Starting phenix.real_space_refine
on Fri Sep 19 03:10:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fm6_50549/09_2025/9fm6_50549.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fm6_50549/09_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_50549/09_2025/9fm6_50549.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fm6_50549/09_2025/9fm6_50549.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fm6_50549/09_2025/9fm6_50549.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fm6_50549/09_2025/9fm6_50549.cif"
  }
  resolution = 2.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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:
    B, C, D, E, F, G
  Time building chain proxies: 3.46, per 1000 atoms: 0.15
  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 B 159 " - pdb=" SG  CYS B 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 159 " - pdb=" SG  CYS C 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 159 " - pdb=" SG  CYS D 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 159 " - pdb=" SG  CYS F 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G 159 " - pdb=" SG  CYS G 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: 2.10
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.72
  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: 4.01

  Time building geometry restraints manager: 2.87 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             3.920
  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:             0.020
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     19.570
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.870
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  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
 ARG   0.011   0.001   ARG B  10 
 TYR   0.029   0.004   TYR D  61 
 PHE   0.029   0.004   PHE B 321 
 TRP   0.020   0.003   TRP B 370 
 HIS   0.004   0.002   HIS B 186 

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

*********************** 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  : 0.937 
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: 0.7696
  time to fit residues: 338.3545
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  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 197 optimal weight:    3.9990
   chunk 215 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 132 optimal weight:    6.9990
   chunk 261 optimal weight:    0.8980
   chunk 248 optimal weight:    0.6980
   chunk 207 optimal weight:    0.5980
   chunk 155 optimal weight:    8.9990
   chunk 244 optimal weight:    7.9990
   chunk 183 optimal weight:    6.9990
   chunk 111 optimal weight:    2.9990
   overall best weight:    1.4384

-------------------------------------------------------------------------------
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 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: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.161519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.131478 restraints weight = 19399.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.44
r_work: 0.3178 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018  23408  Z= 0.202
  Angle     :  0.640   4.627  31969  Z= 0.369
  Chirality :  0.048   0.148   3353
  Planarity :  0.005   0.032   4151
  Dihedral  :  4.905  16.723   3129
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 0.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  4.46 %
    Favored  : 94.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.15), residues: 2856
  helix:  0.77 (0.21), residues: 497
  sheet:  1.73 (0.14), residues: 1176
  loop :  0.40 (0.17), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 220 
 TYR   0.018   0.002   TYR G  61 
 PHE   0.016   0.002   PHE G 321 
 TRP   0.017   0.001   TRP G 370 
 HIS   0.005   0.001   HIS F 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (23401)
  covalent geometry    : angle       0.63877 (31955)
  SS BOND              : bond        0.00444 (    7)
  SS BOND              : angle       1.63406 (   14)
  hydrogen bonds       : bond        0.05882 (  875)
  hydrogen bonds       : angle       5.44913 ( 2478)

*********************** 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
  279 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 260
  time to evaluate  : 0.664 
Fit side-chains
REVERT: A    2 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6885 (tt0)
REVERT: A   42 MET cc_start: 0.4410 (mtp) cc_final: 0.4165 (mtp)
REVERT: A  114 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8438 (mptt)
REVERT: A  138 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7371 (mm-30)
REVERT: A  171 LYS cc_start: 0.8844 (mttt) cc_final: 0.8216 (tptp)
REVERT: A  378 GLN cc_start: 0.7822 (mt0) cc_final: 0.7550 (mm110)
REVERT: A  385 MET cc_start: 0.8952 (mmm) cc_final: 0.8422 (mmm)
REVERT: B    2 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6808 (tt0)
REVERT: B  114 LYS cc_start: 0.8678 (mmmt) cc_final: 0.8458 (mptt)
REVERT: B  138 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7109 (mm-30)
REVERT: B  171 LYS cc_start: 0.8838 (mttt) cc_final: 0.8136 (tptm)
REVERT: B  378 GLN cc_start: 0.7954 (mt0) cc_final: 0.7549 (mp10)
REVERT: C   42 MET cc_start: 0.4327 (mtp) cc_final: 0.4116 (mtp)
REVERT: C  114 LYS cc_start: 0.8662 (mmmt) cc_final: 0.8450 (mptt)
REVERT: C  171 LYS cc_start: 0.8849 (mttt) cc_final: 0.8200 (tptm)
REVERT: C  378 GLN cc_start: 0.7730 (mt0) cc_final: 0.7457 (mm110)
REVERT: D  114 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8415 (mptt)
REVERT: D  171 LYS cc_start: 0.8881 (mttt) cc_final: 0.8179 (tptp)
REVERT: E  114 LYS cc_start: 0.8669 (mmmt) cc_final: 0.8442 (mptt)
REVERT: E  138 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7078 (mm-30)
REVERT: E  171 LYS cc_start: 0.8903 (mttt) cc_final: 0.8151 (tptm)
REVERT: E  258 GLU cc_start: 0.8370 (tt0) cc_final: 0.8131 (tt0)
REVERT: E  378 GLN cc_start: 0.7790 (mt0) cc_final: 0.7585 (mm110)
REVERT: E  385 MET cc_start: 0.8876 (mmm) cc_final: 0.8440 (mmm)
REVERT: F    2 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6894 (tt0)
REVERT: F  114 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8397 (mptt)
REVERT: F  138 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7146 (mm-30)
REVERT: F  171 LYS cc_start: 0.8848 (mttt) cc_final: 0.8212 (tptp)
REVERT: F  378 GLN cc_start: 0.7806 (mt0) cc_final: 0.7529 (mm110)
REVERT: G   42 MET cc_start: 0.4466 (mtp) cc_final: 0.4156 (mtp)
REVERT: G  114 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8359 (mptt)
REVERT: G  171 LYS cc_start: 0.8843 (mttt) cc_final: 0.8199 (tptm)
REVERT: G  254 GLU cc_start: 0.7756 (tt0) cc_final: 0.7534 (tt0)
REVERT: G  378 GLN cc_start: 0.7806 (mt0) cc_final: 0.7471 (mp10)
  outliers start: 19
  outliers final: 6
  residues processed: 278
  average time/residue: 0.5840
  time to fit residues: 186.1769
Evaluate side-chains
  235 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 225
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
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 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 114 optimal weight:    5.9990
   chunk 233 optimal weight:    6.9990
   chunk 106 optimal weight:    3.9990
   chunk 4 optimal weight:   20.0000
   chunk 86 optimal weight:   10.0000
   chunk 277 optimal weight:   10.0000
   chunk 103 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 98 optimal weight:    7.9990
   chunk 257 optimal weight:   20.0000
   chunk 152 optimal weight:    6.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 174 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
F 341 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.158601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.126635 restraints weight = 19411.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 1.57
r_work: 0.3219 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 2.53 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050  23408  Z= 0.367
  Angle     :  0.920   8.300  31969  Z= 0.530
  Chirality :  0.062   0.252   3353
  Planarity :  0.007   0.062   4151
  Dihedral  :  5.889  21.166   3129
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 1.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  :  4.83 %
    Favored  : 93.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.14), residues: 2856
  helix:  0.08 (0.20), residues: 497
  sheet:  1.40 (0.15), residues: 1036
  loop : -0.24 (0.15), residues: 1323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 282 
 TYR   0.026   0.004   TYR A 233 
 PHE   0.030   0.005   PHE E 245 
 TRP   0.022   0.003   TRP G 370 
 HIS   0.012   0.003   HIS C 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00688 (23401)
  covalent geometry    : angle       0.92008 (31955)
  SS BOND              : bond        0.00507 (    7)
  SS BOND              : angle       1.48444 (   14)
  hydrogen bonds       : bond        0.09056 (  875)
  hydrogen bonds       : angle       5.61910 ( 2478)

*********************** 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
  279 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 233
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A    2 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7047 (mt-10)
REVERT: A   42 MET cc_start: 0.4639 (mtp) cc_final: 0.4283 (mtp)
REVERT: A  114 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8327 (mptt)
REVERT: A  138 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7450 (mm-30)
REVERT: A  152 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8210 (ttt180)
REVERT: A  171 LYS cc_start: 0.8795 (mttt) cc_final: 0.8120 (tptm)
REVERT: A  258 GLU cc_start: 0.8417 (tt0) cc_final: 0.8180 (tt0)
REVERT: A  378 GLN cc_start: 0.8008 (mt0) cc_final: 0.7652 (mm110)
REVERT: B   42 MET cc_start: 0.4324 (mtp) cc_final: 0.3839 (mtp)
REVERT: B  114 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8306 (mptt)
REVERT: B  138 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.6937 (mm-30)
REVERT: B  171 LYS cc_start: 0.8797 (mttt) cc_final: 0.8024 (tptm)
REVERT: B  258 GLU cc_start: 0.8308 (tt0) cc_final: 0.8103 (tt0)
REVERT: B  277 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8257 (tt)
REVERT: B  378 GLN cc_start: 0.8056 (mt0) cc_final: 0.7497 (mm110)
REVERT: C   42 MET cc_start: 0.4524 (mtp) cc_final: 0.4050 (mtp)
REVERT: C  114 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8364 (mptt)
REVERT: C  134 GLN cc_start: 0.6848 (pm20) cc_final: 0.6398 (mm-40)
REVERT: C  171 LYS cc_start: 0.8800 (mttt) cc_final: 0.8087 (tptm)
REVERT: C  277 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8574 (tp)
REVERT: C  378 GLN cc_start: 0.7939 (mt0) cc_final: 0.7507 (mm110)
REVERT: D    2 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6574 (tt0)
REVERT: D   42 MET cc_start: 0.4395 (mtp) cc_final: 0.4066 (mtm)
REVERT: D  138 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7157 (mm-30)
REVERT: D  171 LYS cc_start: 0.8800 (mttt) cc_final: 0.8052 (tptm)
REVERT: E   42 MET cc_start: 0.4557 (mtp) cc_final: 0.4149 (mtp)
REVERT: E   57 MET cc_start: 0.6621 (mtm) cc_final: 0.6381 (mtp)
REVERT: E  114 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8339 (mptt)
REVERT: E  138 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7031 (mm-30)
REVERT: E  171 LYS cc_start: 0.8827 (mttt) cc_final: 0.8022 (tptm)
REVERT: E  378 GLN cc_start: 0.8092 (mt0) cc_final: 0.7578 (mm110)
REVERT: F    2 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6868 (tt0)
REVERT: F  114 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8307 (mptt)
REVERT: F  138 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7163 (mm-30)
REVERT: F  171 LYS cc_start: 0.8847 (mttt) cc_final: 0.8172 (tptp)
REVERT: F  378 GLN cc_start: 0.8090 (mt0) cc_final: 0.7633 (mm110)
REVERT: G   10 ARG cc_start: 0.2409 (OUTLIER) cc_final: 0.2056 (ptt90)
REVERT: G   42 MET cc_start: 0.4379 (mtp) cc_final: 0.4091 (mtp)
REVERT: G   57 MET cc_start: 0.6616 (mtm) cc_final: 0.6120 (mtp)
REVERT: G  114 LYS cc_start: 0.8512 (mmmt) cc_final: 0.8262 (mptt)
REVERT: G  138 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7370 (mm-30)
REVERT: G  171 LYS cc_start: 0.8845 (mttt) cc_final: 0.8098 (tptp)
REVERT: G  378 GLN cc_start: 0.8041 (mt0) cc_final: 0.7611 (mm110)
  outliers start: 46
  outliers final: 19
  residues processed: 267
  average time/residue: 0.6187
  time to fit residues: 187.8391
Evaluate side-chains
  250 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 220
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
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  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 E residue    2 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 F residue   55 VAL
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  138 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 279 optimal weight:    4.9990
   chunk 120 optimal weight:    4.9990
   chunk 278 optimal weight:    5.9990
   chunk 180 optimal weight:    4.9990
   chunk 166 optimal weight:    0.8980
   chunk 167 optimal weight:    0.8980
   chunk 271 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 223 optimal weight:    9.9990
   chunk 114 optimal weight:    5.9990
   chunk 237 optimal weight:    0.0370
   overall best weight:    1.5460

-------------------------------------------------------------------------------
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 174 ASN
D 231 ASN
D 338 ASN
E 174 ASN
F 174 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.163187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.131419 restraints weight = 19541.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.31
r_work: 0.3295 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 2.54 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  23408  Z= 0.192
  Angle     :  0.616   5.348  31969  Z= 0.354
  Chirality :  0.048   0.160   3353
  Planarity :  0.004   0.034   4151
  Dihedral  :  5.200  19.049   3129
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 1.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  5.73 %
    Favored  : 92.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.15), residues: 2856
  helix:  0.68 (0.21), residues: 497
  sheet:  1.10 (0.14), residues: 1204
  loop : -0.07 (0.17), residues: 1155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 220 
 TYR   0.014   0.002   TYR C 215 
 PHE   0.015   0.002   PHE G 321 
 TRP   0.015   0.001   TRP G 370 
 HIS   0.005   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (23401)
  covalent geometry    : angle       0.61536 (31955)
  SS BOND              : bond        0.00228 (    7)
  SS BOND              : angle       1.01158 (   14)
  hydrogen bonds       : bond        0.05873 (  875)
  hydrogen bonds       : angle       5.29018 ( 2478)

*********************** 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
  265 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 233
  time to evaluate  : 0.557 
Fit side-chains
REVERT: A    2 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6732 (tt0)
REVERT: A   30 GLU cc_start: 0.6649 (mt-10) cc_final: 0.5728 (mm-30)
REVERT: A   42 MET cc_start: 0.4511 (mtp) cc_final: 0.4149 (mtp)
REVERT: A  114 LYS cc_start: 0.8561 (mmmt) cc_final: 0.8354 (mptt)
REVERT: A  171 LYS cc_start: 0.8806 (mttt) cc_final: 0.8151 (tptm)
REVERT: A  258 GLU cc_start: 0.8355 (tt0) cc_final: 0.8121 (tt0)
REVERT: A  378 GLN cc_start: 0.7968 (mt0) cc_final: 0.7555 (mm110)
REVERT: A  385 MET cc_start: 0.8893 (mmm) cc_final: 0.8354 (mmm)
REVERT: B    2 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6702 (tt0)
REVERT: B   10 ARG cc_start: 0.2739 (OUTLIER) cc_final: 0.2019 (ptt90)
REVERT: B   42 MET cc_start: 0.4274 (mtp) cc_final: 0.3742 (mtp)
REVERT: B  114 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8323 (mptt)
REVERT: B  171 LYS cc_start: 0.8780 (mttt) cc_final: 0.8022 (tptm)
REVERT: B  378 GLN cc_start: 0.8012 (mt0) cc_final: 0.7395 (mm110)
REVERT: C   42 MET cc_start: 0.4429 (mtp) cc_final: 0.4166 (mtp)
REVERT: C  114 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8390 (mptt)
REVERT: C  171 LYS cc_start: 0.8811 (mttt) cc_final: 0.8072 (tptm)
REVERT: C  242 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7763 (ttmt)
REVERT: C  378 GLN cc_start: 0.7827 (mt0) cc_final: 0.7385 (mm110)
REVERT: D    2 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6594 (tt0)
REVERT: D   42 MET cc_start: 0.4408 (mtp) cc_final: 0.4119 (mtm)
REVERT: D  171 LYS cc_start: 0.8801 (mttt) cc_final: 0.8047 (tptm)
REVERT: E   10 ARG cc_start: 0.2615 (OUTLIER) cc_final: 0.2045 (ptt90)
REVERT: E   42 MET cc_start: 0.4415 (mtp) cc_final: 0.4054 (mtp)
REVERT: E  114 LYS cc_start: 0.8599 (mmmt) cc_final: 0.8337 (mptt)
REVERT: E  138 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.6940 (mm-30)
REVERT: E  171 LYS cc_start: 0.8811 (mttt) cc_final: 0.8034 (tptm)
REVERT: E  378 GLN cc_start: 0.7931 (mt0) cc_final: 0.7446 (mm110)
REVERT: F    2 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6850 (tt0)
REVERT: F  114 LYS cc_start: 0.8561 (mmmt) cc_final: 0.8303 (mptt)
REVERT: F  171 LYS cc_start: 0.8808 (mttt) cc_final: 0.8155 (tptm)
REVERT: F  378 GLN cc_start: 0.7971 (mt0) cc_final: 0.7538 (mm110)
REVERT: G   42 MET cc_start: 0.4404 (mtp) cc_final: 0.4132 (mtp)
REVERT: G   57 MET cc_start: 0.6719 (mtm) cc_final: 0.6272 (mtp)
REVERT: G  114 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8297 (mptt)
REVERT: G  138 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7355 (mm-30)
REVERT: G  171 LYS cc_start: 0.8823 (mttt) cc_final: 0.8087 (tptp)
REVERT: G  378 GLN cc_start: 0.7894 (mt0) cc_final: 0.7488 (mm110)
  outliers start: 32
  outliers final: 14
  residues processed: 253
  average time/residue: 0.6300
  time to fit residues: 181.9589
Evaluate side-chains
  245 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 226
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
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   91 LEU
Chi-restraints excluded: chain B residue  147 ASP
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain C residue    2 GLU
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   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 G residue  138 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 143 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 4 optimal weight:    9.9990
   chunk 145 optimal weight:    2.9990
   chunk 162 optimal weight:    0.9980
   chunk 9 optimal weight:   10.0000
   chunk 272 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 136 optimal weight:    7.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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
E 338 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 = 0.3835 r_free = 0.3835 target = 0.163044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.131203 restraints weight = 19412.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.32
r_work: 0.3299 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 2.46 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  23408  Z= 0.193
  Angle     :  0.606   4.900  31969  Z= 0.348
  Chirality :  0.048   0.163   3353
  Planarity :  0.005   0.034   4151
  Dihedral  :  5.033  18.138   3129
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 1.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  6.39 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.15), residues: 2856
  helix:  0.97 (0.22), residues: 497
  sheet:  1.15 (0.14), residues: 1176
  loop : -0.17 (0.16), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 362 
 TYR   0.013   0.002   TYR C 215 
 PHE   0.014   0.002   PHE D 321 
 TRP   0.014   0.001   TRP G 370 
 HIS   0.006   0.001   HIS C 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (23401)
  covalent geometry    : angle       0.60563 (31955)
  SS BOND              : bond        0.00176 (    7)
  SS BOND              : angle       0.76547 (   14)
  hydrogen bonds       : bond        0.05895 (  875)
  hydrogen bonds       : angle       5.18446 ( 2478)

*********************** 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
  270 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 237
  time to evaluate  : 0.926 
Fit side-chains
REVERT: A   30 GLU cc_start: 0.6591 (mt-10) cc_final: 0.5666 (mm-30)
REVERT: A   42 MET cc_start: 0.4426 (mtp) cc_final: 0.4068 (mtp)
REVERT: A  114 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8354 (mptt)
REVERT: A  171 LYS cc_start: 0.8804 (mttt) cc_final: 0.8137 (tptm)
REVERT: A  378 GLN cc_start: 0.7918 (mt0) cc_final: 0.7500 (mm110)
REVERT: A  385 MET cc_start: 0.8894 (mmm) cc_final: 0.8383 (mmm)
REVERT: B    2 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6659 (tt0)
REVERT: B   10 ARG cc_start: 0.2572 (OUTLIER) cc_final: 0.1900 (ptt90)
REVERT: B   42 MET cc_start: 0.4211 (mtp) cc_final: 0.3702 (mtp)
REVERT: B  114 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8314 (mptt)
REVERT: B  171 LYS cc_start: 0.8749 (mttt) cc_final: 0.7975 (tptm)
REVERT: B  277 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8033 (tt)
REVERT: B  378 GLN cc_start: 0.7961 (mt0) cc_final: 0.7387 (mm110)
REVERT: C   42 MET cc_start: 0.4301 (mtp) cc_final: 0.3884 (mtp)
REVERT: C  114 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8372 (mptt)
REVERT: C  171 LYS cc_start: 0.8791 (mttt) cc_final: 0.8046 (tptm)
REVERT: C  242 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7747 (ttmt)
REVERT: C  378 GLN cc_start: 0.7784 (mt0) cc_final: 0.7387 (mm110)
REVERT: D    2 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6558 (tt0)
REVERT: D   42 MET cc_start: 0.4485 (mtp) cc_final: 0.4163 (mtm)
REVERT: D  171 LYS cc_start: 0.8776 (mttt) cc_final: 0.8021 (tptp)
REVERT: E   42 MET cc_start: 0.4402 (mtp) cc_final: 0.4054 (mtp)
REVERT: E  114 LYS cc_start: 0.8600 (mmmt) cc_final: 0.8318 (mptt)
REVERT: E  138 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.6918 (mm-30)
REVERT: E  171 LYS cc_start: 0.8806 (mttt) cc_final: 0.8019 (tptm)
REVERT: E  378 GLN cc_start: 0.7946 (mt0) cc_final: 0.7490 (mm110)
REVERT: F    2 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6855 (tt0)
REVERT: F   10 ARG cc_start: 0.2152 (OUTLIER) cc_final: 0.1859 (ptt180)
REVERT: F  114 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8302 (mptt)
REVERT: F  171 LYS cc_start: 0.8816 (mttt) cc_final: 0.8135 (tptm)
REVERT: F  378 GLN cc_start: 0.7933 (mt0) cc_final: 0.7453 (mm110)
REVERT: G   42 MET cc_start: 0.4466 (mtp) cc_final: 0.4186 (mtp)
REVERT: G   57 MET cc_start: 0.6691 (mtm) cc_final: 0.6369 (mtp)
REVERT: G  114 LYS cc_start: 0.8471 (mmmt) cc_final: 0.8240 (mptt)
REVERT: G  138 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7382 (mm-30)
REVERT: G  171 LYS cc_start: 0.8856 (mttt) cc_final: 0.8072 (tptp)
REVERT: G  242 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7947 (ttpp)
REVERT: G  378 GLN cc_start: 0.7866 (mt0) cc_final: 0.7513 (tp40)
  outliers start: 33
  outliers final: 15
  residues processed: 264
  average time/residue: 0.6527
  time to fit residues: 197.5857
Evaluate side-chains
  254 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 233
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
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  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  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 D residue   55 VAL
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   10 ARG
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain G residue   55 VAL
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 163 optimal weight:    1.9990
   chunk 235 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 98 optimal weight:    8.9990
   chunk 196 optimal weight:    0.0870
   chunk 268 optimal weight:    6.9990
   chunk 282 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0000
   chunk 67 optimal weight:   10.0000
   chunk 168 optimal weight:    5.9990
   overall best weight:    0.7564

-------------------------------------------------------------------------------
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 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: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.166468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.135976 restraints weight = 19789.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 1.38
r_work: 0.3348 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  23408  Z= 0.138
  Angle     :  0.512   4.973  31969  Z= 0.290
  Chirality :  0.045   0.140   3353
  Planarity :  0.004   0.029   4151
  Dihedral  :  4.590  17.078   3129
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 1.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  7.12 %
    Favored  : 91.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.15), residues: 2856
  helix:  1.33 (0.22), residues: 497
  sheet:  1.11 (0.14), residues: 1204
  loop : -0.03 (0.17), residues: 1155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 220 
 TYR   0.009   0.001   TYR C 215 
 PHE   0.009   0.001   PHE D 321 
 TRP   0.009   0.001   TRP G 370 
 HIS   0.003   0.001   HIS F 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (23401)
  covalent geometry    : angle       0.51163 (31955)
  SS BOND              : bond        0.00325 (    7)
  SS BOND              : angle       0.53853 (   14)
  hydrogen bonds       : bond        0.04406 (  875)
  hydrogen bonds       : angle       4.99444 ( 2478)

*********************** 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
  269 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 247
  time to evaluate  : 0.935 
Fit side-chains
REVERT: A    2 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6673 (tt0)
REVERT: A   30 GLU cc_start: 0.6606 (mt-10) cc_final: 0.5739 (mm-30)
REVERT: A   42 MET cc_start: 0.4395 (mtp) cc_final: 0.4086 (mtp)
REVERT: A  114 LYS cc_start: 0.8646 (mmmt) cc_final: 0.8411 (mptt)
REVERT: A  171 LYS cc_start: 0.8842 (mttt) cc_final: 0.8191 (tptm)
REVERT: A  378 GLN cc_start: 0.7899 (mt0) cc_final: 0.7574 (mm110)
REVERT: A  385 MET cc_start: 0.8879 (mmm) cc_final: 0.8412 (mmm)
REVERT: B    2 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6731 (tt0)
REVERT: B   10 ARG cc_start: 0.2707 (OUTLIER) cc_final: 0.1992 (ptt90)
REVERT: B   42 MET cc_start: 0.4333 (mtp) cc_final: 0.3828 (mtp)
REVERT: B  114 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8395 (mptt)
REVERT: B  171 LYS cc_start: 0.8781 (mttt) cc_final: 0.8059 (tptm)
REVERT: C   42 MET cc_start: 0.4280 (mtp) cc_final: 0.3943 (mtp)
REVERT: C  171 LYS cc_start: 0.8802 (mttt) cc_final: 0.8093 (tptm)
REVERT: C  242 LYS cc_start: 0.8172 (ttmm) cc_final: 0.7772 (ttmt)
REVERT: C  378 GLN cc_start: 0.7761 (mt0) cc_final: 0.7383 (mm110)
REVERT: D    2 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6610 (tt0)
REVERT: D   42 MET cc_start: 0.4546 (mtp) cc_final: 0.4306 (mtm)
REVERT: D  171 LYS cc_start: 0.8832 (mttt) cc_final: 0.8113 (tptm)
REVERT: E   42 MET cc_start: 0.4396 (mtp) cc_final: 0.4093 (mtp)
REVERT: E  114 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8418 (mptt)
REVERT: E  171 LYS cc_start: 0.8845 (mttt) cc_final: 0.8091 (tptm)
REVERT: E  378 GLN cc_start: 0.7931 (mt0) cc_final: 0.7508 (mm110)
REVERT: F   10 ARG cc_start: 0.2089 (OUTLIER) cc_final: 0.1761 (ptt180)
REVERT: F  114 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8391 (mptt)
REVERT: F  171 LYS cc_start: 0.8863 (mttt) cc_final: 0.8208 (tptm)
REVERT: F  378 GLN cc_start: 0.7847 (mt0) cc_final: 0.7518 (mm110)
REVERT: G   42 MET cc_start: 0.4502 (mtp) cc_final: 0.4227 (mtp)
REVERT: G   57 MET cc_start: 0.6795 (mtm) cc_final: 0.6406 (mtp)
REVERT: G  114 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8347 (mptt)
REVERT: G  171 LYS cc_start: 0.8885 (mttt) cc_final: 0.8123 (tptp)
REVERT: G  242 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7949 (ttpp)
REVERT: G  378 GLN cc_start: 0.7754 (mt0) cc_final: 0.7553 (tp40)
  outliers start: 22
  outliers final: 10
  residues processed: 264
  average time/residue: 0.5825
  time to fit residues: 178.4028
Evaluate side-chains
  246 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 233
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
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 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 F residue   10 ARG
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain G residue   55 VAL
Chi-restraints excluded: chain G residue   89 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 157 optimal weight:    1.9990
   chunk 247 optimal weight:   10.0000
   chunk 222 optimal weight:    4.9990
   chunk 111 optimal weight:    4.9990
   chunk 163 optimal weight:    6.9990
   chunk 169 optimal weight:    4.9990
   chunk 139 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 174 optimal weight:    9.9990
   chunk 218 optimal weight:   10.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
A 231 ASN
B 174 ASN
B 231 ASN
B 338 ASN
B 378 GLN
C 174 ASN
C 231 ASN
C 338 ASN
D 231 ASN
D 338 ASN
E 174 ASN
E 231 ASN
E 338 ASN
F 174 ASN
F 231 ASN
G 231 ASN
G 338 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.160402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.128571 restraints weight = 19374.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.34
r_work: 0.3259 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 2.45 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  23408  Z= 0.261
  Angle     :  0.723   6.174  31969  Z= 0.415
  Chirality :  0.053   0.174   3353
  Planarity :  0.006   0.044   4151
  Dihedral  :  5.317  18.988   3129
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 1.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  7.04 %
    Favored  : 91.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.15), residues: 2856
  helix:  0.77 (0.21), residues: 497
  sheet:  1.16 (0.14), residues: 1176
  loop : -0.26 (0.16), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 362 
 TYR   0.017   0.003   TYR G 233 
 PHE   0.021   0.003   PHE A 321 
 TRP   0.016   0.002   TRP G 370 
 HIS   0.009   0.002   HIS F 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 (23401)
  covalent geometry    : angle       0.72262 (31955)
  SS BOND              : bond        0.00311 (    7)
  SS BOND              : angle       0.84722 (   14)
  hydrogen bonds       : bond        0.07400 (  875)
  hydrogen bonds       : angle       5.27560 ( 2478)

*********************** 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
  262 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 229
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A   42 MET cc_start: 0.4475 (mtp) cc_final: 0.4138 (mtp)
REVERT: A  114 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8379 (mptt)
REVERT: A  138 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7393 (mm-30)
REVERT: A  171 LYS cc_start: 0.8816 (mttt) cc_final: 0.8137 (tptm)
REVERT: A  378 GLN cc_start: 0.7964 (mt0) cc_final: 0.7558 (mm110)
REVERT: A  385 MET cc_start: 0.8927 (mmm) cc_final: 0.8387 (mmm)
REVERT: B   10 ARG cc_start: 0.2596 (OUTLIER) cc_final: 0.1902 (ptt90)
REVERT: B   42 MET cc_start: 0.4271 (mtp) cc_final: 0.3677 (mtp)
REVERT: B  114 LYS cc_start: 0.8574 (mmmt) cc_final: 0.8312 (mptt)
REVERT: B  138 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.6991 (mm-30)
REVERT: B  171 LYS cc_start: 0.8722 (mttt) cc_final: 0.7967 (tptp)
REVERT: B  277 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8174 (tt)
REVERT: C   42 MET cc_start: 0.4501 (mtp) cc_final: 0.3950 (mtp)
REVERT: C  114 LYS cc_start: 0.8584 (mmmt) cc_final: 0.8367 (mptt)
REVERT: C  171 LYS cc_start: 0.8806 (mttt) cc_final: 0.8054 (tptp)
REVERT: C  242 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7769 (ttmt)
REVERT: C  378 GLN cc_start: 0.7843 (mt0) cc_final: 0.7461 (mm110)
REVERT: D    2 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6571 (tt0)
REVERT: D  171 LYS cc_start: 0.8792 (mttt) cc_final: 0.8024 (tptp)
REVERT: D  277 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8439 (tt)
REVERT: E   10 ARG cc_start: 0.2827 (OUTLIER) cc_final: 0.2157 (ptt90)
REVERT: E   42 MET cc_start: 0.4498 (mtp) cc_final: 0.4117 (mtp)
REVERT: E  114 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8345 (mptt)
REVERT: E  138 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.6985 (mm-30)
REVERT: E  171 LYS cc_start: 0.8829 (mttt) cc_final: 0.8028 (tptm)
REVERT: E  277 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8453 (tp)
REVERT: E  378 GLN cc_start: 0.7989 (mt0) cc_final: 0.7524 (mm110)
REVERT: F    2 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6600 (mm-30)
REVERT: F   10 ARG cc_start: 0.2266 (OUTLIER) cc_final: 0.2000 (ptt180)
REVERT: F  114 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8317 (mptt)
REVERT: F  171 LYS cc_start: 0.8857 (mttt) cc_final: 0.8166 (tptp)
REVERT: F  378 GLN cc_start: 0.8022 (mt0) cc_final: 0.7536 (mm110)
REVERT: G   42 MET cc_start: 0.4521 (mtp) cc_final: 0.4228 (mtp)
REVERT: G   57 MET cc_start: 0.6820 (mtm) cc_final: 0.6409 (mtp)
REVERT: G  114 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8282 (mptt)
REVERT: G  138 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7436 (mm-30)
REVERT: G  171 LYS cc_start: 0.8872 (mttt) cc_final: 0.8090 (tptp)
REVERT: G  254 GLU cc_start: 0.7823 (tt0) cc_final: 0.7583 (tt0)
REVERT: G  378 GLN cc_start: 0.7899 (mt0) cc_final: 0.7526 (tp40)
  outliers start: 33
  outliers final: 15
  residues processed: 256
  average time/residue: 0.5868
  time to fit residues: 173.9068
Evaluate side-chains
  251 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 224
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
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  138 GLU
Chi-restraints excluded: chain B residue  241 THR
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  277 LEU
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  277 LEU
Chi-restraints excluded: chain F residue    2 GLU
Chi-restraints excluded: chain F residue   10 ARG
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain G residue   55 VAL
Chi-restraints excluded: chain G residue   89 SER
Chi-restraints excluded: chain G residue  138 GLU
Chi-restraints excluded: chain G residue  241 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 175 optimal weight:   20.0000
   chunk 160 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 284 optimal weight:    0.3980
   chunk 144 optimal weight:    3.9990
   chunk 100 optimal weight:    9.9990
   chunk 238 optimal weight:    9.9990
   chunk 277 optimal weight:   10.0000
   chunk 150 optimal weight:    2.9990
   overall best weight:    3.0788

-------------------------------------------------------------------------------
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 231 ASN
B 338 ASN
B 378 GLN
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 231 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.160519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.129513 restraints weight = 19385.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.53
r_work: 0.3262 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 2.53 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  23408  Z= 0.242
  Angle     :  0.693   5.640  31969  Z= 0.398
  Chirality :  0.051   0.155   3353
  Planarity :  0.005   0.036   4151
  Dihedral  :  5.299  18.724   3129
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 1.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  7.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.14), residues: 2856
  helix:  0.64 (0.21), residues: 497
  sheet:  1.13 (0.14), residues: 1176
  loop : -0.33 (0.16), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 362 
 TYR   0.015   0.003   TYR C 215 
 PHE   0.019   0.003   PHE A 321 
 TRP   0.016   0.002   TRP G 370 
 HIS   0.007   0.002   HIS F 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (23401)
  covalent geometry    : angle       0.69268 (31955)
  SS BOND              : bond        0.00251 (    7)
  SS BOND              : angle       0.75324 (   14)
  hydrogen bonds       : bond        0.06838 (  875)
  hydrogen bonds       : angle       5.28384 ( 2478)

*********************** 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
  263 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 227
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A   42 MET cc_start: 0.4597 (mtp) cc_final: 0.4230 (mtp)
REVERT: A  114 LYS cc_start: 0.8620 (mmmt) cc_final: 0.8401 (mptt)
REVERT: A  138 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7446 (mm-30)
REVERT: A  171 LYS cc_start: 0.8825 (mttt) cc_final: 0.8155 (tptm)
REVERT: A  378 GLN cc_start: 0.8004 (mt0) cc_final: 0.7596 (mm110)
REVERT: A  385 MET cc_start: 0.8931 (mmm) cc_final: 0.8412 (mmm)
REVERT: B   10 ARG cc_start: 0.2634 (OUTLIER) cc_final: 0.1937 (ptt90)
REVERT: B   42 MET cc_start: 0.4398 (mtp) cc_final: 0.3809 (mtp)
REVERT: B  114 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8354 (mptt)
REVERT: B  138 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7016 (mm-30)
REVERT: B  171 LYS cc_start: 0.8741 (mttt) cc_final: 0.7995 (tptp)
REVERT: B  277 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8157 (tt)
REVERT: C   42 MET cc_start: 0.4450 (mtp) cc_final: 0.3898 (mtp)
REVERT: C  114 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8405 (mptt)
REVERT: C  171 LYS cc_start: 0.8833 (mttt) cc_final: 0.8075 (tptp)
REVERT: C  242 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7813 (ttmt)
REVERT: C  378 GLN cc_start: 0.7892 (mt0) cc_final: 0.7446 (mm110)
REVERT: D    2 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6584 (tt0)
REVERT: D   42 MET cc_start: 0.4494 (mtp) cc_final: 0.4159 (mtm)
REVERT: D  171 LYS cc_start: 0.8814 (mttt) cc_final: 0.8045 (tptp)
REVERT: D  277 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8353 (tt)
REVERT: E   10 ARG cc_start: 0.2938 (OUTLIER) cc_final: 0.2287 (ptt90)
REVERT: E   42 MET cc_start: 0.4491 (mtp) cc_final: 0.4141 (mtp)
REVERT: E  114 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8373 (mptt)
REVERT: E  138 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7006 (mm-30)
REVERT: E  171 LYS cc_start: 0.8844 (mttt) cc_final: 0.8055 (tptm)
REVERT: E  378 GLN cc_start: 0.7993 (mt0) cc_final: 0.7486 (mm110)
REVERT: F    2 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6635 (mm-30)
REVERT: F   10 ARG cc_start: 0.2326 (OUTLIER) cc_final: 0.2021 (ptt180)
REVERT: F  114 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8321 (mptt)
REVERT: F  171 LYS cc_start: 0.8894 (mttt) cc_final: 0.8192 (tptp)
REVERT: F  378 GLN cc_start: 0.8022 (mt0) cc_final: 0.7573 (mm110)
REVERT: G   42 MET cc_start: 0.4526 (mtp) cc_final: 0.4222 (mtp)
REVERT: G   57 MET cc_start: 0.6778 (mtm) cc_final: 0.6416 (mtp)
REVERT: G  114 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8278 (mptt)
REVERT: G  138 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7392 (mm-30)
REVERT: G  171 LYS cc_start: 0.8871 (mttt) cc_final: 0.8110 (tptp)
REVERT: G  378 GLN cc_start: 0.7915 (mt0) cc_final: 0.7562 (tp40)
  outliers start: 36
  outliers final: 17
  residues processed: 255
  average time/residue: 0.5839
  time to fit residues: 171.9338
Evaluate side-chains
  249 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 221
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
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  241 THR
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  138 GLU
Chi-restraints excluded: chain B residue  241 THR
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue  241 THR
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   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 F residue    2 GLU
Chi-restraints excluded: chain F residue   10 ARG
Chi-restraints excluded: chain F residue   55 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
Chi-restraints excluded: chain G residue  241 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 195 optimal weight:    9.9990
   chunk 168 optimal weight:    9.9990
   chunk 142 optimal weight:    6.9990
   chunk 43 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9990
   chunk 197 optimal weight:    6.9990
   chunk 105 optimal weight:    5.9990
   chunk 127 optimal weight:    8.9990
   chunk 271 optimal weight:    9.9990
   chunk 172 optimal weight:    7.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 231 ASN
B 338 ASN
B 341 HIS
B 378 GLN
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 231 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.158397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.126462 restraints weight = 19335.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.39
r_work: 0.3234 rms_B_bonded: 1.49 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.2512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053  23408  Z= 0.349
  Angle     :  0.881   7.763  31969  Z= 0.504
  Chirality :  0.059   0.300   3353
  Planarity :  0.007   0.056   4151
  Dihedral  :  5.770  20.525   3129
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 1.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  6.88 %
    Favored  : 91.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.14), residues: 2856
  helix:  0.15 (0.20), residues: 497
  sheet:  1.29 (0.15), residues: 1036
  loop : -0.61 (0.15), residues: 1323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 362 
 TYR   0.024   0.004   TYR A  61 
 PHE   0.024   0.004   PHE G 321 
 TRP   0.019   0.003   TRP G 370 
 HIS   0.009   0.002   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00654 (23401)
  covalent geometry    : angle       0.88121 (31955)
  SS BOND              : bond        0.00414 (    7)
  SS BOND              : angle       1.08536 (   14)
  hydrogen bonds       : bond        0.08775 (  875)
  hydrogen bonds       : angle       5.50936 ( 2478)

*********************** 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
  265 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 224
  time to evaluate  : 0.888 
Fit side-chains
REVERT: A   42 MET cc_start: 0.4685 (mtp) cc_final: 0.4311 (mtp)
REVERT: A   57 MET cc_start: 0.6415 (mtm) cc_final: 0.5993 (mtp)
REVERT: A  114 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8373 (mptt)
REVERT: A  138 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7449 (mm-30)
REVERT: A  171 LYS cc_start: 0.8815 (mttt) cc_final: 0.8145 (tptm)
REVERT: A  258 GLU cc_start: 0.8306 (tt0) cc_final: 0.8071 (tt0)
REVERT: A  378 GLN cc_start: 0.8055 (mt0) cc_final: 0.7611 (mm110)
REVERT: B   10 ARG cc_start: 0.2690 (OUTLIER) cc_final: 0.1958 (ptt180)
REVERT: B   42 MET cc_start: 0.4475 (mtp) cc_final: 0.3845 (mtp)
REVERT: B  114 LYS cc_start: 0.8589 (mmmt) cc_final: 0.8327 (mptt)
REVERT: B  138 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.6975 (mm-30)
REVERT: B  171 LYS cc_start: 0.8748 (mttt) cc_final: 0.8000 (tptp)
REVERT: B  277 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8253 (tt)
REVERT: C   42 MET cc_start: 0.4662 (mtp) cc_final: 0.4062 (mtp)
REVERT: C  114 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8380 (mptt)
REVERT: C  134 GLN cc_start: 0.6989 (pm20) cc_final: 0.6427 (mm-40)
REVERT: C  171 LYS cc_start: 0.8805 (mttt) cc_final: 0.8069 (tptp)
REVERT: C  242 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7869 (ttmt)
REVERT: C  378 GLN cc_start: 0.7967 (mt0) cc_final: 0.7521 (mm110)
REVERT: D    2 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6561 (tt0)
REVERT: D   42 MET cc_start: 0.4395 (mtp) cc_final: 0.4067 (mtm)
REVERT: D  138 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7243 (mm-30)
REVERT: D  171 LYS cc_start: 0.8789 (mttt) cc_final: 0.8026 (tptp)
REVERT: E   10 ARG cc_start: 0.2953 (OUTLIER) cc_final: 0.2305 (ptt90)
REVERT: E   42 MET cc_start: 0.4677 (mtp) cc_final: 0.4313 (mtp)
REVERT: E  114 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8364 (mptt)
REVERT: E  138 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7009 (mm-30)
REVERT: E  171 LYS cc_start: 0.8824 (mttt) cc_final: 0.8033 (tptm)
REVERT: E  378 GLN cc_start: 0.8063 (mt0) cc_final: 0.7539 (mm110)
REVERT: F    2 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6638 (mm-30)
REVERT: F   10 ARG cc_start: 0.2567 (OUTLIER) cc_final: 0.2308 (ptt180)
REVERT: F  114 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8304 (mptt)
REVERT: F  138 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7212 (mm-30)
REVERT: F  171 LYS cc_start: 0.8875 (mttt) cc_final: 0.8182 (tptp)
REVERT: F  378 GLN cc_start: 0.8087 (mt0) cc_final: 0.7603 (mm110)
REVERT: G   10 ARG cc_start: 0.2836 (OUTLIER) cc_final: 0.2476 (ptt180)
REVERT: G   42 MET cc_start: 0.4550 (mtp) cc_final: 0.4237 (mtp)
REVERT: G   57 MET cc_start: 0.6751 (mtm) cc_final: 0.6385 (mtp)
REVERT: G  114 LYS cc_start: 0.8544 (mmmt) cc_final: 0.8302 (mptt)
REVERT: G  138 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7399 (mm-30)
REVERT: G  171 LYS cc_start: 0.8820 (mttt) cc_final: 0.8089 (tptp)
REVERT: G  378 GLN cc_start: 0.7965 (mt0) cc_final: 0.7538 (mm110)
  outliers start: 41
  outliers final: 21
  residues processed: 257
  average time/residue: 0.6266
  time to fit residues: 184.5272
Evaluate side-chains
  253 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 219
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
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  241 THR
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  138 GLU
Chi-restraints excluded: chain B residue  241 THR
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue  241 THR
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 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 F residue    2 GLU
Chi-restraints excluded: chain F 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 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   91 LEU
Chi-restraints excluded: chain G residue  138 GLU
Chi-restraints excluded: chain G residue  241 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 202 optimal weight:    4.9990
   chunk 227 optimal weight:    6.9990
   chunk 277 optimal weight:    9.9990
   chunk 136 optimal weight:    1.9990
   chunk 226 optimal weight:    5.9990
   chunk 112 optimal weight:   10.0000
   chunk 216 optimal weight:    9.9990
   chunk 160 optimal weight:    6.9990
   chunk 178 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0030
   chunk 164 optimal weight:    2.9990
   overall best weight:    2.1996

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

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.161544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.129955 restraints weight = 19361.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.31
r_work: 0.3277 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 2.49 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025  23408  Z= 0.215
  Angle     :  0.652   6.304  31969  Z= 0.374
  Chirality :  0.049   0.151   3353
  Planarity :  0.005   0.033   4151
  Dihedral  :  5.267  19.048   3129
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 1.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  7.65 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.14), residues: 2856
  helix:  0.58 (0.21), residues: 497
  sheet:  1.08 (0.14), residues: 1176
  loop : -0.45 (0.16), residues: 1183

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (23401)
  covalent geometry    : angle       0.65218 (31955)
  SS BOND              : bond        0.00170 (    7)
  SS BOND              : angle       0.79469 (   14)
  hydrogen bonds       : bond        0.06277 (  875)
  hydrogen bonds       : angle       5.27334 ( 2478)

********************** 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
  246 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 220
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A   42 MET cc_start: 0.4577 (mtp) cc_final: 0.4226 (mtp)
REVERT: A  114 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8365 (mptt)
REVERT: A  138 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7381 (mm-30)
REVERT: A  171 LYS cc_start: 0.8835 (mttt) cc_final: 0.8145 (tptm)
REVERT: A  378 GLN cc_start: 0.8011 (mt0) cc_final: 0.7603 (mm110)
REVERT: A  385 MET cc_start: 0.8911 (mmm) cc_final: 0.8393 (mmm)
REVERT: B   10 ARG cc_start: 0.2625 (OUTLIER) cc_final: 0.1922 (ptt90)
REVERT: B   42 MET cc_start: 0.4327 (mtp) cc_final: 0.3715 (mtp)
REVERT: B  114 LYS cc_start: 0.8582 (mmmt) cc_final: 0.8315 (mptt)
REVERT: B  171 LYS cc_start: 0.8730 (mttt) cc_final: 0.7975 (tptp)
REVERT: B  277 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8120 (tt)
REVERT: C   42 MET cc_start: 0.4374 (mtp) cc_final: 0.4032 (mtp)
REVERT: C  114 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8385 (mptt)
REVERT: C  171 LYS cc_start: 0.8818 (mttt) cc_final: 0.8055 (tptp)
REVERT: C  242 LYS cc_start: 0.8162 (ttmm) cc_final: 0.7767 (ttmt)
REVERT: C  378 GLN cc_start: 0.7925 (mt0) cc_final: 0.7456 (mm110)
REVERT: D    2 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6550 (tt0)
REVERT: D   42 MET cc_start: 0.4298 (mtp) cc_final: 0.4011 (mtm)
REVERT: D  171 LYS cc_start: 0.8797 (mttt) cc_final: 0.8018 (tptp)
REVERT: E   10 ARG cc_start: 0.2797 (OUTLIER) cc_final: 0.2182 (ptt90)
REVERT: E   42 MET cc_start: 0.4495 (mtp) cc_final: 0.4115 (mtp)
REVERT: E  171 LYS cc_start: 0.8836 (mttt) cc_final: 0.8033 (tptm)
REVERT: E  378 GLN cc_start: 0.7978 (mt0) cc_final: 0.7490 (mm110)
REVERT: F    2 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6621 (mm-30)
REVERT: F   10 ARG cc_start: 0.2260 (OUTLIER) cc_final: 0.1922 (ptt180)
REVERT: F  114 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8299 (mptt)
REVERT: F  171 LYS cc_start: 0.8884 (mttt) cc_final: 0.8164 (tptp)
REVERT: F  378 GLN cc_start: 0.7968 (mt0) cc_final: 0.7504 (mm110)
REVERT: G   42 MET cc_start: 0.4431 (mtp) cc_final: 0.4131 (mtp)
REVERT: G   57 MET cc_start: 0.6771 (mtm) cc_final: 0.6453 (mtp)
REVERT: G  114 LYS cc_start: 0.8516 (mmmt) cc_final: 0.8274 (mptt)
REVERT: G  171 LYS cc_start: 0.8830 (mttt) cc_final: 0.8069 (tptm)
REVERT: G  378 GLN cc_start: 0.7914 (mt0) cc_final: 0.7536 (tp40)
  outliers start: 26
  outliers final: 18
  residues processed: 241
  average time/residue: 0.5633
  time to fit residues: 157.1151
Evaluate side-chains
  240 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 215
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
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  241 THR
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  241 THR
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 F residue    2 GLU
Chi-restraints excluded: chain F residue   10 ARG
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   89 SER
Chi-restraints excluded: chain G residue   91 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 206 optimal weight:    9.9990
   chunk 174 optimal weight:    6.9990
   chunk 273 optimal weight:    0.0010
   chunk 165 optimal weight:   10.0000
   chunk 185 optimal weight:    6.9990
   chunk 247 optimal weight:    8.9990
   chunk 134 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 74 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 111 optimal weight:    6.9990
   overall best weight:    3.9994

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

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.159639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.128047 restraints weight = 19250.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 1.27
r_work: 0.3245 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 2.50 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  23408  Z= 0.281
  Angle     :  0.768   6.471  31969  Z= 0.440
  Chirality :  0.054   0.216   3353
  Planarity :  0.006   0.043   4151
  Dihedral  :  5.518  19.801   3129
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  7.45 %
    Favored  : 91.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.14), residues: 2856
  helix:  0.37 (0.21), residues: 497
  sheet:  1.09 (0.14), residues: 1176
  loop : -0.48 (0.16), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G 282 
 TYR   0.020   0.003   TYR A  61 
 PHE   0.021   0.003   PHE A 321 
 TRP   0.019   0.002   TRP G 370 
 HIS   0.008   0.002   HIS F 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 (23401)
  covalent geometry    : angle       0.76763 (31955)
  SS BOND              : bond        0.00261 (    7)
  SS BOND              : angle       0.89912 (   14)
  hydrogen bonds       : bond        0.07684 (  875)
  hydrogen bonds       : angle       5.37721 ( 2478)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11060.53 seconds
wall clock time: 187 minutes 59.57 seconds (11279.57 seconds total)