00
     O    4389      8.00
     N    3899      7.00
     C   14399      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 159 " - pdb=" SG  CYS A 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 159 " - pdb=" SG  CYS C 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 159 " - pdb=" SG  CYS B 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 159 " - pdb=" SG  CYS D 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G 159 " - pdb=" SG  CYS G 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 159 " - pdb=" SG  CYS F 164 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.99
  Conformation dependent library (CDL) restraints added in 2.8 seconds
  

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5236

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 16 sheets defined
      19.4% alpha, 32.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 9
    Processing helix  chain 'A' and resid 27 through 34
    Processing helix  chain 'A' and resid 34 through 41
    Processing helix  chain 'A' and resid 97 through 107
    Processing helix  chain 'A' and resid 112 through 123
    Processing helix  chain 'A' and resid 354 through 361
    Processing helix  chain 'A' and resid 364 through 368
    Processing helix  chain 'A' and resid 372 through 381
      removed outlier: 3.558A  pdb=" N   THR A 376 " --> pdb=" O   ASP A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 393
    Processing helix  chain 'B' and resid 5 through 9
    Processing helix  chain 'B' and resid 27 through 34
    Processing helix  chain 'B' and resid 34 through 41
    Processing helix  chain 'B' and resid 97 through 107
    Processing helix  chain 'B' and resid 112 through 123
    Processing helix  chain 'B' and resid 354 through 361
    Processing helix  chain 'B' and resid 364 through 368
    Processing helix  chain 'B' and resid 372 through 381
      removed outlier: 3.558A  pdb=" N   THR B 376 " --> pdb=" O   ASP B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 393
    Processing helix  chain 'C' and resid 5 through 9
    Processing helix  chain 'C' and resid 27 through 34
    Processing helix  chain 'C' and resid 34 through 41
    Processing helix  chain 'C' and resid 97 through 107
    Processing helix  chain 'C' and resid 112 through 123
    Processing helix  chain 'C' and resid 354 through 361
    Processing helix  chain 'C' and resid 364 through 368
    Processing helix  chain 'C' and resid 372 through 381
      removed outlier: 3.558A  pdb=" N   THR C 376 " --> pdb=" O   ASP C 372 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 381 through 393
    Processing helix  chain 'D' and resid 5 through 9
    Processing helix  chain 'D' and resid 27 through 34
    Processing helix  chain 'D' and resid 34 through 41
    Processing helix  chain 'D' and resid 97 through 107
    Processing helix  chain 'D' and resid 112 through 123
    Processing helix  chain 'D' and resid 354 through 361
    Processing helix  chain 'D' and resid 364 through 368
    Processing helix  chain 'D' and resid 372 through 381
      removed outlier: 3.558A  pdb=" N   THR D 376 " --> pdb=" O   ASP D 372 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 381 through 393
    Processing helix  chain 'E' and resid 5 through 9
    Processing helix  chain 'E' and resid 27 through 34
    Processing helix  chain 'E' and resid 34 through 41
    Processing helix  chain 'E' and resid 97 through 107
    Processing helix  chain 'E' and resid 112 through 123
    Processing helix  chain 'E' and resid 354 through 361
    Processing helix  chain 'E' and resid 364 through 368
    Processing helix  chain 'E' and resid 372 through 381
      removed outlier: 3.559A  pdb=" N   THR E 376 " --> pdb=" O   ASP E 372 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 381 through 393
    Processing helix  chain 'F' and resid 5 through 9
    Processing helix  chain 'F' and resid 27 through 34
    Processing helix  chain 'F' and resid 34 through 41
    Processing helix  chain 'F' and resid 97 through 107
    Processing helix  chain 'F' and resid 112 through 123
    Processing helix  chain 'F' and resid 354 through 361
    Processing helix  chain 'F' and resid 364 through 368
    Processing helix  chain 'F' and resid 372 through 381
      removed outlier: 3.558A  pdb=" N   THR F 376 " --> pdb=" O   ASP F 372 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 381 through 393
    Processing helix  chain 'G' and resid 5 through 9
    Processing helix  chain 'G' and resid 27 through 34
    Processing helix  chain 'G' and resid 34 through 41
    Processing helix  chain 'G' and resid 97 through 107
    Processing helix  chain 'G' and resid 112 through 123
    Processing helix  chain 'G' and resid 354 through 361
    Processing helix  chain 'G' and resid 364 through 368
    Processing helix  chain 'G' and resid 372 through 381
      removed outlier: 3.559A  pdb=" N   THR G 376 " --> pdb=" O   ASP G 372 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 381 through 393
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12
    Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 96
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 91 through 96
    current: chain 'A' and resid 148 through 153
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 169 through 179
    current: chain 'A' and resid 289 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 338 through 345
    current: chain 'B' and resid 148 through 153
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 169 through 179
    current: chain 'B' and resid 289 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 338 through 345
    current: chain 'C' and resid 148 through 153
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 169 through 179
    current: chain 'C' and resid 289 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 338 through 345
    current: chain 'D' and resid 148 through 153
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 169 through 179
    current: chain 'D' and resid 289 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 338 through 345
    current: chain 'E' and resid 148 through 153
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 169 through 179
    current: chain 'E' and resid 289 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 338 through 345
    current: chain 'F' and resid 148 through 153
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 169 through 179
    current: chain 'F' and resid 289 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 338 through 345
    current: chain 'G' and resid 148 through 153
  WARNING: can't find start of bonding for strands!
    previous: chain 'G' and resid 169 through 179
    current: chain 'G' and resid 289 through 321
    Processing sheet with id=AA4, first strand: chain 'A' and resid 215 through 247
      removed outlier: 7.061A  pdb=" N   GLU A 252 " --> pdb=" O   LYS G 244 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   LYS G 244 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   GLU G 252 " --> pdb=" O   LYS F 244 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   LYS F 244 " --> pdb=" O   GLU G 252 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   GLU F 252 " --> pdb=" O   LYS E 244 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   LYS E 244 " --> pdb=" O   GLU F 252 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   GLU E 252 " --> pdb=" O   LYS D 244 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   LYS D 244 " --> pdb=" O   GLU E 252 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   GLU D 252 " --> pdb=" O   LYS C 244 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   LYS C 244 " --> pdb=" O   GLU D 252 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   GLU C 252 " --> pdb=" O   LYS B 244 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   LYS B 244 " --> pdb=" O   GLU C 252 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   GLU B 252 " --> pdb=" O   LYS A 244 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   LYS A 244 " --> pdb=" O   GLU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12
    Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 49
    Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12
    Processing sheet with id=AA8, first strand: chain 'C' and resid 47 through 49
    Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 12
    Processing sheet with id=AB1, first strand: chain 'D' and resid 47 through 49
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
    Processing sheet with id=AB3, first strand: chain 'E' and resid 47 through 49
    Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 12
    Processing sheet with id=AB5, first strand: chain 'F' and resid 47 through 49
    Processing sheet with id=AB6, first strand: chain 'G' and resid 10 through 12
    Processing sheet with id=AB7, first strand: chain 'G' and resid 47 through 49

    875 hydrogen bonds defined for protein.
    2478 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: 6.23

  Time building geometry restraints manager: 5.85 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 6571
        1.34 -     1.46: 5980
        1.46 -     1.59: 10759
        1.59 -     1.71: 0
        1.71 -     1.84: 91
  Bond restraints: 23401
  Sorted by residual:
  bond pdb=" C   ARG F 336 "
       pdb=" O   ARG F 336 "
    ideal  model  delta    sigma   weight residual
    1.235  1.215  0.019 4.70e-03 4.53e+04 1.72e+01
  bond pdb=" C   ARG E 336 "
       pdb=" O   ARG E 336 "
    ideal  model  delta    sigma   weight residual
    1.235  1.216  0.019 4.70e-03 4.53e+04 1.70e+01
  bond pdb=" C   ARG C 336 "
       pdb=" O   ARG C 336 "
    ideal  model  delta    sigma   weight residual
    1.235  1.216  0.019 4.70e-03 4.53e+04 1.63e+01
  bond pdb=" C   ARG G 336 "
       pdb=" O   ARG G 336 "
    ideal  model  delta    sigma   weight residual
    1.235  1.216  0.019 4.70e-03 4.53e+04 1.59e+01
  bond pdb=" C   ARG B 336 "
       pdb=" O   ARG B 336 "
    ideal  model  delta    sigma   weight residual
    1.235  1.216  0.018 4.70e-03 4.53e+04 1.53e+01
  ... (remaining 23396 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 26155
        1.32 -     2.64: 4310
        2.64 -     3.96: 1126
        3.96 -     5.28: 315
        5.28 -     6.60: 49
  Bond angle restraints: 31955
  Sorted by residual:
  angle pdb=" N   ALA B 310 "
        pdb=" CA  ALA B 310 "
        pdb=" C   ALA B 310 "
      ideal   model   delta    sigma   weight residual
     108.96  115.22   -6.26 1.49e+00 4.50e-01 1.76e+01
  angle pdb=" N   ALA A 310 "
        pdb=" CA  ALA A 310 "
        pdb=" C   ALA A 310 "
      ideal   model   delta    sigma   weight residual
     108.96  115.22   -6.26 1.49e+00 4.50e-01 1.76e+01
  angle pdb=" N   ALA D 310 "
        pdb=" CA  ALA D 310 "
        pdb=" C   ALA D 310 "
      ideal   model   delta    sigma   weight residual
     108.96  115.19   -6.23 1.49e+00 4.50e-01 1.75e+01
  angle pdb=" N   ALA E 310 "
        pdb=" CA  ALA E 310 "
        pdb=" C   ALA E 310 "
      ideal   model   delta    sigma   weight residual
     108.96  115.17   -6.21 1.49e+00 4.50e-01 1.74e+01
  angle pdb=" N   ALA G 310 "
        pdb=" CA  ALA G 310 "
        pdb=" C   ALA G 310 "
      ideal   model   delta    sigma   weight residual
     108.96  115.17   -6.21 1.49e+00 4.50e-01 1.74e+01
  ... (remaining 31950 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 13041
       17.93 -    35.86: 378
       35.86 -    53.80: 91
       53.80 -    71.73: 42
       71.73 -    89.66: 7
  Dihedral angle restraints: 13559
    sinusoidal: 5313
      harmonic: 8246
  Sorted by residual:
  dihedral pdb=" CA  ASP G 311 "
           pdb=" CB  ASP G 311 "
           pdb=" CG  ASP G 311 "
           pdb=" OD1 ASP G 311 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.40   56.40     1      2.00e+01 2.50e-03 1.07e+01
  dihedral pdb=" CA  ASP C 311 "
           pdb=" CB  ASP C 311 "
           pdb=" CG  ASP C 311 "
           pdb=" OD1 ASP C 311 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.39   56.39     1      2.00e+01 2.50e-03 1.07e+01
  dihedral pdb=" CA  ASP D 311 "
           pdb=" CB  ASP D 311 "
           pdb=" CG  ASP D 311 "
           pdb=" OD1 ASP D 311 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.39   56.39     1      2.00e+01 2.50e-03 1.07e+01
  ... (remaining 13556 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1820
       0.039 -    0.078: 959
       0.078 -    0.117: 417
       0.117 -    0.156: 143
       0.156 -    0.195: 14
  Chirality restraints: 3353
  Sorted by residual:
  chirality pdb=" CA  ILE G 416 "
            pdb=" N   ILE G 416 "
            pdb=" C   ILE G 416 "
            pdb=" CB  ILE G 416 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.47e-01
  chirality pdb=" CA  ILE B 416 "
            pdb=" N   ILE B 416 "
            pdb=" C   ILE B 416 "
            pdb=" CB  ILE B 416 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.39e-01
  chirality pdb=" CA  ILE F 416 "
            pdb=" N   ILE F 416 "
            pdb=" C   ILE F 416 "
            pdb=" CB  ILE F 416 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.38e-01
  ... (remaining 3350 not shown)

  Planarity restraints: 4151
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 249 "   -0.021 2.00e-02 2.50e+03   4.19e-02 1.75e+01
        pdb=" C   LEU D 249 "    0.072 2.00e-02 2.50e+03
        pdb=" O   LEU D 249 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   VAL D 250 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 249 "   -0.021 2.00e-02 2.50e+03   4.18e-02 1.75e+01
        pdb=" C   LEU B 249 "    0.072 2.00e-02 2.50e+03
        pdb=" O   LEU B 249 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   VAL B 250 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 249 "   -0.021 2.00e-02 2.50e+03   4.18e-02 1.74e+01
        pdb=" C   LEU E 249 "    0.072 2.00e-02 2.50e+03
        pdb=" O   LEU E 249 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   VAL E 250 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 4148 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     2.99: 11277
        2.99 -     3.47: 19575
        3.47 -     3.95: 38037
        3.95 -     4.42: 40659
        4.42 -     4.90: 68884
  Nonbonded interactions: 178432
  Sorted by model distance:
  nonbonded pdb=" N   ASP G 334 "
            pdb=" OD1 ASP G 334 "
     model   vdw
     2.516 3.120
  nonbonded pdb=" N   ASP E 334 "
            pdb=" OD1 ASP E 334 "
     model   vdw
     2.516 3.120
  nonbonded pdb=" N   ASP C 334 "
            pdb=" OD1 ASP C 334 "
     model   vdw
     2.516 3.120
  nonbonded pdb=" N   ASP D 334 "
            pdb=" OD1 ASP D 334 "
     model   vdw
     2.516 3.120
  nonbonded pdb=" N   ASP F 334 "
            pdb=" OD1 ASP F 334 "
     model   vdw
     2.517 3.120
  ... (remaining 178427 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: 0.18
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.840
  Check model and map are aligned:         0.170
  Set scattering table:                    0.210
  Process input model:                     41.880
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.050
  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:11.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   57.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
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      :  0.009   0.069  23408  Z= 0.474
  Angle     :  1.156   6.599  31969  Z= 0.728
  Chirality :  0.056   0.195   3353
  Planarity :  0.009   0.128   4151
  Dihedral  : 10.566  89.660   8302
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 0.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  0.29 %
    Favored  : 99.14 %
  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:  1.39 (0.15), residues: 2856
  helix: -0.37 (0.19), residues: 497
  sheet:  2.35 (0.15), residues: 994
  loop :  0.41 (0.16), residues: 1365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP B 370 
 HIS   0.004   0.002   HIS B 186 
 PHE   0.029   0.004   PHE B 321 
 TYR   0.029   0.004   TYR D  61 
 ARG   0.011   0.001   ARG B  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17054 (  875)
  hydrogen bonds       : angle       6.91411 ( 2478)
  SS BOND              : bond        0.00915 (    7)
  SS BOND              : angle       2.52641 (   14)
  covalent geometry    : bond        0.00853 (23401)
  covalent geometry    : angle       1.15547 (31955)

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

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

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  393 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 379
  time to evaluate  : 2.482 
Fit side-chains
REVERT: A    2 GLU cc_start: 0.6277 (mm-30) cc_final: 0.5308 (tt0)
REVERT: A   30 GLU cc_start: 0.5674 (mt-10) cc_final: 0.4712 (mm-30)
REVERT: A   57 MET cc_start: 0.5888 (mtp) cc_final: 0.5640 (mtm)
REVERT: A  114 LYS cc_start: 0.7161 (mmmt) cc_final: 0.6573 (mptt)
REVERT: A  135 TYR cc_start: 0.6002 (m-80) cc_final: 0.5754 (m-80)
REVERT: A  147 ASP cc_start: 0.6741 (m-30) cc_final: 0.6371 (t0)
REVERT: A  171 LYS cc_start: 0.7922 (mttt) cc_final: 0.6602 (tptm)
REVERT: A  258 GLU cc_start: 0.7588 (tt0) cc_final: 0.7341 (tt0)
REVERT: A  259 ILE cc_start: 0.7665 (mm) cc_final: 0.7341 (mm)
REVERT: A  378 GLN cc_start: 0.7017 (mt0) cc_final: 0.6214 (mm110)
REVERT: A  385 MET cc_start: 0.7902 (mmm) cc_final: 0.7196 (mmm)
REVERT: A  408 SER cc_start: 0.8268 (m) cc_final: 0.8056 (t)
REVERT: B    2 GLU cc_start: 0.6345 (mm-30) cc_final: 0.5875 (mt-10)
REVERT: B   30 GLU cc_start: 0.5601 (mt-10) cc_final: 0.4598 (mm-30)
REVERT: B   42 MET cc_start: 0.3774 (mtp) cc_final: 0.3563 (mtp)
REVERT: B  114 LYS cc_start: 0.7062 (mmmt) cc_final: 0.6471 (mptt)
REVERT: B  147 ASP cc_start: 0.6694 (m-30) cc_final: 0.6330 (t0)
REVERT: B  171 LYS cc_start: 0.7725 (mttt) cc_final: 0.6290 (tptm)
REVERT: B  258 GLU cc_start: 0.7480 (tt0) cc_final: 0.7188 (tt0)
REVERT: B  378 GLN cc_start: 0.6805 (mt0) cc_final: 0.5710 (mp10)
REVERT: C    2 GLU cc_start: 0.6227 (mm-30) cc_final: 0.5648 (mt-10)
REVERT: C   30 GLU cc_start: 0.5586 (mt-10) cc_final: 0.4667 (mm-30)
REVERT: C  114 LYS cc_start: 0.7024 (mmmt) cc_final: 0.6424 (mptt)
REVERT: C  145 ASP cc_start: 0.7116 (t0) cc_final: 0.6895 (t70)
REVERT: C  147 ASP cc_start: 0.6718 (m-30) cc_final: 0.6340 (t0)
REVERT: C  171 LYS cc_start: 0.7704 (mttt) cc_final: 0.6211 (tptp)
REVERT: C  299 LYS cc_start: 0.8049 (mttt) cc_final: 0.7773 (mttt)
REVERT: C  323 ARG cc_start: 0.6913 (mtm180) cc_final: 0.6645 (mtm-85)
REVERT: C  378 GLN cc_start: 0.6595 (mt0) cc_final: 0.5772 (mm110)
REVERT: C  407 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7511 (mt-10)
REVERT: D    2 GLU cc_start: 0.6468 (mm-30) cc_final: 0.6073 (mm-30)
REVERT: D   57 MET cc_start: 0.6171 (mtp) cc_final: 0.5924 (mtm)
REVERT: D  114 LYS cc_start: 0.7023 (mmmt) cc_final: 0.6388 (mptt)
REVERT: D  147 ASP cc_start: 0.6777 (m-30) cc_final: 0.6408 (t0)
REVERT: D  171 LYS cc_start: 0.7754 (mttt) cc_final: 0.6235 (tptm)
REVERT: D  243 ASN cc_start: 0.7114 (m110) cc_final: 0.6894 (m110)
REVERT: D  378 GLN cc_start: 0.6737 (mt0) cc_final: 0.5972 (mm110)
REVERT: D  408 SER cc_start: 0.8239 (m) cc_final: 0.8031 (t)
REVERT: E    2 GLU cc_start: 0.6214 (mm-30) cc_final: 0.5732 (mt-10)
REVERT: E   30 GLU cc_start: 0.5471 (mt-10) cc_final: 0.4561 (mm-30)
REVERT: E   57 MET cc_start: 0.6043 (mtp) cc_final: 0.5818 (mtm)
REVERT: E  114 LYS cc_start: 0.7030 (mmmt) cc_final: 0.6367 (mptt)
REVERT: E  147 ASP cc_start: 0.6733 (m-30) cc_final: 0.6196 (t0)
REVERT: E  171 LYS cc_start: 0.7705 (mttt) cc_final: 0.6277 (tptp)
REVERT: E  258 GLU cc_start: 0.7503 (tt0) cc_final: 0.7162 (tt0)
REVERT: E  378 GLN cc_start: 0.6810 (mt0) cc_final: 0.5958 (mm110)
REVERT: E  385 MET cc_start: 0.7600 (mmm) cc_final: 0.7207 (mmm)
REVERT: E  408 SER cc_start: 0.8263 (m) cc_final: 0.8038 (t)
REVERT: F    2 GLU cc_start: 0.6196 (mm-30) cc_final: 0.5369 (tt0)
REVERT: F   30 GLU cc_start: 0.5894 (mt-10) cc_final: 0.4799 (mm-30)
REVERT: F   57 MET cc_start: 0.6155 (mtp) cc_final: 0.5925 (mtp)
REVERT: F  114 LYS cc_start: 0.7313 (mmmt) cc_final: 0.6626 (mptt)
REVERT: F  147 ASP cc_start: 0.6635 (m-30) cc_final: 0.6249 (t0)
REVERT: F  171 LYS cc_start: 0.7869 (mttt) cc_final: 0.6515 (tptm)
REVERT: F  258 GLU cc_start: 0.7534 (tt0) cc_final: 0.7231 (tt0)
REVERT: F  307 GLU cc_start: 0.7989 (pt0) cc_final: 0.7773 (pt0)
REVERT: F  323 ARG cc_start: 0.7136 (mtm180) cc_final: 0.6849 (mtp180)
REVERT: F  378 GLN cc_start: 0.6710 (mt0) cc_final: 0.5849 (mm110)
REVERT: G    2 GLU cc_start: 0.6445 (mm-30) cc_final: 0.5839 (mt-10)
REVERT: G   30 GLU cc_start: 0.5569 (mt-10) cc_final: 0.4625 (mm-30)
REVERT: G  114 LYS cc_start: 0.7090 (mmmt) cc_final: 0.6458 (mptt)
REVERT: G  147 ASP cc_start: 0.6758 (m-30) cc_final: 0.6388 (t0)
REVERT: G  171 LYS cc_start: 0.7859 (mttt) cc_final: 0.6476 (tptp)
REVERT: G  378 GLN cc_start: 0.6647 (mt0) cc_final: 0.5594 (mp10)
  outliers start: 14
  outliers final: 0
  residues processed: 393
  average time/residue: 1.5159
  time to fit residues: 668.4567
Evaluate side-chains
  242 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 2.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 242 optimal weight:    0.5980
   chunk 217 optimal weight:    0.0010
   chunk 120 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 146 optimal weight:    4.9990
   chunk 116 optimal weight:    1.9990
   chunk 224 optimal weight:    0.8980
   chunk 87 optimal weight:   30.0000
   chunk 136 optimal weight:    3.9990
   chunk 167 optimal weight:    2.9990
   chunk 260 optimal weight:    6.9990
   overall best weight:    1.0990

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

Flipped N/Q/H residues before XYZ refinement:
A 174 ASN
B 338 ASN
C 174 ASN
C 338 ASN
D 174 ASN
D 231 ASN
D 338 ASN
E 174 ASN
E 243 ASN
F 174 ASN
G 243 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.162860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.133456 restraints weight = 19344.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.37
r_work: 0.3206 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015  23408  Z= 0.187
  Angle     :  0.613   4.450  31969  Z= 0.352
  Chirality :  0.047   0.149   3353
  Planarity :  0.004   0.031   4151
  Dihedral  :  4.819  16.539   3129
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 0.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  4.42 %
    Favored  : 94.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.53 (0.15), residues: 2856
  helix:  0.85 (0.21), residues: 497
  sheet:  1.74 (0.14), residues: 1176
  loop :  0.41 (0.17), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP G 370 
 HIS   0.004   0.001   HIS F 186 
 PHE   0.016   0.002   PHE G 321 
 TYR   0.018   0.002   TYR G  61 
 ARG   0.003   0.001   ARG D 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05678 (  875)
  hydrogen bonds       : angle       5.43336 ( 2478)
  SS BOND              : bond        0.00420 (    7)
  SS BOND              : angle       1.61965 (   14)
  covalent geometry    : bond        0.00291 (23401)
  covalent geometry    : angle       0.61230 (31955)

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

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

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 258
  time to evaluate  : 2.662 
Fit side-chains
REVERT: A    2 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6850 (tt0)
REVERT: A   42 MET cc_start: 0.4382 (mtp) cc_final: 0.4110 (mtp)
REVERT: A  114 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8404 (mptt)
REVERT: A  138 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7328 (mm-30)
REVERT: A  171 LYS cc_start: 0.8795 (mttt) cc_final: 0.8178 (tptp)
REVERT: A  378 GLN cc_start: 0.7756 (mt0) cc_final: 0.7504 (mm110)
REVERT: A  385 MET cc_start: 0.8920 (mmm) cc_final: 0.8450 (mmm)
REVERT: B    2 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6784 (tt0)
REVERT: B  114 LYS cc_start: 0.8619 (mmmt) cc_final: 0.8395 (mptt)
REVERT: B  138 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7030 (mm-30)
REVERT: B  171 LYS cc_start: 0.8820 (mttt) cc_final: 0.8118 (tptp)
REVERT: B  378 GLN cc_start: 0.7874 (mt0) cc_final: 0.7495 (mp10)
REVERT: C  114 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8408 (mptt)
REVERT: C  171 LYS cc_start: 0.8795 (mttt) cc_final: 0.8149 (tptm)
REVERT: C  378 GLN cc_start: 0.7657 (mt0) cc_final: 0.7400 (mm110)
REVERT: D  171 LYS cc_start: 0.8855 (mttt) cc_final: 0.8154 (tptp)
REVERT: E  114 LYS cc_start: 0.8636 (mmmt) cc_final: 0.8406 (mptt)
REVERT: E  138 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7048 (mm-30)
REVERT: E  171 LYS cc_start: 0.8878 (mttt) cc_final: 0.8120 (tptm)
REVERT: E  385 MET cc_start: 0.8852 (mmm) cc_final: 0.8531 (mmm)
REVERT: F    2 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6875 (tt0)
REVERT: F  114 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8353 (mptt)
REVERT: F  138 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7075 (mm-30)
REVERT: F  171 LYS cc_start: 0.8821 (mttt) cc_final: 0.8188 (tptp)
REVERT: F  378 GLN cc_start: 0.7723 (mt0) cc_final: 0.7456 (mm110)
REVERT: G   42 MET cc_start: 0.4503 (mtp) cc_final: 0.4189 (mtp)
REVERT: G  114 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8332 (mptt)
REVERT: G  171 LYS cc_start: 0.8808 (mttt) cc_final: 0.8168 (tptp)
REVERT: G  254 GLU cc_start: 0.7701 (tt0) cc_final: 0.7470 (tt0)
REVERT: G  378 GLN cc_start: 0.7749 (mt0) cc_final: 0.7469 (mp10)
  outliers start: 19
  outliers final: 7
  residues processed: 276
  average time/residue: 1.2591
  time to fit residues: 400.2335
Evaluate side-chains
  235 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 224
  time to evaluate  : 2.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain C residue  408 SER
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue  138 GLU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain F residue  138 GLU
Chi-restraints excluded: chain F residue  408 SER
Chi-restraints excluded: chain G residue  408 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 259 optimal weight:   10.0000
   chunk 96 optimal weight:    0.3980
   chunk 195 optimal weight:   10.0000
   chunk 146 optimal weight:    2.9990
   chunk 203 optimal weight:    4.9990
   chunk 184 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 231 optimal weight:    5.9990
   chunk 89 optimal weight:    8.9990
   chunk 239 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
A 174 ASN
A 243 ASN
B 174 ASN
B 338 ASN
C 174 ASN
C 231 ASN
C 338 ASN
D 174 ASN
D 338 ASN
E 174 ASN
E 338 ASN
F 174 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.163193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.131294 restraints weight = 19312.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.39
r_work: 0.3283 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 2.56 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021  23408  Z= 0.220
  Angle     :  0.659   5.436  31969  Z= 0.381
  Chirality :  0.050   0.150   3353
  Planarity :  0.005   0.037   4151
  Dihedral  :  5.150  18.165   3129
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 0.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  5.16 %
    Favored  : 93.41 %
  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:  1.16 (0.15), residues: 2856
  helix:  1.03 (0.22), residues: 497
  sheet:  1.24 (0.14), residues: 1204
  loop :  0.25 (0.17), residues: 1155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP G 370 
 HIS   0.009   0.002   HIS F 186 
 PHE   0.019   0.003   PHE G 321 
 TYR   0.021   0.002   TYR A  61 
 ARG   0.005   0.001   ARG C 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06629 (  875)
  hydrogen bonds       : angle       5.23156 ( 2478)
  SS BOND              : bond        0.00312 (    7)
  SS BOND              : angle       1.02120 (   14)
  covalent geometry    : bond        0.00366 (23401)
  covalent geometry    : angle       0.65891 (31955)

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

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

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 241
  time to evaluate  : 2.466 
Fit side-chains
REVERT: A    2 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6808 (tt0)
REVERT: A   30 GLU cc_start: 0.6773 (mt-10) cc_final: 0.5869 (mm-30)
REVERT: A   42 MET cc_start: 0.4458 (mtp) cc_final: 0.4143 (mtp)
REVERT: A  114 LYS cc_start: 0.8602 (mmmt) cc_final: 0.8392 (mptt)
REVERT: A  171 LYS cc_start: 0.8807 (mttt) cc_final: 0.8219 (tptp)
REVERT: A  258 GLU cc_start: 0.8384 (tt0) cc_final: 0.8155 (tt0)
REVERT: A  378 GLN cc_start: 0.7887 (mt0) cc_final: 0.7650 (mm110)
REVERT: A  385 MET cc_start: 0.8929 (mmm) cc_final: 0.8400 (mmm)
REVERT: B    2 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6779 (tt0)
REVERT: B   10 ARG cc_start: 0.2884 (OUTLIER) cc_final: 0.2101 (ptt90)
REVERT: B   42 MET cc_start: 0.4167 (mtp) cc_final: 0.3680 (mtm)
REVERT: B  114 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8393 (mptt)
REVERT: B  171 LYS cc_start: 0.8803 (mttt) cc_final: 0.8117 (tptm)
REVERT: C  114 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8406 (mptt)
REVERT: C  171 LYS cc_start: 0.8762 (mttt) cc_final: 0.8119 (tptm)
REVERT: C  242 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7766 (ttmt)
REVERT: C  378 GLN cc_start: 0.7835 (mt0) cc_final: 0.7499 (mm110)
REVERT: D    2 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6640 (tt0)
REVERT: D  171 LYS cc_start: 0.8811 (mttt) cc_final: 0.8140 (tptm)
REVERT: E   42 MET cc_start: 0.4443 (mtp) cc_final: 0.4076 (mtp)
REVERT: E   57 MET cc_start: 0.6659 (mtm) cc_final: 0.6431 (mtp)
REVERT: E  114 LYS cc_start: 0.8615 (mmmt) cc_final: 0.8376 (mptt)
REVERT: E  138 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7002 (mm-30)
REVERT: E  171 LYS cc_start: 0.8830 (mttt) cc_final: 0.8098 (tptm)
REVERT: E  385 MET cc_start: 0.8882 (mmm) cc_final: 0.8354 (mmm)
REVERT: F    2 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6852 (tt0)
REVERT: F   92 ASP cc_start: 0.8707 (m-30) cc_final: 0.8503 (m-30)
REVERT: F  114 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8353 (mptt)
REVERT: F  171 LYS cc_start: 0.8805 (mttt) cc_final: 0.8215 (tptm)
REVERT: F  378 GLN cc_start: 0.7860 (mt0) cc_final: 0.7562 (mm110)
REVERT: G   42 MET cc_start: 0.4572 (mtp) cc_final: 0.4288 (mtp)
REVERT: G  138 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7400 (mm-30)
REVERT: G  171 LYS cc_start: 0.8803 (mttt) cc_final: 0.8125 (tptp)
REVERT: G  254 GLU cc_start: 0.7761 (tt0) cc_final: 0.7513 (tt0)
REVERT: G  378 GLN cc_start: 0.7795 (mt0) cc_final: 0.7416 (mp10)
  outliers start: 35
  outliers final: 19
  residues processed: 264
  average time/residue: 1.2051
  time to fit residues: 367.2390
Evaluate side-chains
  249 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 226
  time to evaluate  : 2.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain B residue   10 ARG
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue  147 ASP
Chi-restraints excluded: chain D residue    2 GLU
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue  350 ASP
Chi-restraints excluded: chain D residue  408 SER
Chi-restraints excluded: chain E residue    2 GLU
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue   55 VAL
Chi-restraints excluded: chain E residue  138 GLU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue  239 VAL
Chi-restraints excluded: chain G residue   55 VAL
Chi-restraints excluded: chain G residue  138 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 206 optimal weight:   20.0000
   chunk 14 optimal weight:    5.9990
   chunk 168 optimal weight:   10.0000
   chunk 152 optimal weight:    9.9990
   chunk 209 optimal weight:    9.9990
   chunk 236 optimal weight:   10.0000
   chunk 213 optimal weight:   10.0000
   chunk 271 optimal weight:   10.0000
   chunk 81 optimal weight:    6.9990
   chunk 204 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 174 ASN
B 231 ASN
B 338 ASN
B 341 HIS
B 378 GLN
C 174 ASN
C 231 ASN
C 338 ASN
D 174 ASN
D 231 ASN
D 338 ASN
E 174 ASN
E 338 ASN
F 174 ASN
F 231 ASN
F 341 HIS
G 338 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.157990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.125542 restraints weight = 19425.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 1.45
r_work: 0.3214 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 2.56 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.052  23408  Z= 0.397
  Angle     :  0.968   8.506  31969  Z= 0.554
  Chirality :  0.065   0.305   3353
  Planarity :  0.008   0.060   4151
  Dihedral  :  5.978  21.584   3129
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  :  5.16 %
    Favored  : 92.84 %
  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:  0.45 (0.14), residues: 2856
  helix: -0.00 (0.20), residues: 497
  sheet:  1.34 (0.15), residues: 1036
  loop : -0.39 (0.15), residues: 1323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.004   TRP G 370 
 HIS   0.013   0.003   HIS F 186 
 PHE   0.029   0.005   PHE E 245 
 TYR   0.029   0.004   TYR A 233 
 ARG   0.011   0.002   ARG G 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09427 (  875)
  hydrogen bonds       : angle       5.63182 ( 2478)
  SS BOND              : bond        0.00549 (    7)
  SS BOND              : angle       1.45758 (   14)
  covalent geometry    : bond        0.00763 (23401)
  covalent geometry    : angle       0.96769 (31955)

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

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

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 227
  time to evaluate  : 2.430 
Fit side-chains
REVERT: A   42 MET cc_start: 0.4771 (mtp) cc_final: 0.4417 (mtp)
REVERT: A  114 LYS cc_start: 0.8600 (mmmt) cc_final: 0.8381 (mptt)
REVERT: A  138 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7484 (mm-30)
REVERT: A  152 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8222 (ttt180)
REVERT: A  171 LYS cc_start: 0.8804 (mttt) cc_final: 0.8146 (tptm)
REVERT: A  258 GLU cc_start: 0.8390 (tt0) cc_final: 0.8171 (tt0)
REVERT: A  378 GLN cc_start: 0.8066 (mt0) cc_final: 0.7649 (mm110)
REVERT: B    2 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6736 (tt0)
REVERT: B   10 ARG cc_start: 0.3000 (OUTLIER) cc_final: 0.2254 (ptt90)
REVERT: B   42 MET cc_start: 0.4521 (mtp) cc_final: 0.3875 (mtp)
REVERT: B  114 LYS cc_start: 0.8599 (mmmt) cc_final: 0.8339 (mptt)
REVERT: B  138 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.6996 (mm-30)
REVERT: B  171 LYS cc_start: 0.8791 (mttt) cc_final: 0.8035 (tptp)
REVERT: B  277 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8316 (tt)
REVERT: C  114 LYS cc_start: 0.8616 (mmmt) cc_final: 0.8401 (mptt)
REVERT: C  134 GLN cc_start: 0.6913 (pm20) cc_final: 0.6428 (mm-40)
REVERT: C  171 LYS cc_start: 0.8822 (mttt) cc_final: 0.8087 (tptm)
REVERT: C  277 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8620 (tt)
REVERT: C  378 GLN cc_start: 0.8009 (mt0) cc_final: 0.7536 (mm110)
REVERT: D    2 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6561 (tt0)
REVERT: D  138 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7261 (mm-30)
REVERT: D  171 LYS cc_start: 0.8831 (mttt) cc_final: 0.8080 (tptp)
REVERT: E   42 MET cc_start: 0.4451 (mtp) cc_final: 0.4040 (mtp)
REVERT: E  114 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8355 (mptt)
REVERT: E  138 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7010 (mm-30)
REVERT: E  171 LYS cc_start: 0.8829 (mttt) cc_final: 0.8038 (tptm)
REVERT: E  385 MET cc_start: 0.8872 (mmm) cc_final: 0.8405 (mmm)
REVERT: F    2 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6856 (tt0)
REVERT: F  114 LYS cc_start: 0.8555 (mmmt) cc_final: 0.8308 (mptt)
REVERT: F  138 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7213 (mm-30)
REVERT: F  171 LYS cc_start: 0.8830 (mttt) cc_final: 0.8164 (tptp)
REVERT: F  378 GLN cc_start: 0.8115 (mt0) cc_final: 0.7634 (mm110)
REVERT: G   10 ARG cc_start: 0.2630 (OUTLIER) cc_final: 0.2311 (ptt90)
REVERT: G   42 MET cc_start: 0.4526 (mtp) cc_final: 0.4225 (mtp)
REVERT: G   57 MET cc_start: 0.6649 (mtm) cc_final: 0.6078 (mtp)
REVERT: G  138 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7374 (mm-30)
REVERT: G  171 LYS cc_start: 0.8844 (mttt) cc_final: 0.8088 (tptp)
REVERT: G  378 GLN cc_start: 0.8046 (mt0) cc_final: 0.7599 (mm110)
  outliers start: 49
  outliers final: 21
  residues processed: 263
  average time/residue: 1.2702
  time to fit residues: 383.5987
Evaluate side-chains
  253 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 220
  time to evaluate  : 2.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain B residue   10 ARG
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue  147 ASP
Chi-restraints excluded: chain C residue  277 LEU
Chi-restraints excluded: chain D residue    2 GLU
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue  138 GLU
Chi-restraints excluded: chain D residue  277 LEU
Chi-restraints excluded: chain E residue    2 GLU
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue   55 VAL
Chi-restraints excluded: chain E residue  138 GLU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   89 SER
Chi-restraints excluded: chain F residue  138 GLU
Chi-restraints excluded: chain F residue  239 VAL
Chi-restraints excluded: chain G residue   10 ARG
Chi-restraints excluded: chain G residue   55 VAL
Chi-restraints excluded: chain G residue   89 SER
Chi-restraints excluded: chain G residue  138 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 156 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 202 optimal weight:    5.9990
   chunk 190 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 249 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 149 optimal weight:    7.9990
   chunk 223 optimal weight:    7.9990
   chunk 39 optimal weight:    7.9990
   chunk 97 optimal weight:    9.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 174 ASN
B 338 ASN
C 174 ASN
C 231 ASN
D 338 ASN
E 174 ASN
F 174 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.160853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.129088 restraints weight = 19391.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 1.32
r_work: 0.3267 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 2.47 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  23408  Z= 0.242
  Angle     :  0.703   5.981  31969  Z= 0.405
  Chirality :  0.051   0.252   3353
  Planarity :  0.005   0.035   4151
  Dihedral  :  5.446  19.411   3129
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 1.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  :  5.89 %
    Favored  : 92.26 %
  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:  0.61 (0.14), residues: 2856
  helix:  0.41 (0.21), residues: 497
  sheet:  1.15 (0.14), residues: 1176
  loop : -0.29 (0.16), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP G 370 
 HIS   0.007   0.002   HIS C 186 
 PHE   0.018   0.003   PHE G 321 
 TYR   0.015   0.003   TYR C 215 
 ARG   0.004   0.001   ARG B 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06830 (  875)
  hydrogen bonds       : angle       5.33387 ( 2478)
  SS BOND              : bond        0.00285 (    7)
  SS BOND              : angle       1.01742 (   14)
  covalent geometry    : bond        0.00412 (23401)
  covalent geometry    : angle       0.70311 (31955)

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

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

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 231
  time to evaluate  : 2.660 
Fit side-chains
REVERT: A   30 GLU cc_start: 0.6651 (mt-10) cc_final: 0.5716 (mm-30)
REVERT: A   42 MET cc_start: 0.4692 (mtp) cc_final: 0.4359 (mtp)
REVERT: A  114 LYS cc_start: 0.8582 (mmmt) cc_final: 0.8377 (mptt)
REVERT: A  138 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7420 (mm-30)
REVERT: A  171 LYS cc_start: 0.8817 (mttt) cc_final: 0.8160 (tptm)
REVERT: A  258 GLU cc_start: 0.8341 (tt0) cc_final: 0.8118 (tt0)
REVERT: A  378 GLN cc_start: 0.8016 (mt0) cc_final: 0.7636 (mm110)
REVERT: A  385 MET cc_start: 0.8917 (mmm) cc_final: 0.8380 (mmm)
REVERT: B    2 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6761 (tt0)
REVERT: B   10 ARG cc_start: 0.2551 (OUTLIER) cc_final: 0.1828 (ptt90)
REVERT: B   42 MET cc_start: 0.4461 (mtp) cc_final: 0.3808 (mtp)
REVERT: B  114 LYS cc_start: 0.8581 (mmmt) cc_final: 0.8319 (mptt)
REVERT: B  138 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7028 (mm-30)
REVERT: B  171 LYS cc_start: 0.8778 (mttt) cc_final: 0.8026 (tptp)
REVERT: B  277 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8156 (tt)
REVERT: C  114 LYS cc_start: 0.8620 (mmmt) cc_final: 0.8403 (mptt)
REVERT: C  171 LYS cc_start: 0.8815 (mttt) cc_final: 0.8082 (tptm)
REVERT: C  242 LYS cc_start: 0.8233 (ttmm) cc_final: 0.7880 (ttmt)
REVERT: C  378 GLN cc_start: 0.7940 (mt0) cc_final: 0.7481 (mm110)
REVERT: D    2 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6581 (tt0)
REVERT: D  171 LYS cc_start: 0.8821 (mttt) cc_final: 0.8063 (tptm)
REVERT: D  277 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8399 (tt)
REVERT: E   42 MET cc_start: 0.4384 (mtp) cc_final: 0.3954 (mtp)
REVERT: E   57 MET cc_start: 0.6577 (mtm) cc_final: 0.6364 (mtp)
REVERT: E  114 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8353 (mptt)
REVERT: E  138 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7005 (mm-30)
REVERT: E  171 LYS cc_start: 0.8816 (mttt) cc_final: 0.8043 (tptm)
REVERT: E  385 MET cc_start: 0.8843 (mmm) cc_final: 0.8363 (mmm)
REVERT: F  114 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8317 (mptt)
REVERT: F  171 LYS cc_start: 0.8824 (mttt) cc_final: 0.8153 (tptm)
REVERT: F  378 GLN cc_start: 0.8056 (mt0) cc_final: 0.7594 (mm110)
REVERT: G   42 MET cc_start: 0.4465 (mtp) cc_final: 0.4167 (mtp)
REVERT: G   57 MET cc_start: 0.6699 (mtm) cc_final: 0.6305 (mtp)
REVERT: G  138 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7376 (mm-30)
REVERT: G  171 LYS cc_start: 0.8841 (mttt) cc_final: 0.8104 (tptp)
REVERT: G  378 GLN cc_start: 0.7902 (mt0) cc_final: 0.7512 (mm110)
  outliers start: 45
  outliers final: 15
  residues processed: 264
  average time/residue: 1.2573
  time to fit residues: 382.0694
Evaluate side-chains
  243 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 220
  time to evaluate  : 2.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain B residue   10 ARG
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  147 ASP
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain C residue    2 GLU
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain D residue    2 GLU
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue  277 LEU
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue   55 VAL
Chi-restraints excluded: chain E residue  138 GLU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  277 LEU
Chi-restraints excluded: chain F residue   89 SER
Chi-restraints excluded: chain G residue   55 VAL
Chi-restraints excluded: chain G residue   89 SER
Chi-restraints excluded: chain G residue  138 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 106 optimal weight:    7.9990
   chunk 245 optimal weight:    0.9990
   chunk 146 optimal weight:    0.9980
   chunk 175 optimal weight:   20.0000
   chunk 226 optimal weight:    8.9990
   chunk 133 optimal weight:    7.9990
   chunk 14 optimal weight:    7.9990
   chunk 256 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   chunk 138 optimal weight:    9.9990
   chunk 104 optimal weight:    5.9990
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
B 174 ASN
B 338 ASN
C 174 ASN
C 231 ASN
D 231 ASN
D 338 ASN
E 174 ASN
E 231 ASN
E 338 ASN
F 174 ASN
F 231 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.158851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.126739 restraints weight = 19264.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 1.38
r_work: 0.3241 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 2.40 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  23408  Z= 0.314
  Angle     :  0.829   7.305  31969  Z= 0.475
  Chirality :  0.057   0.337   3353
  Planarity :  0.006   0.046   4151
  Dihedral  :  5.743  20.216   3129
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  6.47 %
    Favored  : 91.77 %
  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:  0.47 (0.14), residues: 2856
  helix:  0.12 (0.20), residues: 497
  sheet:  1.14 (0.14), residues: 1176
  loop : -0.39 (0.16), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP G 370 
 HIS   0.007   0.002   HIS A 186 
 PHE   0.020   0.004   PHE F 245 
 TYR   0.021   0.003   TYR A 233 
 ARG   0.007   0.001   ARG B 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08326 (  875)
  hydrogen bonds       : angle       5.47203 ( 2478)
  SS BOND              : bond        0.00361 (    7)
  SS BOND              : angle       1.16887 (   14)
  covalent geometry    : bond        0.00572 (23401)
  covalent geometry    : angle       0.82919 (31955)

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

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

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 225
  time to evaluate  : 2.392 
Fit side-chains
REVERT: A   42 MET cc_start: 0.4724 (mtp) cc_final: 0.4381 (mtp)
REVERT: A  114 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8379 (mptt)
REVERT: A  138 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7425 (mm-30)
REVERT: A  171 LYS cc_start: 0.8801 (mttt) cc_final: 0.8135 (tptm)
REVERT: A  258 GLU cc_start: 0.8356 (tt0) cc_final: 0.8142 (tt0)
REVERT: A  378 GLN cc_start: 0.8029 (mt0) cc_final: 0.7617 (mm110)
REVERT: B    2 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6718 (tt0)
REVERT: B   10 ARG cc_start: 0.2643 (OUTLIER) cc_final: 0.1911 (ptt90)
REVERT: B   42 MET cc_start: 0.4450 (mtp) cc_final: 0.3907 (mtp)
REVERT: B  114 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8291 (mptt)
REVERT: B  138 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.6986 (mm-30)
REVERT: B  171 LYS cc_start: 0.8754 (mttt) cc_final: 0.7973 (tptp)
REVERT: B  277 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8251 (tt)
REVERT: C  114 LYS cc_start: 0.8599 (mmmt) cc_final: 0.8371 (mptt)
REVERT: C  171 LYS cc_start: 0.8815 (mttt) cc_final: 0.8065 (tptm)
REVERT: C  242 LYS cc_start: 0.8251 (ttmm) cc_final: 0.7893 (ttmt)
REVERT: C  378 GLN cc_start: 0.7996 (mt0) cc_final: 0.7540 (mm110)
REVERT: D    2 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6574 (tt0)
REVERT: D  138 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7217 (mm-30)
REVERT: D  171 LYS cc_start: 0.8801 (mttt) cc_final: 0.8033 (tptp)
REVERT: E   10 ARG cc_start: 0.2588 (OUTLIER) cc_final: 0.1883 (ptt180)
REVERT: E   42 MET cc_start: 0.4553 (mtp) cc_final: 0.4134 (mtp)
REVERT: E   57 MET cc_start: 0.6575 (mtm) cc_final: 0.6327 (mtp)
REVERT: E  114 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8330 (mptt)
REVERT: E  138 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7002 (mm-30)
REVERT: E  171 LYS cc_start: 0.8795 (mttt) cc_final: 0.8020 (tptm)
REVERT: E  385 MET cc_start: 0.8840 (mmm) cc_final: 0.8396 (mmm)
REVERT: F    2 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6586 (mm-30)
REVERT: F  114 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8285 (mptt)
REVERT: F  138 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7171 (mm-30)
REVERT: F  152 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7603 (ttt180)
REVERT: F  171 LYS cc_start: 0.8874 (mttt) cc_final: 0.8175 (tptp)
REVERT: F  378 GLN cc_start: 0.8013 (mt0) cc_final: 0.7521 (mm110)
REVERT: G   42 MET cc_start: 0.4434 (mtp) cc_final: 0.4132 (mtp)
REVERT: G   57 MET cc_start: 0.6726 (mtm) cc_final: 0.6270 (mtp)
REVERT: G  138 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7368 (mm-30)
REVERT: G  171 LYS cc_start: 0.8847 (mttt) cc_final: 0.8087 (tptp)
REVERT: G  378 GLN cc_start: 0.7931 (mt0) cc_final: 0.7531 (mm110)
  outliers start: 43
  outliers final: 19
  residues processed: 261
  average time/residue: 1.2284
  time to fit residues: 371.2150
Evaluate side-chains
  250 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 219
  time to evaluate  : 2.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain B residue   10 ARG
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain D residue    2 GLU
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue  138 GLU
Chi-restraints excluded: chain E residue   10 ARG
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue   55 VAL
Chi-restraints excluded: chain E residue  138 GLU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  277 LEU
Chi-restraints excluded: chain F residue    2 GLU
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   89 SER
Chi-restraints excluded: chain F residue  138 GLU
Chi-restraints excluded: chain F residue  152 ARG
Chi-restraints excluded: chain F residue  239 VAL
Chi-restraints excluded: chain G residue   55 VAL
Chi-restraints excluded: chain G residue   89 SER
Chi-restraints excluded: chain G residue   91 LEU
Chi-restraints excluded: chain G residue  138 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 152 optimal weight:    8.9990
   chunk 178 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 213 optimal weight:    7.9990
   chunk 49 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 142 optimal weight:    7.9990
   chunk 179 optimal weight:    1.9990
   chunk 187 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 185 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 174 ASN
B 338 ASN
C 174 ASN
C 231 ASN
D 231 ASN
D 338 ASN
E 174 ASN
E 231 ASN
F 174 ASN
F 231 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.161047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.129735 restraints weight = 19499.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.19
r_work: 0.3248 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  23408  Z= 0.224
  Angle     :  0.671   5.454  31969  Z= 0.385
  Chirality :  0.050   0.219   3353
  Planarity :  0.005   0.033   4151
  Dihedral  :  5.344  18.921   3129
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 1.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  7.04 %
    Favored  : 91.81 %
  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:  0.55 (0.14), residues: 2856
  helix:  0.51 (0.21), residues: 497
  sheet:  1.11 (0.14), residues: 1176
  loop : -0.40 (0.16), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP G 370 
 HIS   0.006   0.001   HIS C 186 
 PHE   0.017   0.002   PHE D 321 
 TYR   0.015   0.002   TYR A  61 
 ARG   0.003   0.000   ARG B 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06519 (  875)
  hydrogen bonds       : angle       5.26879 ( 2478)
  SS BOND              : bond        0.00183 (    7)
  SS BOND              : angle       0.85824 (   14)
  covalent geometry    : bond        0.00378 (23401)
  covalent geometry    : angle       0.67090 (31955)

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

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

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 222
  time to evaluate  : 2.501 
Fit side-chains
REVERT: A   30 GLU cc_start: 0.6722 (mt-10) cc_final: 0.5813 (mm-30)
REVERT: A   42 MET cc_start: 0.4642 (mtp) cc_final: 0.4286 (mtp)
REVERT: A  114 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8487 (mptt)
REVERT: A  138 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7496 (mm-30)
REVERT: A  171 LYS cc_start: 0.8921 (mttt) cc_final: 0.8248 (tptm)
REVERT: A  378 GLN cc_start: 0.8105 (mt0) cc_final: 0.7699 (mm110)
REVERT: A  385 MET cc_start: 0.8946 (mmm) cc_final: 0.8438 (mmm)
REVERT: B    2 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6795 (tt0)
REVERT: B   10 ARG cc_start: 0.2662 (OUTLIER) cc_final: 0.1929 (ptt90)
REVERT: B   42 MET cc_start: 0.4435 (mtp) cc_final: 0.3887 (mtp)
REVERT: B  114 LYS cc_start: 0.8662 (mmmt) cc_final: 0.8421 (mptt)
REVERT: B  171 LYS cc_start: 0.8831 (mttt) cc_final: 0.8086 (tptp)
REVERT: B  277 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8123 (tt)
REVERT: B  378 GLN cc_start: 0.8020 (tp40) cc_final: 0.7770 (mp10)
REVERT: C  171 LYS cc_start: 0.8902 (mttt) cc_final: 0.8172 (tptp)
REVERT: C  242 LYS cc_start: 0.8319 (ttmm) cc_final: 0.8023 (ttmt)
REVERT: C  378 GLN cc_start: 0.8049 (mt0) cc_final: 0.7598 (mm110)
REVERT: D    2 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6645 (tt0)
REVERT: D  171 LYS cc_start: 0.8871 (mttt) cc_final: 0.8135 (tptm)
REVERT: E   10 ARG cc_start: 0.2597 (OUTLIER) cc_final: 0.1866 (ptt180)
REVERT: E   42 MET cc_start: 0.4472 (mtp) cc_final: 0.4100 (mtp)
REVERT: E  114 LYS cc_start: 0.8716 (mmmt) cc_final: 0.8456 (mptt)
REVERT: E  138 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7087 (mm-30)
REVERT: E  171 LYS cc_start: 0.8895 (mttt) cc_final: 0.8147 (tptm)
REVERT: E  385 MET cc_start: 0.8864 (mmm) cc_final: 0.8377 (mmm)
REVERT: F  114 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8421 (mptt)
REVERT: F  171 LYS cc_start: 0.8952 (mttt) cc_final: 0.8272 (tptp)
REVERT: F  378 GLN cc_start: 0.8096 (mt0) cc_final: 0.7665 (mm110)
REVERT: G   42 MET cc_start: 0.4521 (mtp) cc_final: 0.4221 (mtp)
REVERT: G   57 MET cc_start: 0.6887 (mtm) cc_final: 0.6470 (mtp)
REVERT: G  138 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7475 (mm-30)
REVERT: G  171 LYS cc_start: 0.8942 (mttt) cc_final: 0.8197 (tptp)
REVERT: G  242 LYS cc_start: 0.8332 (ttpt) cc_final: 0.8058 (ttpp)
REVERT: G  254 GLU cc_start: 0.7930 (tt0) cc_final: 0.7692 (tt0)
REVERT: G  378 GLN cc_start: 0.8004 (mt0) cc_final: 0.7637 (mm110)
  outliers start: 28
  outliers final: 17
  residues processed: 245
  average time/residue: 1.2629
  time to fit residues: 356.0942
Evaluate side-chains
  240 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 216
  time to evaluate  : 2.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain B residue   10 ARG
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  147 ASP
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue  147 ASP
Chi-restraints excluded: chain C residue  350 ASP
Chi-restraints excluded: chain D residue    2 GLU
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain E residue   10 ARG
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue   55 VAL
Chi-restraints excluded: chain E residue  138 GLU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  277 LEU
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   89 SER
Chi-restraints excluded: chain G residue  138 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 262 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 210 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 157 optimal weight:    3.9990
   chunk 133 optimal weight:    8.9990
   chunk 211 optimal weight:    0.6980
   chunk 261 optimal weight:    7.9990
   chunk 228 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
B 174 ASN
B 338 ASN
C 231 ASN
D 231 ASN
D 338 ASN
E 174 ASN
E 231 ASN
E 338 ASN
F 174 ASN
F 231 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.163168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.132101 restraints weight = 19486.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.26
r_work: 0.3315 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 2.32 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  23408  Z= 0.181
  Angle     :  0.591   5.472  31969  Z= 0.338
  Chirality :  0.047   0.146   3353
  Planarity :  0.004   0.032   4151
  Dihedral  :  4.999  18.288   3129
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 1.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  7.25 %
    Favored  : 91.73 %
  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:  0.70 (0.15), residues: 2856
  helix:  0.92 (0.21), residues: 497
  sheet:  1.03 (0.14), residues: 1204
  loop : -0.28 (0.16), residues: 1155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP G 370 
 HIS   0.004   0.001   HIS F 186 
 PHE   0.013   0.002   PHE D 321 
 TYR   0.012   0.002   TYR C  61 
 ARG   0.002   0.000   ARG C 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05533 (  875)
  hydrogen bonds       : angle       5.08878 ( 2478)
  SS BOND              : bond        0.00110 (    7)
  SS BOND              : angle       0.67967 (   14)
  covalent geometry    : bond        0.00299 (23401)
  covalent geometry    : angle       0.59101 (31955)

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

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

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 229
  time to evaluate  : 2.477 
Fit side-chains
REVERT: A   30 GLU cc_start: 0.6585 (mt-10) cc_final: 0.5679 (mm-30)
REVERT: A   42 MET cc_start: 0.4564 (mtp) cc_final: 0.4125 (mtp)
REVERT: A  114 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8363 (mptt)
REVERT: A  171 LYS cc_start: 0.8829 (mttt) cc_final: 0.8138 (tptm)
REVERT: A  378 GLN cc_start: 0.7909 (mt0) cc_final: 0.7485 (mm110)
REVERT: A  385 MET cc_start: 0.8876 (mmm) cc_final: 0.8369 (mmm)
REVERT: B    2 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6735 (tt0)
REVERT: B   10 ARG cc_start: 0.2454 (OUTLIER) cc_final: 0.1761 (ptt90)
REVERT: B   42 MET cc_start: 0.4325 (mtp) cc_final: 0.3766 (mtp)
REVERT: B  114 LYS cc_start: 0.8561 (mmmt) cc_final: 0.8296 (mptt)
REVERT: B  171 LYS cc_start: 0.8713 (mttt) cc_final: 0.7950 (tptp)
REVERT: B  277 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.7983 (tt)
REVERT: B  378 GLN cc_start: 0.7879 (tp40) cc_final: 0.7629 (mp10)
REVERT: C  171 LYS cc_start: 0.8799 (mttt) cc_final: 0.8038 (tptm)
REVERT: C  242 LYS cc_start: 0.8198 (ttmm) cc_final: 0.7858 (ttmt)
REVERT: C  277 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8341 (tp)
REVERT: C  378 GLN cc_start: 0.7803 (mt0) cc_final: 0.7407 (mm110)
REVERT: D    2 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6533 (tt0)
REVERT: D  171 LYS cc_start: 0.8758 (mttt) cc_final: 0.8001 (tptp)
REVERT: E   10 ARG cc_start: 0.2539 (OUTLIER) cc_final: 0.1886 (ptt180)
REVERT: E   42 MET cc_start: 0.4295 (mtp) cc_final: 0.3901 (mtp)
REVERT: E  114 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8324 (mptt)
REVERT: E  171 LYS cc_start: 0.8784 (mttt) cc_final: 0.8003 (tptm)
REVERT: E  385 MET cc_start: 0.8797 (mmm) cc_final: 0.8384 (mmm)
REVERT: F  114 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8280 (mptt)
REVERT: F  138 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7146 (mm-30)
REVERT: F  171 LYS cc_start: 0.8856 (mttt) cc_final: 0.8146 (tptp)
REVERT: F  378 GLN cc_start: 0.7870 (mt0) cc_final: 0.7413 (mm110)
REVERT: G   42 MET cc_start: 0.4466 (mtp) cc_final: 0.4170 (mtp)
REVERT: G   57 MET cc_start: 0.6752 (mtm) cc_final: 0.6397 (mtp)
REVERT: G  138 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7342 (mm-30)
REVERT: G  171 LYS cc_start: 0.8826 (mttt) cc_final: 0.8059 (tptp)
REVERT: G  242 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7828 (ttpp)
REVERT: G  254 GLU cc_start: 0.7742 (tt0) cc_final: 0.7509 (tt0)
REVERT: G  378 GLN cc_start: 0.7852 (mt0) cc_final: 0.7506 (tp40)
  outliers start: 25
  outliers final: 10
  residues processed: 248
  average time/residue: 1.2040
  time to fit residues: 345.2981
Evaluate side-chains
  238 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 221
  time to evaluate  : 2.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain B residue   10 ARG
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue  147 ASP
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain C residue  147 ASP
Chi-restraints excluded: chain C residue  277 LEU
Chi-restraints excluded: chain D residue    2 GLU
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain E residue   10 ARG
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   89 SER
Chi-restraints excluded: chain F residue  138 GLU
Chi-restraints excluded: chain G residue   55 VAL
Chi-restraints excluded: chain G residue   89 SER
Chi-restraints excluded: chain G residue  138 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 265 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   chunk 220 optimal weight:   10.0000
   chunk 69 optimal weight:    2.9990
   chunk 114 optimal weight:    0.0040
   chunk 123 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 270 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.8000

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

Flipped N/Q/H residues before XYZ refinement:
B 174 ASN
B 231 ASN
B 338 ASN
C 174 ASN
C 231 ASN
D 132 HIS
D 231 ASN
D 338 ASN
E 174 ASN
E 231 ASN
E 338 ASN
F 174 ASN
F 231 ASN
G 338 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.162604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.130616 restraints weight = 19440.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 1.38
r_work: 0.3296 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 2.39 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  23408  Z= 0.194
  Angle     :  0.609   5.133  31969  Z= 0.349
  Chirality :  0.048   0.145   3353
  Planarity :  0.004   0.033   4151
  Dihedral  :  5.025  18.241   3129
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  7.70 %
    Favored  : 91.49 %
  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:  0.70 (0.15), residues: 2856
  helix:  0.96 (0.21), residues: 497
  sheet:  1.09 (0.14), residues: 1176
  loop : -0.35 (0.16), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP G 370 
 HIS   0.005   0.001   HIS E 186 
 PHE   0.015   0.002   PHE C 321 
 TYR   0.013   0.002   TYR C  61 
 ARG   0.002   0.000   ARG F 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05953 (  875)
  hydrogen bonds       : angle       5.07095 ( 2478)
  SS BOND              : bond        0.00139 (    7)
  SS BOND              : angle       0.70494 (   14)
  covalent geometry    : bond        0.00322 (23401)
  covalent geometry    : angle       0.60936 (31955)

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

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

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 221
  time to evaluate  : 2.480 
Fit side-chains
REVERT: A   30 GLU cc_start: 0.6617 (mt-10) cc_final: 0.5677 (mm-30)
REVERT: A   42 MET cc_start: 0.4598 (mtp) cc_final: 0.4230 (mtp)
REVERT: A  114 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8369 (mptt)
REVERT: A  171 LYS cc_start: 0.8829 (mttt) cc_final: 0.8127 (tptm)
REVERT: A  378 GLN cc_start: 0.7923 (mt0) cc_final: 0.7497 (mm110)
REVERT: A  385 MET cc_start: 0.8879 (mmm) cc_final: 0.8370 (mmm)
REVERT: B    2 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6734 (tt0)
REVERT: B   10 ARG cc_start: 0.2478 (OUTLIER) cc_final: 0.1793 (ptt90)
REVERT: B   42 MET cc_start: 0.4352 (mtp) cc_final: 0.3785 (mtp)
REVERT: B  171 LYS cc_start: 0.8744 (mttt) cc_final: 0.7963 (tptp)
REVERT: B  277 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8082 (tt)
REVERT: B  378 GLN cc_start: 0.7878 (tp40) cc_final: 0.7629 (mp10)
REVERT: C  171 LYS cc_start: 0.8789 (mttt) cc_final: 0.8021 (tptp)
REVERT: C  242 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7875 (ttmt)
REVERT: C  378 GLN cc_start: 0.7811 (mt0) cc_final: 0.7409 (mm110)
REVERT: D    2 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6542 (tt0)
REVERT: D  171 LYS cc_start: 0.8779 (mttt) cc_final: 0.8013 (tptm)
REVERT: E   10 ARG cc_start: 0.2614 (OUTLIER) cc_final: 0.1967 (ptt180)
REVERT: E   42 MET cc_start: 0.4300 (mtp) cc_final: 0.3877 (mtp)
REVERT: E  171 LYS cc_start: 0.8814 (mttt) cc_final: 0.8015 (tptm)
REVERT: E  277 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8366 (tp)
REVERT: E  385 MET cc_start: 0.8800 (mmm) cc_final: 0.8375 (mmm)
REVERT: F  114 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8263 (mptt)
REVERT: F  138 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7149 (mm-30)
REVERT: F  171 LYS cc_start: 0.8863 (mttt) cc_final: 0.8139 (tptp)
REVERT: F  378 GLN cc_start: 0.7914 (mt0) cc_final: 0.7443 (mm110)
REVERT: G   42 MET cc_start: 0.4482 (mtp) cc_final: 0.4183 (mtp)
REVERT: G   57 MET cc_start: 0.6756 (mtm) cc_final: 0.6433 (mtp)
REVERT: G  138 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7336 (mm-30)
REVERT: G  171 LYS cc_start: 0.8825 (mttt) cc_final: 0.8042 (tptp)
REVERT: G  242 LYS cc_start: 0.8152 (ttpt) cc_final: 0.7915 (ttpp)
REVERT: G  378 GLN cc_start: 0.7839 (mt0) cc_final: 0.7489 (tp40)
  outliers start: 20
  outliers final: 11
  residues processed: 235
  average time/residue: 1.2023
  time to fit residues: 330.7359
Evaluate side-chains
  238 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 220
  time to evaluate  : 2.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain B residue   10 ARG
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue  147 ASP
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue  147 ASP
Chi-restraints excluded: chain D residue    2 GLU
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain E residue   10 ARG
Chi-restraints excluded: chain E residue  277 LEU
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   89 SER
Chi-restraints excluded: chain F residue  138 GLU
Chi-restraints excluded: chain G residue   55 VAL
Chi-restraints excluded: chain G residue   89 SER
Chi-restraints excluded: chain G residue  138 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 251 optimal weight:    7.9990
   chunk 106 optimal weight:    9.9990
   chunk 257 optimal weight:   10.0000
   chunk 77 optimal weight:    0.7980
   chunk 184 optimal weight:    0.7980
   chunk 276 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 157 optimal weight:    2.9990
   chunk 181 optimal weight:    0.9990
   chunk 134 optimal weight:   20.0000
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
B 174 ASN
B 231 ASN
B 338 ASN
C 174 ASN
C 231 ASN
C 338 ASN
D 231 ASN
D 338 ASN
E 174 ASN
E 231 ASN
F 174 ASN
F 231 ASN
G 338 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.161582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.129597 restraints weight = 19446.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.37
r_work: 0.3281 rms_B_bonded: 1.49 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  23408  Z= 0.215
  Angle     :  0.647   5.028  31969  Z= 0.371
  Chirality :  0.049   0.149   3353
  Planarity :  0.005   0.033   4151
  Dihedral  :  5.151  18.384   3129
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 1.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  7.65 %
    Favored  : 91.40 %
  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:  0.64 (0.15), residues: 2856
  helix:  0.84 (0.21), residues: 497
  sheet:  1.09 (0.14), residues: 1176
  loop : -0.39 (0.16), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP G 370 
 HIS   0.006   0.001   HIS F 186 
 PHE   0.017   0.002   PHE C 321 
 TYR   0.016   0.002   TYR C  61 
 ARG   0.003   0.000   ARG B 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06443 (  875)
  hydrogen bonds       : angle       5.13244 ( 2478)
  SS BOND              : bond        0.00184 (    7)
  SS BOND              : angle       0.76140 (   14)
  covalent geometry    : bond        0.00363 (23401)
  covalent geometry    : angle       0.64724 (31955)

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

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

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5712 Ramachandran restraints generated.
    2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 220
  time to evaluate  : 2.543 
Fit side-chains
REVERT: A   30 GLU cc_start: 0.6651 (mt-10) cc_final: 0.5711 (mm-30)
REVERT: A   42 MET cc_start: 0.4591 (mtp) cc_final: 0.4207 (mtp)
REVERT: A  114 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8378 (mptt)
REVERT: A  171 LYS cc_start: 0.8834 (mttt) cc_final: 0.8134 (tptm)
REVERT: A  378 GLN cc_start: 0.7948 (mt0) cc_final: 0.7531 (mm110)
REVERT: A  385 MET cc_start: 0.8896 (mmm) cc_final: 0.8383 (mmm)
REVERT: B    2 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6742 (tt0)
REVERT: B   10 ARG cc_start: 0.2586 (OUTLIER) cc_final: 0.1891 (ptt90)
REVERT: B   42 MET cc_start: 0.4350 (mtp) cc_final: 0.3767 (mtp)
REVERT: B  114 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8297 (mptt)
REVERT: B  171 LYS cc_start: 0.8752 (mttt) cc_final: 0.7983 (tptp)
REVERT: B  277 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8104 (tt)
REVERT: B  378 GLN cc_start: 0.7910 (tp40) cc_final: 0.7654 (mp10)
REVERT: C  171 LYS cc_start: 0.8812 (mttt) cc_final: 0.8035 (tptp)
REVERT: C  242 LYS cc_start: 0.8237 (ttmm) cc_final: 0.7894 (ttmt)
REVERT: C  378 GLN cc_start: 0.7850 (mt0) cc_final: 0.7424 (mm110)
REVERT: D    2 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6563 (tt0)
REVERT: D  171 LYS cc_start: 0.8773 (mttt) cc_final: 0.8004 (tptp)
REVERT: E   10 ARG cc_start: 0.2603 (OUTLIER) cc_final: 0.1962 (ptt180)
REVERT: E   42 MET cc_start: 0.4376 (mtp) cc_final: 0.3982 (mtp)
REVERT: E  171 LYS cc_start: 0.8826 (mttt) cc_final: 0.8027 (tptm)
REVERT: E  277 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8388 (tp)
REVERT: E  385 MET cc_start: 0.8819 (mmm) cc_final: 0.8336 (mmm)
REVERT: F    2 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6610 (mm-30)
REVERT: F  114 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8274 (mptt)
REVERT: F  138 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7170 (mm-30)
REVERT: F  171 LYS cc_start: 0.8875 (mttt) cc_final: 0.8142 (tptp)
REVERT: F  378 GLN cc_start: 0.7958 (mt0) cc_final: 0.7505 (mm110)
REVERT: G   42 MET cc_start: 0.4483 (mtp) cc_final: 0.4186 (mtp)
REVERT: G   57 MET cc_start: 0.6770 (mtm) cc_final: 0.6457 (mtp)
REVERT: G  138 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7357 (mm-30)
REVERT: G  171 LYS cc_start: 0.8834 (mttt) cc_final: 0.8051 (tptp)
REVERT: G  242 LYS cc_start: 0.8182 (ttpt) cc_final: 0.7932 (ttpp)
REVERT: G  378 GLN cc_start: 0.7859 (mt0) cc_final: 0.7502 (tp40)
  outliers start: 23
  outliers final: 13
  residues processed: 237
  average time/residue: 1.1815
  time to fit residues: 324.7195
Evaluate side-chains
  240 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 219
  time to evaluate  : 2.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain B residue   10 ARG
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue  147 ASP
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue  147 ASP
Chi-restraints excluded: chain D residue    2 GLU
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain E residue   10 ARG
Chi-restraints excluded: chain E residue   55 VAL
Chi-restraints excluded: chain E residue  277 LEU
Chi-restraints excluded: chain F residue    2 GLU
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   89 SER
Chi-restraints excluded: chain F residue  138 GLU
Chi-restraints excluded: chain G residue   55 VAL
Chi-restraints excluded: chain G residue   89 SER
Chi-restraints excluded: chain G residue  138 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 132 optimal weight:   10.0000
   chunk 248 optimal weight:    9.9990
   chunk 240 optimal weight:    0.6980
   chunk 114 optimal weight:    3.9990
   chunk 104 optimal weight:    6.9990
   chunk 163 optimal weight:    0.5980
   chunk 196 optimal weight:    6.9990
   chunk 255 optimal weight:    7.9990
   chunk 267 optimal weight:    2.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
B 174 ASN
B 231 ASN
B 338 ASN
C 174 ASN
C 231 ASN
D 231 ASN
D 338 ASN
E 174 ASN
E 231 ASN
F 174 ASN
F 231 ASN
G 338 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.161671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.130764 restraints weight = 19537.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.26
r_work: 0.3299 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 2.32 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  23408  Z= 0.202
  Angle     :  0.622   5.020  31969  Z= 0.356
  Chirality :  0.049   0.144   3353
  Planarity :  0.004   0.032   4151
  Dihedral  :  5.070  18.363   3129
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 1.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  7.74 %
    Favored  : 91.28 %
  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:  0.65 (0.15), residues: 2856
  helix:  0.89 (0.21), residues: 497
  sheet:  1.08 (0.14), residues: 1176
  loop : -0.38 (0.16), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP G 370 
 HIS   0.005   0.001   HIS E 186 
 PHE   0.016   0.002   PHE C 321 
 TYR   0.015   0.002   TYR C  61 
 ARG   0.002   0.000   ARG B 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06064 (  875)
  hydrogen bonds       : angle       5.09231 ( 2478)
  SS BOND              : bond        0.00161 (    7)
  SS BOND              : angle       0.74468 (   14)
  covalent geometry    : bond        0.00339 (23401)
  covalent geometry    : angle       0.62226 (31955)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 20841.21 seconds
wall clock time: 358 minutes 2.60 seconds (21482.60 seconds total)