Starting phenix.real_space_refine
on Wed Mar  4 06:35:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jlq_22377/03_2026/7jlq_22377.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jlq_22377/03_2026/7jlq_22377.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jlq_22377/03_2026/7jlq_22377.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jlq_22377/03_2026/7jlq_22377.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jlq_22377/03_2026/7jlq_22377.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jlq_22377/03_2026/7jlq_22377.map"
  }
  resolution = 4.0
  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=   0.004
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      66      5.16       5
     C    7725      2.51       5
     N    1962      2.21       5
     O    1947      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 99 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11700
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 474, 3900
          Classifications: {'peptide': 474}
          Link IDs: {'PTRANS': 17, 'TRANS': 456}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 3.12, per 1000 atoms: 0.27
  Number of scatterers: 11700
  At special positions: 0
  Unit cell: (130.41, 123.606, 92.988, 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      66     16.00
     O    1947      8.00
     N    1962      7.00
     C    7725      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  86 " - pdb=" SG  CYS A 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  86 " - pdb=" SG  CYS B 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  86 " - pdb=" SG  CYS C 122 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  Conformation dependent library (CDL) restraints added in 435.4 milliseconds
  

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2712

  Finding SS restraints...
    Secondary structure from input PDB file:
      81 helices and 9 sheets defined
      73.8% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 56
      removed outlier: 3.658A  pdb=" N   HIS A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 86
      removed outlier: 3.820A  pdb=" N   MET A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE A  73 " --> pdb=" O   GLU A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 116
      removed outlier: 4.336A  pdb=" N   ALA A 115 " --> pdb=" O   THR A 111 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   PHE A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 111 through 116'
    Processing helix  chain 'A' and resid 118 through 127
    Processing helix  chain 'A' and resid 132 through 166
      removed outlier: 3.852A  pdb=" N   ILE A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   TRP A 143 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLU A 159 " --> pdb=" O   CYS A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 178
    Processing helix  chain 'A' and resid 179 through 190
      removed outlier: 3.514A  pdb=" N   THR A 190 " --> pdb=" O   ARG A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 213
    Processing helix  chain 'A' and resid 215 through 225
    Processing helix  chain 'A' and resid 244 through 256
    Processing helix  chain 'A' and resid 270 through 277
      removed outlier: 3.789A  pdb=" N   ARG A 275 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   GLY A 276 " --> pdb=" O   TYR A 273 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   GLY A 277 " --> pdb=" O   LYS A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 317
      Proline residue:  A 302  - end of helix
    Processing helix  chain 'A' and resid 318 through 323
    Processing helix  chain 'A' and resid 324 through 328
    Processing helix  chain 'A' and resid 333 through 340
    Processing helix  chain 'A' and resid 346 through 357
      removed outlier: 3.632A  pdb=" N   ARG A 353 " --> pdb=" O   GLU A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 367
    Processing helix  chain 'A' and resid 370 through 398
      removed outlier: 3.581A  pdb=" N   VAL A 390 " --> pdb=" O   SER A 386 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASP A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 404
    Processing helix  chain 'A' and resid 407 through 422
    Processing helix  chain 'A' and resid 435 through 446
      removed outlier: 3.711A  pdb=" N   ARG A 439 " --> pdb=" O   GLU A 435 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   HIS A 444 " --> pdb=" O   VAL A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 453
      removed outlier: 3.820A  pdb=" N   GLN A 453 " --> pdb=" O   ASP A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 466
      removed outlier: 3.628A  pdb=" N   ARG A 462 " --> pdb=" O   ARG A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 481
    Processing helix  chain 'A' and resid 481 through 493
      Proline residue:  A 487  - end of helix
    Processing helix  chain 'A' and resid 494 through 496
      No H-bonds generated for 'chain 'A' and resid 494 through 496'
    Processing helix  chain 'A' and resid 497 through 508
      removed outlier: 3.546A  pdb=" N   ILE A 502 " --> pdb=" O   ALA A 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 56
      removed outlier: 3.658A  pdb=" N   HIS B  54 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 86
      removed outlier: 3.820A  pdb=" N   MET B  62 " --> pdb=" O   GLY B  58 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE B  73 " --> pdb=" O   GLU B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 116
      removed outlier: 4.336A  pdb=" N   ALA B 115 " --> pdb=" O   THR B 111 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   PHE B 116 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 111 through 116'
    Processing helix  chain 'B' and resid 118 through 127
    Processing helix  chain 'B' and resid 132 through 166
      removed outlier: 3.851A  pdb=" N   ILE B 138 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   TRP B 143 " --> pdb=" O   ALA B 139 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLU B 159 " --> pdb=" O   CYS B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 178
    Processing helix  chain 'B' and resid 179 through 190
      removed outlier: 3.516A  pdb=" N   THR B 190 " --> pdb=" O   ARG B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 213
    Processing helix  chain 'B' and resid 215 through 225
    Processing helix  chain 'B' and resid 244 through 256
    Processing helix  chain 'B' and resid 270 through 277
      removed outlier: 3.789A  pdb=" N   ARG B 275 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   GLY B 276 " --> pdb=" O   TYR B 273 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   GLY B 277 " --> pdb=" O   LYS B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 317
      Proline residue:  B 302  - end of helix
    Processing helix  chain 'B' and resid 318 through 323
    Processing helix  chain 'B' and resid 324 through 328
    Processing helix  chain 'B' and resid 333 through 340
    Processing helix  chain 'B' and resid 346 through 357
      removed outlier: 3.632A  pdb=" N   ARG B 353 " --> pdb=" O   GLU B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 367
    Processing helix  chain 'B' and resid 370 through 398
      removed outlier: 3.581A  pdb=" N   VAL B 390 " --> pdb=" O   SER B 386 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASP B 398 " --> pdb=" O   LEU B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 404
    Processing helix  chain 'B' and resid 407 through 422
    Processing helix  chain 'B' and resid 435 through 446
      removed outlier: 3.711A  pdb=" N   ARG B 439 " --> pdb=" O   GLU B 435 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   HIS B 444 " --> pdb=" O   VAL B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 453
      removed outlier: 3.821A  pdb=" N   GLN B 453 " --> pdb=" O   ASP B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 466
      removed outlier: 3.628A  pdb=" N   ARG B 462 " --> pdb=" O   ARG B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 472 through 481
    Processing helix  chain 'B' and resid 481 through 493
      Proline residue:  B 487  - end of helix
    Processing helix  chain 'B' and resid 494 through 496
      No H-bonds generated for 'chain 'B' and resid 494 through 496'
    Processing helix  chain 'B' and resid 497 through 508
      removed outlier: 3.545A  pdb=" N   ILE B 502 " --> pdb=" O   ALA B 498 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 56
      removed outlier: 3.659A  pdb=" N   HIS C  54 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 86
      removed outlier: 3.820A  pdb=" N   MET C  62 " --> pdb=" O   GLY C  58 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE C  73 " --> pdb=" O   GLU C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 116
      removed outlier: 4.336A  pdb=" N   ALA C 115 " --> pdb=" O   THR C 111 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   PHE C 116 " --> pdb=" O   LEU C 112 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 111 through 116'
    Processing helix  chain 'C' and resid 118 through 127
    Processing helix  chain 'C' and resid 132 through 166
      removed outlier: 3.851A  pdb=" N   ILE C 138 " --> pdb=" O   THR C 134 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   TRP C 143 " --> pdb=" O   ALA C 139 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLU C 159 " --> pdb=" O   CYS C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 174 through 178
    Processing helix  chain 'C' and resid 179 through 190
      removed outlier: 3.515A  pdb=" N   THR C 190 " --> pdb=" O   ARG C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 213
    Processing helix  chain 'C' and resid 215 through 225
    Processing helix  chain 'C' and resid 244 through 256
    Processing helix  chain 'C' and resid 270 through 277
      removed outlier: 3.789A  pdb=" N   ARG C 275 " --> pdb=" O   GLU C 272 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   GLY C 276 " --> pdb=" O   TYR C 273 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   GLY C 277 " --> pdb=" O   LYS C 274 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 317
      Proline residue:  C 302  - end of helix
    Processing helix  chain 'C' and resid 318 through 323
    Processing helix  chain 'C' and resid 324 through 328
    Processing helix  chain 'C' and resid 333 through 340
    Processing helix  chain 'C' and resid 346 through 357
      removed outlier: 3.632A  pdb=" N   ARG C 353 " --> pdb=" O   GLU C 349 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 358 through 367
    Processing helix  chain 'C' and resid 370 through 398
      removed outlier: 3.581A  pdb=" N   VAL C 390 " --> pdb=" O   SER C 386 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASP C 398 " --> pdb=" O   LEU C 394 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 399 through 404
    Processing helix  chain 'C' and resid 407 through 422
    Processing helix  chain 'C' and resid 435 through 446
      removed outlier: 3.712A  pdb=" N   ARG C 439 " --> pdb=" O   GLU C 435 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   HIS C 444 " --> pdb=" O   VAL C 440 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 449 through 453
      removed outlier: 3.821A  pdb=" N   GLN C 453 " --> pdb=" O   ASP C 450 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 458 through 466
      removed outlier: 3.627A  pdb=" N   ARG C 462 " --> pdb=" O   ARG C 458 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 472 through 481
    Processing helix  chain 'C' and resid 481 through 493
      Proline residue:  C 487  - end of helix
    Processing helix  chain 'C' and resid 494 through 496
      No H-bonds generated for 'chain 'C' and resid 494 through 496'
    Processing helix  chain 'C' and resid 497 through 508
      removed outlier: 3.546A  pdb=" N   ILE C 502 " --> pdb=" O   ALA C 498 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 234
    Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 332
    Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 512
    Processing sheet with id=AA4, first strand: chain 'B' and resid 232 through 234
    Processing sheet with id=AA5, first strand: chain 'B' and resid 330 through 332
    Processing sheet with id=AA6, first strand: chain 'B' and resid 509 through 512
    Processing sheet with id=AA7, first strand: chain 'C' and resid 232 through 234
    Processing sheet with id=AA8, first strand: chain 'C' and resid 330 through 332
    Processing sheet with id=AA9, first strand: chain 'C' and resid 509 through 512

    696 hydrogen bonds defined for protein.
    1971 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.84

  Time building geometry restraints manager: 1.34 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: 3635
        1.34 -     1.46: 2515
        1.46 -     1.57: 5790
        1.57 -     1.69: 0
        1.69 -     1.81: 87
  Bond restraints: 12027
  Sorted by residual:
  bond pdb=" CA  PHE C 242 "
       pdb=" CB  PHE C 242 "
    ideal  model  delta    sigma   weight residual
    1.526  1.495  0.031 1.53e-02 4.27e+03 4.19e+00
  bond pdb=" CB  GLN B 120 "
       pdb=" CG  GLN B 120 "
    ideal  model  delta    sigma   weight residual
    1.520  1.573 -0.053 3.00e-02 1.11e+03 3.15e+00
  bond pdb=" CB  GLN A 120 "
       pdb=" CG  GLN A 120 "
    ideal  model  delta    sigma   weight residual
    1.520  1.573 -0.053 3.00e-02 1.11e+03 3.09e+00
  bond pdb=" CB  GLN C 120 "
       pdb=" CG  GLN C 120 "
    ideal  model  delta    sigma   weight residual
    1.520  1.573 -0.053 3.00e-02 1.11e+03 3.08e+00
  bond pdb=" CB  TRP B 332 "
       pdb=" CG  TRP B 332 "
    ideal  model  delta    sigma   weight residual
    1.498  1.446  0.052 3.10e-02 1.04e+03 2.79e+00
  ... (remaining 12022 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 15575
        2.05 -     4.10: 634
        4.10 -     6.15: 95
        6.15 -     8.20: 30
        8.20 -    10.25: 4
  Bond angle restraints: 16338
  Sorted by residual:
  angle pdb=" CB  GLN A 120 "
        pdb=" CG  GLN A 120 "
        pdb=" CD  GLN A 120 "
      ideal   model   delta    sigma   weight residual
     112.60  119.42   -6.82 1.70e+00 3.46e-01 1.61e+01
  angle pdb=" CB  GLN B 120 "
        pdb=" CG  GLN B 120 "
        pdb=" CD  GLN B 120 "
      ideal   model   delta    sigma   weight residual
     112.60  119.41   -6.81 1.70e+00 3.46e-01 1.60e+01
  angle pdb=" CB  GLN C 120 "
        pdb=" CG  GLN C 120 "
        pdb=" CD  GLN C 120 "
      ideal   model   delta    sigma   weight residual
     112.60  119.40   -6.80 1.70e+00 3.46e-01 1.60e+01
  angle pdb=" CA  GLN C 120 "
        pdb=" CB  GLN C 120 "
        pdb=" CG  GLN C 120 "
      ideal   model   delta    sigma   weight residual
     114.10  121.76   -7.66 2.00e+00 2.50e-01 1.47e+01
  angle pdb=" CA  GLN B 120 "
        pdb=" CB  GLN B 120 "
        pdb=" CG  GLN B 120 "
      ideal   model   delta    sigma   weight residual
     114.10  121.73   -7.63 2.00e+00 2.50e-01 1.46e+01
  ... (remaining 16333 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 6291
       17.52 -    35.04: 579
       35.04 -    52.56: 114
       52.56 -    70.08: 18
       70.08 -    87.60: 15
  Dihedral angle restraints: 7017
    sinusoidal: 2832
      harmonic: 4185
  Sorted by residual:
  dihedral pdb=" CB  CYS C  86 "
           pdb=" SG  CYS C  86 "
           pdb=" SG  CYS C 122 "
           pdb=" CB  CYS C 122 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -119.71   33.71     1      1.00e+01 1.00e-02 1.61e+01
  dihedral pdb=" CB  CYS B  86 "
           pdb=" SG  CYS B  86 "
           pdb=" SG  CYS B 122 "
           pdb=" CB  CYS B 122 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -119.69   33.69     1      1.00e+01 1.00e-02 1.61e+01
  dihedral pdb=" CB  CYS A  86 "
           pdb=" SG  CYS A  86 "
           pdb=" SG  CYS A 122 "
           pdb=" CB  CYS A 122 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -119.69   33.69     1      1.00e+01 1.00e-02 1.61e+01
  ... (remaining 7014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 964
       0.036 -    0.071: 536
       0.071 -    0.107: 246
       0.107 -    0.143: 69
       0.143 -    0.178: 21
  Chirality restraints: 1836
  Sorted by residual:
  chirality pdb=" CB  ILE A 254 "
            pdb=" CA  ILE A 254 "
            pdb=" CG1 ILE A 254 "
            pdb=" CG2 ILE A 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.96e-01
  chirality pdb=" CB  ILE B 254 "
            pdb=" CA  ILE B 254 "
            pdb=" CG1 ILE B 254 "
            pdb=" CG2 ILE B 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.73e-01
  chirality pdb=" CB  ILE C 254 "
            pdb=" CA  ILE C 254 "
            pdb=" CG1 ILE C 254 "
            pdb=" CG2 ILE C 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.71e-01
  ... (remaining 1833 not shown)

  Planarity restraints: 2031
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 180 "    0.018 2.00e-02 2.50e+03   1.77e-02 7.80e+00
        pdb=" CG  TRP C 180 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 180 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 180 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 180 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 180 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 180 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 180 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 180 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 180 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 180 "    0.019 2.00e-02 2.50e+03   1.76e-02 7.77e+00
        pdb=" CG  TRP A 180 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 180 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 180 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 180 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 180 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 180 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 180 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 180 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 180 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 180 "   -0.019 2.00e-02 2.50e+03   1.76e-02 7.76e+00
        pdb=" CG  TRP B 180 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 180 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 180 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 180 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 180 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 180 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 180 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 180 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 180 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 2028 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 432
        2.70 -     3.25: 12051
        3.25 -     3.80: 18486
        3.80 -     4.35: 23424
        4.35 -     4.90: 38982
  Nonbonded interactions: 93375
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 209 "
            pdb=" OE2 GLU C 349 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" OH  TYR A 209 "
            pdb=" OE2 GLU A 349 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" OH  TYR B 209 "
            pdb=" OE2 GLU B 349 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" NH2 ARG B  49 "
            pdb=" OD1 ASN B 153 "
     model   vdw
     2.161 3.120
  nonbonded pdb=" NH2 ARG A  49 "
            pdb=" OD1 ASN A 153 "
     model   vdw
     2.161 3.120
  ... (remaining 93370 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.030
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6515
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      :  0.007   0.053  12030  Z= 0.340
  Angle     :  0.990  10.250  16344  Z= 0.549
  Chirality :  0.054   0.178   1836
  Planarity :  0.005   0.029   2031
  Dihedral  : 14.269  87.601   4296
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  3.08 %
    Favored  : 96.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.82 (0.21), residues: 1410
  helix: -0.46 (0.16), residues: 942
  sheet: -2.13 (0.85), residues: 30
  loop : -2.63 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 356 
 TYR   0.030   0.004   TYR A 471 
 PHE   0.040   0.003   PHE A 368 
 TRP   0.046   0.004   TRP C 180 
 HIS   0.007   0.002   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00712 (12027)
  covalent geometry    : angle       0.98979 (16338)
  SS BOND              : bond        0.00315 (    3)
  SS BOND              : angle       0.97087 (    6)
  hydrogen bonds       : bond        0.20106 (  696)
  hydrogen bonds       : angle       6.50632 ( 1971)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  420 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 411
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ILE cc_start: 0.9175 (mt) cc_final: 0.8946 (tp)
REVERT: A   79 PHE cc_start: 0.8860 (t80) cc_final: 0.8492 (t80)
REVERT: A   83 LEU cc_start: 0.8269 (mt) cc_final: 0.7593 (mt)
REVERT: A  226 SER cc_start: 0.8013 (m) cc_final: 0.7732 (p)
REVERT: A  321 LYS cc_start: 0.7793 (tptm) cc_final: 0.7006 (mttt)
REVERT: A  363 LYS cc_start: 0.7773 (mttt) cc_final: 0.7507 (mttt)
REVERT: A  364 TYR cc_start: 0.8049 (t80) cc_final: 0.7783 (t80)
REVERT: A  435 GLU cc_start: 0.7716 (tp30) cc_final: 0.7239 (tp30)
REVERT: A  445 ILE cc_start: 0.6461 (pt) cc_final: 0.6250 (pt)
REVERT: B   83 LEU cc_start: 0.8230 (mt) cc_final: 0.7923 (mt)
REVERT: B  143 TRP cc_start: 0.8208 (t60) cc_final: 0.7709 (t60)
REVERT: B  152 TYR cc_start: 0.8314 (t80) cc_final: 0.8038 (t80)
REVERT: B  226 SER cc_start: 0.7959 (m) cc_final: 0.7737 (p)
REVERT: B  364 TYR cc_start: 0.7941 (t80) cc_final: 0.7737 (t80)
REVERT: B  372 LEU cc_start: 0.8949 (tp) cc_final: 0.8539 (mt)
REVERT: B  445 ILE cc_start: 0.6511 (pt) cc_final: 0.6279 (pt)
REVERT: B  471 TYR cc_start: 0.8585 (m-80) cc_final: 0.7338 (m-10)
REVERT: C   62 MET cc_start: 0.7010 (ttp) cc_final: 0.6662 (tmm)
REVERT: C  226 SER cc_start: 0.7880 (m) cc_final: 0.7679 (p)
REVERT: C  471 TYR cc_start: 0.8526 (m-80) cc_final: 0.8311 (m-10)
  outliers start: 9
  outliers final: 0
  residues processed: 416
  average time/residue: 0.1160
  time to fit residues: 67.9373
Evaluate side-chains
  228 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
B 406 HIS
C 406 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.173203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.135462 restraints weight = 16878.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.136972 restraints weight = 11182.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.138330 restraints weight = 8653.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.140107 restraints weight = 6093.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.140383 restraints weight = 5305.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6500
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12030  Z= 0.144
  Angle     :  0.680  11.512  16344  Z= 0.341
  Chirality :  0.043   0.191   1836
  Planarity :  0.005   0.044   2031
  Dihedral  :  4.189  15.688   1557
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 12.48 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.22), residues: 1410
  helix:  0.43 (0.17), residues: 942
  sheet: -1.55 (0.89), residues: 30
  loop : -2.04 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 506 
 TYR   0.015   0.001   TYR A 157 
 PHE   0.024   0.001   PHE B 475 
 TRP   0.014   0.002   TRP B 143 
 HIS   0.006   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (12027)
  covalent geometry    : angle       0.67646 (16338)
  SS BOND              : bond        0.01392 (    3)
  SS BOND              : angle       3.80586 (    6)
  hydrogen bonds       : bond        0.04926 (  696)
  hydrogen bonds       : angle       4.89554 ( 1971)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 263
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ILE cc_start: 0.9248 (mt) cc_final: 0.8969 (tp)
REVERT: A   83 LEU cc_start: 0.8230 (mt) cc_final: 0.7935 (mt)
REVERT: A  310 LEU cc_start: 0.7268 (mt) cc_final: 0.6869 (mt)
REVERT: A  471 TYR cc_start: 0.8414 (m-10) cc_final: 0.8154 (m-10)
REVERT: B  143 TRP cc_start: 0.7956 (t60) cc_final: 0.7383 (t60)
REVERT: B  422 ARG cc_start: 0.7767 (mtp180) cc_final: 0.7522 (mtp180)
REVERT: B  471 TYR cc_start: 0.8449 (m-80) cc_final: 0.6898 (m-10)
REVERT: C   62 MET cc_start: 0.7227 (ttp) cc_final: 0.6617 (tmm)
REVERT: C   75 PHE cc_start: 0.7926 (t80) cc_final: 0.7638 (t80)
REVERT: C   81 THR cc_start: 0.8812 (p) cc_final: 0.8540 (t)
REVERT: C  172 MET cc_start: 0.7588 (ppp) cc_final: 0.7326 (ppp)
REVERT: C  318 GLU cc_start: 0.7306 (tp30) cc_final: 0.7091 (mm-30)
  outliers start: 34
  outliers final: 15
  residues processed: 287
  average time/residue: 0.0907
  time to fit residues: 39.1718
Evaluate side-chains
  227 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 212
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  457 HIS
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  193 GLU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  442 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 112 optimal weight:    0.5980
   chunk 118 optimal weight:    6.9990
   chunk 60 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 139 optimal weight:    0.9990
   chunk 140 optimal weight:   20.0000
   chunk 12 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 14 optimal weight:    0.7980
   chunk 108 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A 216 GLN
** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  57 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.173603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.136326 restraints weight = 17007.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.138237 restraints weight = 10948.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.139638 restraints weight = 8350.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.141812 restraints weight = 6035.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.142102 restraints weight = 5112.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6492
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12030  Z= 0.125
  Angle     :  0.606  12.009  16344  Z= 0.307
  Chirality :  0.040   0.134   1836
  Planarity :  0.004   0.045   2031
  Dihedral  :  4.143  17.203   1557
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.72 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.22), residues: 1410
  helix:  0.58 (0.17), residues: 963
  sheet: -1.35 (0.89), residues: 30
  loop : -2.23 (0.26), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 506 
 TYR   0.019   0.001   TYR C 157 
 PHE   0.024   0.001   PHE A  73 
 TRP   0.018   0.001   TRP C 143 
 HIS   0.003   0.001   HIS A 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (12027)
  covalent geometry    : angle       0.60374 (16338)
  SS BOND              : bond        0.01092 (    3)
  SS BOND              : angle       3.02291 (    6)
  hydrogen bonds       : bond        0.04349 (  696)
  hydrogen bonds       : angle       4.68445 ( 1971)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 231
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ILE cc_start: 0.9252 (mt) cc_final: 0.8727 (tp)
REVERT: A   71 MET cc_start: 0.8443 (mtm) cc_final: 0.8044 (ptp)
REVERT: A   75 PHE cc_start: 0.7432 (m-10) cc_final: 0.7165 (m-10)
REVERT: A  310 LEU cc_start: 0.7261 (mt) cc_final: 0.6963 (mt)
REVERT: B   81 THR cc_start: 0.8586 (p) cc_final: 0.8350 (t)
REVERT: B  143 TRP cc_start: 0.7983 (t60) cc_final: 0.7352 (t60)
REVERT: B  471 TYR cc_start: 0.8283 (m-80) cc_final: 0.6908 (m-10)
REVERT: B  503 ASP cc_start: 0.9003 (m-30) cc_final: 0.8640 (p0)
REVERT: C   71 MET cc_start: 0.8259 (mtm) cc_final: 0.8011 (ptp)
REVERT: C   75 PHE cc_start: 0.7750 (t80) cc_final: 0.7381 (t80)
REVERT: C  471 TYR cc_start: 0.8324 (m-80) cc_final: 0.6921 (m-10)
  outliers start: 35
  outliers final: 19
  residues processed: 251
  average time/residue: 0.0906
  time to fit residues: 34.2075
Evaluate side-chains
  222 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 203
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  150 PHE
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  457 HIS
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  442 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 116 optimal weight:   10.0000
   chunk 87 optimal weight:    0.8980
   chunk 49 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 119 optimal weight:    9.9990
   chunk 42 optimal weight:    5.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 436 GLN
C  57 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.170943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.134603 restraints weight = 17516.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.135244 restraints weight = 10920.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.136530 restraints weight = 8907.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.138750 restraints weight = 6763.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.138884 restraints weight = 5763.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6637
moved from start:          0.4188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12030  Z= 0.152
  Angle     :  0.635  12.190  16344  Z= 0.319
  Chirality :  0.042   0.132   1836
  Planarity :  0.005   0.042   2031
  Dihedral  :  4.191  16.618   1557
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 18.40 %
    Favored  : 77.96 %
  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 are not related in a simple way.
  whole: -0.20 (0.22), residues: 1410
  helix:  0.69 (0.17), residues: 948
  sheet:  None (None), residues: 0
  loop : -1.82 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 506 
 TYR   0.015   0.002   TYR B 471 
 PHE   0.020   0.002   PHE A  73 
 TRP   0.013   0.002   TRP A 158 
 HIS   0.003   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (12027)
  covalent geometry    : angle       0.63296 (16338)
  SS BOND              : bond        0.00976 (    3)
  SS BOND              : angle       2.73120 (    6)
  hydrogen bonds       : bond        0.04308 (  696)
  hydrogen bonds       : angle       4.66229 ( 1971)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 233
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ILE cc_start: 0.9288 (mt) cc_final: 0.8153 (tp)
REVERT: A   71 MET cc_start: 0.8375 (mtm) cc_final: 0.8000 (ptp)
REVERT: A  310 LEU cc_start: 0.7372 (mt) cc_final: 0.6999 (mt)
REVERT: A  365 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.6880 (mpp)
REVERT: B   75 PHE cc_start: 0.7556 (t80) cc_final: 0.7293 (t80)
REVERT: B  363 LYS cc_start: 0.7502 (mttt) cc_final: 0.6948 (tttt)
REVERT: B  471 TYR cc_start: 0.8427 (m-80) cc_final: 0.7064 (m-10)
REVERT: C   75 PHE cc_start: 0.7591 (t80) cc_final: 0.7219 (t80)
REVERT: C   81 THR cc_start: 0.8770 (p) cc_final: 0.8527 (t)
REVERT: C  363 LYS cc_start: 0.6935 (mttt) cc_final: 0.6489 (mtmt)
REVERT: C  365 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6776 (mpp)
REVERT: C  469 PHE cc_start: 0.7343 (t80) cc_final: 0.6765 (t80)
REVERT: C  471 TYR cc_start: 0.8431 (m-80) cc_final: 0.7026 (m-10)
  outliers start: 46
  outliers final: 32
  residues processed: 254
  average time/residue: 0.0897
  time to fit residues: 34.4667
Evaluate side-chains
  237 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 203
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  379 ASN
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  150 PHE
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  216 GLN
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  379 ASN
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  442 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 119 optimal weight:    0.7980
   chunk 137 optimal weight:    2.9990
   chunk 140 optimal weight:    7.9990
   chunk 74 optimal weight:    4.9990
   chunk 23 optimal weight:    0.5980
   chunk 101 optimal weight:   20.0000
   chunk 32 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 107 optimal weight:    9.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A 344 ASN
B  57 ASN
C  57 ASN
C 344 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.173409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.137373 restraints weight = 17191.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.138987 restraints weight = 10579.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.140251 restraints weight = 8219.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.142190 restraints weight = 6261.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.142552 restraints weight = 5481.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6557
moved from start:          0.4536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12030  Z= 0.117
  Angle     :  0.615  13.983  16344  Z= 0.302
  Chirality :  0.040   0.131   1836
  Planarity :  0.004   0.042   2031
  Dihedral  :  4.079  15.669   1557
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 20.22 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.22), residues: 1410
  helix:  0.89 (0.17), residues: 939
  sheet:  None (None), residues: 0
  loop : -1.67 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 495 
 TYR   0.020   0.001   TYR B 152 
 PHE   0.028   0.001   PHE B 251 
 TRP   0.009   0.001   TRP A 158 
 HIS   0.002   0.000   HIS B 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (12027)
  covalent geometry    : angle       0.61369 (16338)
  SS BOND              : bond        0.00958 (    3)
  SS BOND              : angle       2.42636 (    6)
  hydrogen bonds       : bond        0.03985 (  696)
  hydrogen bonds       : angle       4.58652 ( 1971)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 233
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.6552 (mpp)
REVERT: B  164 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.7300 (t80)
REVERT: B  363 LYS cc_start: 0.7437 (mttt) cc_final: 0.6924 (tttt)
REVERT: B  365 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.6713 (mpp)
REVERT: B  471 TYR cc_start: 0.8445 (m-80) cc_final: 0.7115 (m-10)
REVERT: C   66 GLU cc_start: 0.9013 (mp0) cc_final: 0.8753 (mp0)
REVERT: C   75 PHE cc_start: 0.7552 (t80) cc_final: 0.7238 (t80)
REVERT: C   81 THR cc_start: 0.8760 (p) cc_final: 0.8483 (t)
REVERT: C  363 LYS cc_start: 0.6963 (mttt) cc_final: 0.6544 (mtmt)
REVERT: C  365 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.6647 (mpp)
REVERT: C  471 TYR cc_start: 0.8473 (m-80) cc_final: 0.7082 (m-10)
  outliers start: 55
  outliers final: 29
  residues processed: 264
  average time/residue: 0.0950
  time to fit residues: 37.1197
Evaluate side-chains
  244 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 211
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  150 PHE
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain C residue  448 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 85 optimal weight:    6.9990
   chunk 98 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 140 optimal weight:    7.9990
   chunk 90 optimal weight:   10.0000
   chunk 78 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 114 optimal weight:    5.9990
   chunk 136 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   chunk 72 optimal weight:    0.4980
   overall best weight:    3.0786

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

Flipped N/Q/H residues before XYZ refinement:
A  54 HIS
A  57 ASN
A 284 GLN
A 288 ASN
B  54 HIS
C  54 HIS
C  57 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.168005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.132273 restraints weight = 17884.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.134261 restraints weight = 10823.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.135245 restraints weight = 8158.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.135888 restraints weight = 6449.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.136089 restraints weight = 6101.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6722
moved from start:          0.4838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12030  Z= 0.183
  Angle     :  0.680  13.340  16344  Z= 0.344
  Chirality :  0.044   0.138   1836
  Planarity :  0.005   0.045   2031
  Dihedral  :  4.359  18.668   1557
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 21.72 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.22), residues: 1410
  helix:  0.58 (0.17), residues: 939
  sheet:  None (None), residues: 0
  loop : -1.54 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 495 
 TYR   0.023   0.003   TYR B 152 
 PHE   0.037   0.002   PHE A 382 
 TRP   0.017   0.002   TRP A 158 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (12027)
  covalent geometry    : angle       0.67903 (16338)
  SS BOND              : bond        0.00905 (    3)
  SS BOND              : angle       2.41071 (    6)
  hydrogen bonds       : bond        0.04371 (  696)
  hydrogen bonds       : angle       4.84543 ( 1971)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 234
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASN cc_start: 0.6651 (OUTLIER) cc_final: 0.6437 (m-40)
REVERT: A  164 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.6833 (t80)
REVERT: A  354 LEU cc_start: 0.8289 (mt) cc_final: 0.8032 (mp)
REVERT: A  365 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7132 (mpp)
REVERT: A  402 LEU cc_start: 0.5736 (mt) cc_final: 0.5087 (mp)
REVERT: A  430 MET cc_start: 0.6675 (ptt) cc_final: 0.6253 (ptt)
REVERT: A  435 GLU cc_start: 0.7399 (tp30) cc_final: 0.6898 (tp30)
REVERT: A  469 PHE cc_start: 0.7416 (t80) cc_final: 0.6346 (t80)
REVERT: B   81 THR cc_start: 0.8659 (p) cc_final: 0.8365 (t)
REVERT: B  164 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.7310 (t80)
REVERT: B  251 PHE cc_start: 0.7283 (m-10) cc_final: 0.6877 (m-10)
REVERT: B  330 ARG cc_start: 0.7768 (mtt-85) cc_final: 0.7337 (mtt-85)
REVERT: B  363 LYS cc_start: 0.7327 (mttt) cc_final: 0.6952 (tttt)
REVERT: B  365 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7612 (mtp)
REVERT: C   66 GLU cc_start: 0.8937 (mp0) cc_final: 0.8589 (mp0)
REVERT: C   75 PHE cc_start: 0.7591 (t80) cc_final: 0.7268 (t80)
REVERT: C  363 LYS cc_start: 0.7099 (mttt) cc_final: 0.6741 (mtmt)
REVERT: C  365 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.6808 (mpp)
REVERT: C  469 PHE cc_start: 0.7660 (t80) cc_final: 0.7075 (t80)
REVERT: C  471 TYR cc_start: 0.8572 (m-80) cc_final: 0.7261 (m-10)
  outliers start: 57
  outliers final: 34
  residues processed: 262
  average time/residue: 0.0996
  time to fit residues: 38.4552
Evaluate side-chains
  253 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 213
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   57 ASN
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  379 ASN
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  150 PHE
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  379 ASN
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  442 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 35 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 112 optimal weight:    0.7980
   chunk 81 optimal weight:    7.9990
   chunk 15 optimal weight:    0.1980
   chunk 115 optimal weight:    0.0370
   chunk 100 optimal weight:    6.9990
   overall best weight:    0.7860

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

Flipped N/Q/H residues before XYZ refinement:
B  55 GLN
C  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.173718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.136633 restraints weight = 17604.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.136491 restraints weight = 11097.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.138397 restraints weight = 8662.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.138973 restraints weight = 6878.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.139105 restraints weight = 6312.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6673
moved from start:          0.5151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12030  Z= 0.118
  Angle     :  0.624  13.859  16344  Z= 0.311
  Chirality :  0.041   0.163   1836
  Planarity :  0.004   0.043   2031
  Dihedral  :  4.145  17.248   1557
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 21.96 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.22), residues: 1410
  helix:  0.74 (0.17), residues: 957
  sheet:  None (None), residues: 0
  loop : -1.52 (0.27), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 330 
 TYR   0.026   0.002   TYR B 157 
 PHE   0.041   0.001   PHE B  79 
 TRP   0.010   0.001   TRP A 158 
 HIS   0.002   0.000   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (12027)
  covalent geometry    : angle       0.62291 (16338)
  SS BOND              : bond        0.00910 (    3)
  SS BOND              : angle       2.10035 (    6)
  hydrogen bonds       : bond        0.03923 (  696)
  hydrogen bonds       : angle       4.65531 ( 1971)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 243
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.6820 (t80)
REVERT: A  324 PRO cc_start: 0.7985 (Cg_endo) cc_final: 0.7745 (Cg_exo)
REVERT: A  402 LEU cc_start: 0.5674 (mt) cc_final: 0.5174 (mp)
REVERT: A  430 MET cc_start: 0.6586 (ptt) cc_final: 0.6094 (ptt)
REVERT: B   63 LEU cc_start: 0.9031 (tt) cc_final: 0.8642 (mt)
REVERT: B   81 THR cc_start: 0.8783 (p) cc_final: 0.8479 (t)
REVERT: B  164 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.7332 (t80)
REVERT: B  330 ARG cc_start: 0.7558 (mtt-85) cc_final: 0.7101 (mtt-85)
REVERT: B  363 LYS cc_start: 0.7531 (mttt) cc_final: 0.7124 (tttt)
REVERT: B  365 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7586 (mtp)
REVERT: B  503 ASP cc_start: 0.8951 (m-30) cc_final: 0.8671 (p0)
REVERT: C   81 THR cc_start: 0.8815 (p) cc_final: 0.8590 (t)
REVERT: C  226 SER cc_start: 0.8200 (t) cc_final: 0.7536 (p)
REVERT: C  363 LYS cc_start: 0.6978 (mttt) cc_final: 0.6608 (mtmt)
REVERT: C  365 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.6837 (mpp)
REVERT: C  471 TYR cc_start: 0.8483 (m-80) cc_final: 0.7223 (m-10)
  outliers start: 43
  outliers final: 24
  residues processed: 266
  average time/residue: 0.1017
  time to fit residues: 39.9814
Evaluate side-chains
  249 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 221
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   62 MET
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  442 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 115 optimal weight:    9.9990
   chunk 110 optimal weight:    0.6980
   chunk 89 optimal weight:    3.9990
   chunk 136 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0370
   chunk 119 optimal weight:    0.4980
   chunk 2 optimal weight:    7.9990
   chunk 87 optimal weight:    0.0570
   chunk 62 optimal weight:    4.9990
   chunk 93 optimal weight:    0.3980
   chunk 139 optimal weight:    0.9990
   overall best weight:    0.3376

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 284 GLN
B 406 HIS
C  55 GLN
C  57 ASN
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.175538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.138463 restraints weight = 17646.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.140494 restraints weight = 10473.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.141829 restraints weight = 7775.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.142174 restraints weight = 6253.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.142749 restraints weight = 5886.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6607
moved from start:          0.5474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  12030  Z= 0.119
  Angle     :  0.640  13.869  16344  Z= 0.316
  Chirality :  0.041   0.188   1836
  Planarity :  0.004   0.043   2031
  Dihedral  :  4.102  16.073   1557
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.22 %
    Favored  : 74.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.22), residues: 1410
  helix:  0.74 (0.17), residues: 957
  sheet:  None (None), residues: 0
  loop : -1.38 (0.26), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 330 
 TYR   0.027   0.002   TYR B 152 
 PHE   0.038   0.001   PHE B  79 
 TRP   0.009   0.001   TRP C 257 
 HIS   0.003   0.000   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (12027)
  covalent geometry    : angle       0.63867 (16338)
  SS BOND              : bond        0.00882 (    3)
  SS BOND              : angle       1.85185 (    6)
  hydrogen bonds       : bond        0.03910 (  696)
  hydrogen bonds       : angle       4.57844 ( 1971)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 240
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6942 (t80)
REVERT: A  310 LEU cc_start: 0.7399 (mt) cc_final: 0.6907 (mt)
REVERT: A  324 PRO cc_start: 0.8083 (Cg_endo) cc_final: 0.7848 (Cg_exo)
REVERT: A  402 LEU cc_start: 0.5537 (mt) cc_final: 0.4961 (mp)
REVERT: A  430 MET cc_start: 0.6432 (ptt) cc_final: 0.6106 (ptt)
REVERT: B   63 LEU cc_start: 0.8969 (tt) cc_final: 0.8636 (mt)
REVERT: B   81 THR cc_start: 0.8660 (p) cc_final: 0.8334 (t)
REVERT: B  164 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.7318 (t80)
REVERT: B  363 LYS cc_start: 0.7439 (mttt) cc_final: 0.7084 (tttt)
REVERT: B  365 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.6987 (mpp)
REVERT: B  471 TYR cc_start: 0.8511 (m-80) cc_final: 0.7244 (m-10)
REVERT: C  226 SER cc_start: 0.8111 (t) cc_final: 0.7531 (p)
REVERT: C  251 PHE cc_start: 0.6957 (m-10) cc_final: 0.6554 (m-80)
REVERT: C  363 LYS cc_start: 0.7002 (mttt) cc_final: 0.6583 (mtmt)
REVERT: C  365 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.6680 (mpp)
REVERT: C  471 TYR cc_start: 0.8525 (m-80) cc_final: 0.7165 (m-10)
  outliers start: 31
  outliers final: 17
  residues processed: 256
  average time/residue: 0.1024
  time to fit residues: 38.2350
Evaluate side-chains
  241 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 220
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  209 TYR
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  442 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 7 optimal weight:   20.0000
   chunk 39 optimal weight:    7.9990
   chunk 21 optimal weight:   10.0000
   chunk 127 optimal weight:    0.5980
   chunk 110 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 103 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  72 GLN
C  57 ASN
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.173515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.136640 restraints weight = 17807.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.138755 restraints weight = 10899.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.139640 restraints weight = 7864.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.140332 restraints weight = 6732.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.140511 restraints weight = 6165.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6662
moved from start:          0.5595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12030  Z= 0.130
  Angle     :  0.668  14.292  16344  Z= 0.331
  Chirality :  0.042   0.145   1836
  Planarity :  0.005   0.094   2031
  Dihedral  :  4.141  16.474   1557
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 23.54 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.22), residues: 1410
  helix:  0.75 (0.17), residues: 948
  sheet:  None (None), residues: 0
  loop : -1.45 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 330 
 TYR   0.028   0.002   TYR B 152 
 PHE   0.059   0.001   PHE A 382 
 TRP   0.021   0.001   TRP C 143 
 HIS   0.006   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (12027)
  covalent geometry    : angle       0.66698 (16338)
  SS BOND              : bond        0.00866 (    3)
  SS BOND              : angle       1.92180 (    6)
  hydrogen bonds       : bond        0.03977 (  696)
  hydrogen bonds       : angle       4.60701 ( 1971)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 217
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6933 (t80)
REVERT: A  251 PHE cc_start: 0.6731 (m-10) cc_final: 0.6452 (m-10)
REVERT: A  310 LEU cc_start: 0.7463 (mt) cc_final: 0.6968 (mt)
REVERT: A  324 PRO cc_start: 0.8071 (Cg_endo) cc_final: 0.7859 (Cg_exo)
REVERT: A  406 HIS cc_start: 0.6288 (OUTLIER) cc_final: 0.6068 (t-90)
REVERT: A  430 MET cc_start: 0.6543 (ptt) cc_final: 0.6104 (ptt)
REVERT: B   62 MET cc_start: 0.7919 (mtp) cc_final: 0.7690 (mtp)
REVERT: B   63 LEU cc_start: 0.8990 (tt) cc_final: 0.8605 (mt)
REVERT: B   81 THR cc_start: 0.8657 (p) cc_final: 0.8293 (t)
REVERT: B  164 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.7362 (t80)
REVERT: B  363 LYS cc_start: 0.7435 (mttt) cc_final: 0.7031 (tttt)
REVERT: B  365 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.6953 (mpp)
REVERT: B  471 TYR cc_start: 0.8444 (m-80) cc_final: 0.7194 (m-10)
REVERT: C   81 THR cc_start: 0.8580 (p) cc_final: 0.8328 (t)
REVERT: C  226 SER cc_start: 0.8247 (t) cc_final: 0.7668 (p)
REVERT: C  251 PHE cc_start: 0.6982 (m-10) cc_final: 0.6610 (m-80)
REVERT: C  363 LYS cc_start: 0.7123 (mttt) cc_final: 0.6666 (mtmt)
REVERT: C  428 GLN cc_start: 0.8359 (mp10) cc_final: 0.8117 (mp10)
REVERT: C  448 MET cc_start: 0.6434 (pmm) cc_final: 0.6006 (pmm)
REVERT: C  471 TYR cc_start: 0.8490 (m-80) cc_final: 0.7225 (m-10)
  outliers start: 34
  outliers final: 24
  residues processed: 236
  average time/residue: 0.1037
  time to fit residues: 35.5752
Evaluate side-chains
  241 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 213
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  209 TYR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   62 MET
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  216 GLN
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  431 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 108 optimal weight:    0.0870
   chunk 19 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 120 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 81 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    1.3362

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  57 ASN
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 284 GLN
C 406 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.173422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.137574 restraints weight = 17905.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.139018 restraints weight = 10931.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.140350 restraints weight = 8393.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.140696 restraints weight = 6666.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.141178 restraints weight = 6229.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6675
moved from start:          0.5723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12030  Z= 0.129
  Angle     :  0.672  14.352  16344  Z= 0.332
  Chirality :  0.042   0.148   1836
  Planarity :  0.004   0.075   2031
  Dihedral  :  4.142  16.586   1557
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 24.25 %
    Favored  : 73.14 %
  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 are not related in a simple way.
  whole: -0.02 (0.22), residues: 1410
  helix:  0.69 (0.17), residues: 951
  sheet:  None (None), residues: 0
  loop : -1.43 (0.26), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 330 
 TYR   0.029   0.002   TYR B 152 
 PHE   0.032   0.001   PHE B  79 
 TRP   0.019   0.002   TRP C 143 
 HIS   0.007   0.001   HIS C 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (12027)
  covalent geometry    : angle       0.67093 (16338)
  SS BOND              : bond        0.00846 (    3)
  SS BOND              : angle       1.84530 (    6)
  hydrogen bonds       : bond        0.04038 (  696)
  hydrogen bonds       : angle       4.63919 ( 1971)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 220
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6876 (t80)
REVERT: A  248 LYS cc_start: 0.5881 (tptm) cc_final: 0.4905 (tttt)
REVERT: A  310 LEU cc_start: 0.7520 (mt) cc_final: 0.7013 (mt)
REVERT: A  324 PRO cc_start: 0.8143 (Cg_endo) cc_final: 0.7926 (Cg_exo)
REVERT: A  354 LEU cc_start: 0.8213 (mp) cc_final: 0.7973 (mp)
REVERT: A  406 HIS cc_start: 0.6233 (OUTLIER) cc_final: 0.5969 (t70)
REVERT: A  430 MET cc_start: 0.6539 (ptt) cc_final: 0.6126 (ptt)
REVERT: B   63 LEU cc_start: 0.8919 (tt) cc_final: 0.8589 (mt)
REVERT: B  164 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.7392 (t80)
REVERT: B  363 LYS cc_start: 0.7447 (mttt) cc_final: 0.7001 (tttt)
REVERT: B  365 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.6934 (mpp)
REVERT: B  471 TYR cc_start: 0.8483 (m-80) cc_final: 0.7193 (m-10)
REVERT: C   81 THR cc_start: 0.8483 (p) cc_final: 0.8218 (t)
REVERT: C  226 SER cc_start: 0.8206 (t) cc_final: 0.7570 (p)
REVERT: C  251 PHE cc_start: 0.6926 (m-10) cc_final: 0.6562 (m-80)
REVERT: C  363 LYS cc_start: 0.6978 (mttt) cc_final: 0.6548 (mtmt)
REVERT: C  365 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.6611 (mpp)
REVERT: C  428 GLN cc_start: 0.8352 (mp10) cc_final: 0.8030 (mp10)
REVERT: C  448 MET cc_start: 0.6626 (pmm) cc_final: 0.5981 (pmm)
REVERT: C  471 TYR cc_start: 0.8497 (m-80) cc_final: 0.7242 (m-10)
  outliers start: 33
  outliers final: 23
  residues processed: 238
  average time/residue: 0.1007
  time to fit residues: 34.9583
Evaluate side-chains
  246 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 218
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  209 TYR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   62 MET
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  216 GLN
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  406 HIS
Chi-restraints excluded: chain C residue  431 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 57 optimal weight:    7.9990
   chunk 97 optimal weight:    1.9990
   chunk 109 optimal weight:    0.0670
   chunk 94 optimal weight:   20.0000
   chunk 78 optimal weight:    0.6980
   chunk 137 optimal weight:    0.0170
   chunk 127 optimal weight:    9.9990
   chunk 86 optimal weight:    3.9990
   chunk 125 optimal weight:    0.8980
   chunk 131 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0060
   overall best weight:    0.3372

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

Flipped N/Q/H residues before XYZ refinement:
C  57 ASN
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 406 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.176748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.140390 restraints weight = 17767.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.140560 restraints weight = 10823.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.140778 restraints weight = 8704.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.141860 restraints weight = 7679.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.142149 restraints weight = 6892.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6617
moved from start:          0.5916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12030  Z= 0.121
  Angle     :  0.672  14.617  16344  Z= 0.332
  Chirality :  0.042   0.177   1836
  Planarity :  0.004   0.062   2031
  Dihedral  :  4.063  17.195   1557
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 24.64 %
    Favored  : 73.14 %
  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 are not related in a simple way.
  whole:  0.15 (0.22), residues: 1410
  helix:  0.77 (0.17), residues: 960
  sheet:  None (None), residues: 0
  loop : -1.26 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 330 
 TYR   0.031   0.001   TYR B 152 
 PHE   0.034   0.001   PHE B  79 
 TRP   0.018   0.001   TRP C 143 
 HIS   0.009   0.000   HIS C 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (12027)
  covalent geometry    : angle       0.67159 (16338)
  SS BOND              : bond        0.00841 (    3)
  SS BOND              : angle       1.72094 (    6)
  hydrogen bonds       : bond        0.03928 (  696)
  hydrogen bonds       : angle       4.51131 ( 1971)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1956.03 seconds
wall clock time: 34 minutes 32.52 seconds (2072.52 seconds total)