Starting phenix.real_space_refine
on Wed Mar  4 01:28:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nt9_0506/03_2026/6nt9_0506.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nt9_0506/03_2026/6nt9_0506.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nt9_0506/03_2026/6nt9_0506.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nt9_0506/03_2026/6nt9_0506.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nt9_0506/03_2026/6nt9_0506.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nt9_0506/03_2026/6nt9_0506.cif"
  }
  resolution = 3.3
  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=   0.001 sd=   0.009
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      48      5.16       5
     C    6314      2.51       5
     N    1692      2.21       5
     O    1852      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  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: 9906
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 605, 4881
          Classifications: {'peptide': 605}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 19, 'TRANS': 585}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 72
          Classifications: {'peptide': 9}
          Link IDs: {'PTRANS': 2, 'TRANS': 6}
  Restraints were copied for chains:
    B, D
  Time building chain proxies: 3.67, per 1000 atoms: 0.37
  Number of scatterers: 9906
  At special positions: 0
  Unit cell: (80.25, 114.49, 144.45, 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      48     16.00
     O    1852      8.00
     N    1692      7.00
     C    6314      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 351.0 milliseconds
  

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2320

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 10 sheets defined
      55.4% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 61
      removed outlier: 3.751A  pdb=" N   LYS A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 99
      removed outlier: 3.524A  pdb=" N   VAL A  97 " --> pdb=" O   SER A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 104
    Processing helix  chain 'A' and resid 108 through 130
      removed outlier: 3.684A  pdb=" N   ASN A 129 " --> pdb=" O   HIS A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 217
    Processing helix  chain 'A' and resid 232 through 240
      removed outlier: 3.731A  pdb=" N   GLY A 240 " --> pdb=" O   LYS A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 285
      removed outlier: 3.943A  pdb=" N   LEU A 276 " --> pdb=" O   GLY A 272 " (cutoff:3.500A)
      Proline residue:  A 279  - end of helix
    Processing helix  chain 'A' and resid 294 through 307
      removed outlier: 3.836A  pdb=" N   PHE A 298 " --> pdb=" O   GLY A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 344
      removed outlier: 3.597A  pdb=" N   PHE A 335 " --> pdb=" O   THR A 331 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLN A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 370
      removed outlier: 3.776A  pdb=" N   PHE A 370 " --> pdb=" O   ALA A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 483
      removed outlier: 3.802A  pdb=" N   SER A 413 " --> pdb=" O   ASP A 409 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   GLU A 448 " --> pdb=" O   ARG A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 527
      removed outlier: 3.882A  pdb=" N   LYS A 504 " --> pdb=" O   ASP A 500 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   THR A 517 " --> pdb=" O   GLY A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 539
      removed outlier: 3.857A  pdb=" N   HIS A 538 " --> pdb=" O   ALA A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 572
      removed outlier: 3.751A  pdb=" N   LEU A 555 " --> pdb=" O   LYS A 551 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ALA A 571 " --> pdb=" O   LYS A 567 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLU A 572 " --> pdb=" O   LYS A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 605
      removed outlier: 3.808A  pdb=" N   TYR A 591 " --> pdb=" O   LYS A 587 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   THR A 602 " --> pdb=" O   MET A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 658
      removed outlier: 4.057A  pdb=" N   GLU A 618 " --> pdb=" O   ASN A 614 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU A 631 " --> pdb=" O   ARG A 627 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   LYS A 646 " --> pdb=" O   GLU A 642 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LEU A 658 " --> pdb=" O   LEU A 654 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 61
      removed outlier: 3.751A  pdb=" N   LYS B  61 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 99
      removed outlier: 3.525A  pdb=" N   VAL B  97 " --> pdb=" O   SER B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 104
    Processing helix  chain 'B' and resid 108 through 130
      removed outlier: 3.683A  pdb=" N   ASN B 129 " --> pdb=" O   HIS B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 217
    Processing helix  chain 'B' and resid 232 through 240
      removed outlier: 3.731A  pdb=" N   GLY B 240 " --> pdb=" O   LYS B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 285
      removed outlier: 3.943A  pdb=" N   LEU B 276 " --> pdb=" O   GLY B 272 " (cutoff:3.500A)
      Proline residue:  B 279  - end of helix
    Processing helix  chain 'B' and resid 294 through 307
      removed outlier: 3.835A  pdb=" N   PHE B 298 " --> pdb=" O   GLY B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 344
      removed outlier: 3.598A  pdb=" N   PHE B 335 " --> pdb=" O   THR B 331 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLN B 342 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 370
      removed outlier: 3.775A  pdb=" N   PHE B 370 " --> pdb=" O   ALA B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 483
      removed outlier: 3.803A  pdb=" N   SER B 413 " --> pdb=" O   ASP B 409 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   GLU B 448 " --> pdb=" O   ARG B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 527
      removed outlier: 3.883A  pdb=" N   LYS B 504 " --> pdb=" O   ASP B 500 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   THR B 517 " --> pdb=" O   GLY B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 535 through 539
      removed outlier: 3.857A  pdb=" N   HIS B 538 " --> pdb=" O   ALA B 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 572
      removed outlier: 3.750A  pdb=" N   LEU B 555 " --> pdb=" O   LYS B 551 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ALA B 571 " --> pdb=" O   LYS B 567 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLU B 572 " --> pdb=" O   LYS B 568 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 576 through 605
      removed outlier: 3.808A  pdb=" N   TYR B 591 " --> pdb=" O   LYS B 587 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   THR B 602 " --> pdb=" O   MET B 598 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 605 through 658
      removed outlier: 4.057A  pdb=" N   GLU B 618 " --> pdb=" O   ASN B 614 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU B 631 " --> pdb=" O   ARG B 627 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   LYS B 646 " --> pdb=" O   GLU B 642 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU B 658 " --> pdb=" O   LEU B 654 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3
      removed outlier: 6.548A  pdb=" N   ARG A  25 " --> pdb=" O   ILE A  14 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ILE A  14 " --> pdb=" O   ARG A  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 3
      removed outlier: 5.055A  pdb=" N   LYS A  82 " --> pdb=" O   PHE A  40 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA A  72 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 145
    Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 222
      removed outlier: 3.593A  pdb=" N   SER A 247 " --> pdb=" O   SER A 260 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 320 through 326
      removed outlier: 9.695A  pdb=" N   ILE A 379 " --> pdb=" O   VAL A 310 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   HIS A 312 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   VAL A 381 " --> pdb=" O   HIS A 312 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   PHE A 314 " --> pdb=" O   VAL A 381 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   LEU A 352 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 3
      removed outlier: 6.548A  pdb=" N   ARG B  25 " --> pdb=" O   ILE B  14 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ILE B  14 " --> pdb=" O   ARG B  25 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 3
      removed outlier: 5.055A  pdb=" N   LYS B  82 " --> pdb=" O   PHE B  40 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA B  72 " --> pdb=" O   ILE B  85 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 141 through 145
    Processing sheet with id=AA9, first strand: chain 'B' and resid 221 through 222
      removed outlier: 3.593A  pdb=" N   SER B 247 " --> pdb=" O   SER B 260 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 320 through 326
      removed outlier: 9.695A  pdb=" N   ILE B 379 " --> pdb=" O   VAL B 310 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   HIS B 312 " --> pdb=" O   ILE B 379 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   VAL B 381 " --> pdb=" O   HIS B 312 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   PHE B 314 " --> pdb=" O   VAL B 381 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   LEU B 352 " --> pdb=" O   LEU B 359 " (cutoff:3.500A)

    596 hydrogen bonds defined for protein.
    1728 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: 1.48

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2878
        1.33 -     1.45: 1642
        1.45 -     1.57: 5508
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 10104
  Sorted by residual:
  bond pdb=" CB  VAL B 381 "
       pdb=" CG2 VAL B 381 "
    ideal  model  delta    sigma   weight residual
    1.521  1.449  0.072 3.30e-02 9.18e+02 4.82e+00
  bond pdb=" CB  VAL A 381 "
       pdb=" CG2 VAL A 381 "
    ideal  model  delta    sigma   weight residual
    1.521  1.450  0.071 3.30e-02 9.18e+02 4.64e+00
  bond pdb=" CB  ILE B 418 "
       pdb=" CG2 ILE B 418 "
    ideal  model  delta    sigma   weight residual
    1.521  1.451  0.070 3.30e-02 9.18e+02 4.56e+00
  bond pdb=" CB  ILE A 418 "
       pdb=" CG2 ILE A 418 "
    ideal  model  delta    sigma   weight residual
    1.521  1.451  0.070 3.30e-02 9.18e+02 4.51e+00
  bond pdb=" CG  LEU C 374 "
       pdb=" CD2 LEU C 374 "
    ideal  model  delta    sigma   weight residual
    1.521  1.468  0.053 3.30e-02 9.18e+02 2.58e+00
  ... (remaining 10099 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 13210
        2.26 -     4.52: 399
        4.52 -     6.78: 27
        6.78 -     9.04: 2
        9.04 -    11.30: 4
  Bond angle restraints: 13642
  Sorted by residual:
  angle pdb=" C   GLY A 175 "
        pdb=" N   THR A 176 "
        pdb=" CA  THR A 176 "
      ideal   model   delta    sigma   weight residual
     121.54  131.08   -9.54 1.91e+00 2.74e-01 2.49e+01
  angle pdb=" C   GLY B 175 "
        pdb=" N   THR B 176 "
        pdb=" CA  THR B 176 "
      ideal   model   delta    sigma   weight residual
     121.54  131.07   -9.53 1.91e+00 2.74e-01 2.49e+01
  angle pdb=" C   PRO D 371 "
        pdb=" N   GLN D 372 "
        pdb=" CA  GLN D 372 "
      ideal   model   delta    sigma   weight residual
     122.15  133.45  -11.30 3.47e+00 8.31e-02 1.06e+01
  angle pdb=" C   PRO C 371 "
        pdb=" N   GLN C 372 "
        pdb=" CA  GLN C 372 "
      ideal   model   delta    sigma   weight residual
     122.15  133.41  -11.26 3.47e+00 8.31e-02 1.05e+01
  angle pdb=" C   GLY B 294 "
        pdb=" N   PHE B 295 "
        pdb=" CA  PHE B 295 "
      ideal   model   delta    sigma   weight residual
     122.09  116.95    5.14 1.79e+00 3.12e-01 8.23e+00
  ... (remaining 13637 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.55: 5778
       14.55 -    29.10: 232
       29.10 -    43.64: 76
       43.64 -    58.19: 6
       58.19 -    72.74: 6
  Dihedral angle restraints: 6098
    sinusoidal: 2516
      harmonic: 3582
  Sorted by residual:
  dihedral pdb=" CA  TRP A 293 "
           pdb=" C   TRP A 293 "
           pdb=" N   GLY A 294 "
           pdb=" CA  GLY A 294 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.32  -16.68     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  TRP B 293 "
           pdb=" C   TRP B 293 "
           pdb=" N   GLY B 294 "
           pdb=" CA  GLY B 294 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.33  -16.67     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  ARG B 308 "
           pdb=" C   ARG B 308 "
           pdb=" N   MET B 309 "
           pdb=" CA  MET B 309 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.72   16.28     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 6095 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1015
       0.051 -    0.103: 424
       0.103 -    0.154: 81
       0.154 -    0.205: 8
       0.205 -    0.257: 4
  Chirality restraints: 1532
  Sorted by residual:
  chirality pdb=" CB  ILE A  73 "
            pdb=" CA  ILE A  73 "
            pdb=" CG1 ILE A  73 "
            pdb=" CG2 ILE A  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CB  ILE B  73 "
            pdb=" CA  ILE B  73 "
            pdb=" CG1 ILE B  73 "
            pdb=" CG2 ILE B  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CA  THR B 176 "
            pdb=" N   THR B 176 "
            pdb=" C   THR B 176 "
            pdb=" CB  THR B 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.31    0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 1529 not shown)

  Planarity restraints: 1732
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 137 "    0.044 5.00e-02 4.00e+02   6.65e-02 7.07e+00
        pdb=" N   PRO B 138 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO B 138 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 138 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 137 "    0.044 5.00e-02 4.00e+02   6.63e-02 7.04e+00
        pdb=" N   PRO A 138 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 138 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 138 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 325 "   -0.019 2.00e-02 2.50e+03   1.86e-02 6.94e+00
        pdb=" CG  TYR A 325 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 325 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 325 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 325 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 325 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 325 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 325 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1729 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2114
        2.78 -     3.31: 8637
        3.31 -     3.84: 15360
        3.84 -     4.37: 17261
        4.37 -     4.90: 31485
  Nonbonded interactions: 74857
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 111 "
            pdb=" OH  TYR B 153 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OE2 GLU A 111 "
            pdb=" OH  TYR A 153 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" NH2 ARG A 357 "
            pdb=" OD2 ASP B 452 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" O   ASP A 523 "
            pdb=" OG  SER A 527 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" O   ASP B 523 "
            pdb=" OG  SER B 527 "
     model   vdw
     2.342 3.040
  ... (remaining 74852 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'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.860
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.260
  Find NCS groups from input model:        0.070
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
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      :  0.010   0.074  10104  Z= 0.416
  Angle     :  0.894  11.305  13642  Z= 0.489
  Chirality :  0.056   0.257   1532
  Planarity :  0.007   0.066   1732
  Dihedral  :  9.659  72.738   3778
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 1.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.73 %
    Favored  : 98.09 %
  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: -2.03 (0.20), residues: 1200
  helix: -0.77 (0.17), residues: 628
  sheet: -1.48 (0.39), residues: 146
  loop : -1.98 (0.25), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 357 
 TYR   0.043   0.003   TYR A 325 
 PHE   0.030   0.003   PHE A 585 
 TRP   0.029   0.003   TRP A 619 
 HIS   0.015   0.003   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.01029 (10104)
  covalent geometry    : angle       0.89404 (13642)
  hydrogen bonds       : bond        0.14260 (  588)
  hydrogen bonds       : angle       5.44051 ( 1728)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 196
  time to evaluate  : 0.442 
Fit side-chains
REVERT: A   13 ASP cc_start: 0.7775 (m-30) cc_final: 0.7526 (m-30)
REVERT: A   61 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8243 (mtmm)
REVERT: A  234 MET cc_start: 0.7488 (tpt) cc_final: 0.7121 (mmm)
REVERT: A  320 THR cc_start: 0.8756 (p) cc_final: 0.8534 (p)
REVERT: A  351 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7538 (mt-10)
REVERT: A  409 ASP cc_start: 0.8086 (m-30) cc_final: 0.7717 (m-30)
REVERT: A  414 MET cc_start: 0.8321 (tmm) cc_final: 0.8026 (ttp)
REVERT: A  564 TYR cc_start: 0.8038 (m-10) cc_final: 0.7720 (m-10)
REVERT: A  648 GLN cc_start: 0.7530 (tt0) cc_final: 0.7195 (tp40)
REVERT: B   53 MET cc_start: 0.7450 (mmm) cc_final: 0.7221 (mmp)
REVERT: B   61 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8105 (mtmm)
REVERT: B  234 MET cc_start: 0.7409 (tpt) cc_final: 0.7047 (mmm)
REVERT: B  374 THR cc_start: 0.9056 (p) cc_final: 0.8813 (m)
REVERT: B  376 GLU cc_start: 0.8084 (mp0) cc_final: 0.7712 (mp0)
REVERT: B  462 THR cc_start: 0.7978 (m) cc_final: 0.7571 (p)
REVERT: B  534 ASP cc_start: 0.8503 (p0) cc_final: 0.8260 (p0)
REVERT: B  564 TYR cc_start: 0.8174 (m-10) cc_final: 0.7695 (m-10)
REVERT: B  648 GLN cc_start: 0.7670 (tt0) cc_final: 0.7053 (tp-100)
  outliers start: 2
  outliers final: 0
  residues processed: 198
  average time/residue: 0.1047
  time to fit residues: 28.3284
Evaluate side-chains
  111 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 117 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  81 HIS
A 369 HIS
** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 GLN
B  81 HIS
B 312 HIS
B 369 HIS
** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 581 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.122966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.094060 restraints weight = 14072.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.00
r_work: 0.2989 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10104  Z= 0.135
  Angle     :  0.498   6.856  13642  Z= 0.265
  Chirality :  0.040   0.130   1532
  Planarity :  0.004   0.038   1732
  Dihedral  :  3.933  16.324   1318
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  6.28 %
    Favored  : 93.08 %
  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:  0.54 (0.24), residues: 1200
  helix:  1.87 (0.20), residues: 626
  sheet: -1.49 (0.39), residues: 136
  loop : -1.27 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  80 
 TYR   0.012   0.001   TYR B 325 
 PHE   0.021   0.001   PHE B 470 
 TRP   0.019   0.001   TRP B 619 
 HIS   0.009   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10104)
  covalent geometry    : angle       0.49792 (13642)
  hydrogen bonds       : bond        0.06639 (  588)
  hydrogen bonds       : angle       3.96722 ( 1728)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 140
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A   37 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8994 (mp)
REVERT: A   61 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8383 (mtmm)
REVERT: A  234 MET cc_start: 0.7495 (tpt) cc_final: 0.7201 (mmm)
REVERT: A  337 GLU cc_start: 0.8560 (tt0) cc_final: 0.8280 (mm-30)
REVERT: A  351 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7960 (mt-10)
REVERT: A  409 ASP cc_start: 0.8514 (m-30) cc_final: 0.8109 (m-30)
REVERT: A  648 GLN cc_start: 0.7619 (tt0) cc_final: 0.6955 (tp-100)
REVERT: B   57 GLU cc_start: 0.8502 (tp30) cc_final: 0.7367 (mt-10)
REVERT: B   61 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8309 (mtmm)
REVERT: B  234 MET cc_start: 0.7362 (tpt) cc_final: 0.7008 (mmm)
REVERT: B  376 GLU cc_start: 0.8821 (mp0) cc_final: 0.8445 (mp0)
REVERT: B  462 THR cc_start: 0.7953 (m) cc_final: 0.7488 (p)
REVERT: B  561 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8212 (mm-30)
REVERT: B  564 TYR cc_start: 0.8582 (m-10) cc_final: 0.8271 (m-10)
  outliers start: 7
  outliers final: 3
  residues processed: 142
  average time/residue: 0.1026
  time to fit residues: 20.8486
Evaluate side-chains
  114 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 110
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  522 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   chunk 56 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   chunk 108 optimal weight:    6.9990
   chunk 102 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 289 GLN
B 312 HIS
** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.123089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.094449 restraints weight = 14203.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 2.06
r_work: 0.2930 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10104  Z= 0.194
  Angle     :  0.535   6.109  13642  Z= 0.282
  Chirality :  0.043   0.143   1532
  Planarity :  0.004   0.044   1732
  Dihedral  :  3.770  14.756   1318
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  7.83 %
    Favored  : 90.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.22 (0.24), residues: 1200
  helix:  2.42 (0.20), residues: 630
  sheet: -1.45 (0.40), residues: 136
  loop : -0.86 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 440 
 TYR   0.020   0.001   TYR B 325 
 PHE   0.017   0.002   PHE A 470 
 TRP   0.013   0.002   TRP B 619 
 HIS   0.007   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (10104)
  covalent geometry    : angle       0.53463 (13642)
  hydrogen bonds       : bond        0.06900 (  588)
  hydrogen bonds       : angle       3.95962 ( 1728)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8986 (mp)
REVERT: A   61 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8349 (mtmm)
REVERT: A  351 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7980 (mt-10)
REVERT: A  409 ASP cc_start: 0.8586 (m-30) cc_final: 0.8243 (m-30)
REVERT: A  516 GLU cc_start: 0.8245 (tp30) cc_final: 0.7855 (tp30)
REVERT: A  648 GLN cc_start: 0.7551 (tt0) cc_final: 0.6955 (tp-100)
REVERT: B   37 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8918 (mp)
REVERT: B   61 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8259 (mtmm)
REVERT: B  234 MET cc_start: 0.7511 (tpt) cc_final: 0.7249 (mmm)
REVERT: B  462 THR cc_start: 0.7983 (m) cc_final: 0.7415 (p)
REVERT: B  564 TYR cc_start: 0.8676 (m-10) cc_final: 0.8417 (m-10)
  outliers start: 15
  outliers final: 10
  residues processed: 123
  average time/residue: 0.0995
  time to fit residues: 17.6568
Evaluate side-chains
  122 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   86 MET
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 116 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 459 HIS
C 372 GLN
B 459 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.121012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.092429 restraints weight = 14372.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 2.04
r_work: 0.2897 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.2492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  10104  Z= 0.248
  Angle     :  0.573   7.423  13642  Z= 0.302
  Chirality :  0.045   0.148   1532
  Planarity :  0.004   0.046   1732
  Dihedral  :  3.855  14.463   1318
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  8.11 %
    Favored  : 90.07 %
  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:  1.31 (0.24), residues: 1200
  helix:  2.49 (0.20), residues: 630
  sheet: -1.44 (0.40), residues: 136
  loop : -0.82 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 440 
 TYR   0.023   0.002   TYR A 325 
 PHE   0.016   0.002   PHE B 470 
 TRP   0.010   0.001   TRP A 619 
 HIS   0.007   0.001   HIS A 593 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 (10104)
  covalent geometry    : angle       0.57298 (13642)
  hydrogen bonds       : bond        0.07255 (  588)
  hydrogen bonds       : angle       4.03780 ( 1728)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A   37 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8954 (mp)
REVERT: A   61 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8220 (mtmm)
REVERT: A  351 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8059 (mt-10)
REVERT: A  376 GLU cc_start: 0.8745 (mp0) cc_final: 0.8480 (mp0)
REVERT: A  409 ASP cc_start: 0.8559 (m-30) cc_final: 0.8172 (m-30)
REVERT: A  516 GLU cc_start: 0.8318 (tp30) cc_final: 0.7886 (tp30)
REVERT: A  648 GLN cc_start: 0.7464 (tt0) cc_final: 0.6780 (tp-100)
REVERT: B   37 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8937 (mp)
REVERT: B   57 GLU cc_start: 0.8549 (tp30) cc_final: 0.7692 (mt-10)
REVERT: B   61 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8292 (mtmm)
REVERT: B  376 GLU cc_start: 0.8763 (mp0) cc_final: 0.8510 (mp0)
REVERT: B  564 TYR cc_start: 0.8658 (m-10) cc_final: 0.8395 (m-10)
REVERT: B  648 GLN cc_start: 0.7171 (tt0) cc_final: 0.6381 (tp-100)
  outliers start: 20
  outliers final: 13
  residues processed: 131
  average time/residue: 0.0984
  time to fit residues: 18.7277
Evaluate side-chains
  124 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   86 MET
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 103 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 119 optimal weight:    2.9990
   chunk 84 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 117 optimal weight:    0.6980
   chunk 104 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.123927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.094815 restraints weight = 14289.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 2.07
r_work: 0.2852 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10104  Z= 0.140
  Angle     :  0.479   6.093  13642  Z= 0.253
  Chirality :  0.041   0.141   1532
  Planarity :  0.003   0.043   1732
  Dihedral  :  3.548  13.890   1318
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.11 %
    Favored  : 89.16 %
  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:  1.76 (0.25), residues: 1200
  helix:  2.91 (0.20), residues: 630
  sheet: -1.32 (0.41), residues: 142
  loop : -0.63 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 405 
 TYR   0.009   0.001   TYR B 153 
 PHE   0.016   0.001   PHE A 470 
 TRP   0.010   0.001   TRP A 619 
 HIS   0.006   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10104)
  covalent geometry    : angle       0.47927 (13642)
  hydrogen bonds       : bond        0.06178 (  588)
  hydrogen bonds       : angle       3.77068 ( 1728)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.420 
Fit side-chains
REVERT: A   37 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8904 (mp)
REVERT: A   61 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8285 (mtmm)
REVERT: A  351 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7994 (mt-10)
REVERT: A  376 GLU cc_start: 0.8703 (mp0) cc_final: 0.8455 (mp0)
REVERT: A  409 ASP cc_start: 0.8555 (m-30) cc_final: 0.8120 (m-30)
REVERT: A  648 GLN cc_start: 0.7355 (tt0) cc_final: 0.6696 (tp-100)
REVERT: B   37 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8902 (mp)
REVERT: B   61 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8282 (mtmm)
REVERT: B  523 ASP cc_start: 0.8117 (t70) cc_final: 0.7753 (t0)
REVERT: B  648 GLN cc_start: 0.7138 (tt0) cc_final: 0.6376 (tp-100)
  outliers start: 19
  outliers final: 14
  residues processed: 132
  average time/residue: 0.0934
  time to fit residues: 18.0113
Evaluate side-chains
  128 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   86 MET
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  293 TRP
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 110 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 44 optimal weight:   10.0000
   chunk 98 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.125630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.097202 restraints weight = 14258.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 2.00
r_work: 0.2926 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2789 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  10104  Z= 0.179
  Angle     :  0.506   5.989  13642  Z= 0.266
  Chirality :  0.042   0.141   1532
  Planarity :  0.004   0.046   1732
  Dihedral  :  3.542  13.460   1318
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  :  9.20 %
    Favored  : 88.34 %
  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:  1.81 (0.25), residues: 1200
  helix:  2.93 (0.20), residues: 630
  sheet: -1.37 (0.41), residues: 142
  loop : -0.57 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 222 
 TYR   0.011   0.001   TYR A 325 
 PHE   0.016   0.001   PHE A 470 
 TRP   0.009   0.001   TRP A 619 
 HIS   0.005   0.001   HIS B 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (10104)
  covalent geometry    : angle       0.50574 (13642)
  hydrogen bonds       : bond        0.06484 (  588)
  hydrogen bonds       : angle       3.82184 ( 1728)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A   37 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8870 (mp)
REVERT: A   61 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8304 (mtmm)
REVERT: A  351 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7991 (mt-10)
REVERT: A  376 GLU cc_start: 0.8679 (mp0) cc_final: 0.8435 (mp0)
REVERT: A  409 ASP cc_start: 0.8558 (m-30) cc_final: 0.8088 (m-30)
REVERT: A  516 GLU cc_start: 0.8252 (tp30) cc_final: 0.7826 (tp30)
REVERT: A  648 GLN cc_start: 0.7330 (tt0) cc_final: 0.6645 (tp-100)
REVERT: B   37 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8864 (mp)
REVERT: B   61 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8248 (mtmm)
REVERT: B  376 GLU cc_start: 0.8726 (mp0) cc_final: 0.8459 (mp0)
REVERT: B  523 ASP cc_start: 0.8095 (t70) cc_final: 0.7744 (t0)
  outliers start: 27
  outliers final: 16
  residues processed: 136
  average time/residue: 0.0834
  time to fit residues: 16.7887
Evaluate side-chains
  125 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   86 MET
Chi-restraints excluded: chain A residue  293 TRP
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  293 TRP
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 112 optimal weight:    0.7980
   chunk 96 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 93 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0570
   chunk 47 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 372 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.126524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.097922 restraints weight = 14217.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.02
r_work: 0.2816 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2675 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.3050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  10104  Z= 0.116
  Angle     :  0.452   5.601  13642  Z= 0.237
  Chirality :  0.040   0.129   1532
  Planarity :  0.003   0.045   1732
  Dihedral  :  3.293  12.931   1318
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  9.93 %
    Favored  : 88.25 %
  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:  2.20 (0.25), residues: 1200
  helix:  3.24 (0.20), residues: 630
  sheet: -1.25 (0.42), residues: 136
  loop : -0.35 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 357 
 TYR   0.009   0.001   TYR B 153 
 PHE   0.017   0.001   PHE A 470 
 TRP   0.009   0.001   TRP A 619 
 HIS   0.009   0.001   HIS A 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (10104)
  covalent geometry    : angle       0.45175 (13642)
  hydrogen bonds       : bond        0.05520 (  588)
  hydrogen bonds       : angle       3.60023 ( 1728)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A   61 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8310 (mtmm)
REVERT: A  376 GLU cc_start: 0.8674 (mp0) cc_final: 0.8439 (mp0)
REVERT: B   37 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8897 (mp)
REVERT: B   61 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8227 (mtmm)
REVERT: B   65 LYS cc_start: 0.8808 (ptmt) cc_final: 0.8531 (pttt)
REVERT: B  561 GLU cc_start: 0.8261 (tm-30) cc_final: 0.8013 (tm-30)
  outliers start: 20
  outliers final: 14
  residues processed: 134
  average time/residue: 0.0839
  time to fit residues: 16.6485
Evaluate side-chains
  127 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   86 MET
Chi-restraints excluded: chain A residue  293 TRP
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  293 TRP
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  462 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 44 optimal weight:   20.0000
   chunk 5 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 115 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0570
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
A 133 HIS
** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 372 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.132128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.103375 restraints weight = 13877.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 1.89
r_work: 0.2950 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2805 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10104  Z= 0.119
  Angle     :  0.462   6.894  13642  Z= 0.241
  Chirality :  0.039   0.131   1532
  Planarity :  0.003   0.043   1732
  Dihedral  :  3.196  12.282   1318
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 10.47 %
    Favored  : 87.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.37 (0.25), residues: 1200
  helix:  3.34 (0.20), residues: 632
  sheet: -1.23 (0.42), residues: 136
  loop : -0.20 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 627 
 TYR   0.009   0.001   TYR A 153 
 PHE   0.016   0.001   PHE A 470 
 TRP   0.008   0.001   TRP B 619 
 HIS   0.003   0.001   HIS A 593 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (10104)
  covalent geometry    : angle       0.46177 (13642)
  hydrogen bonds       : bond        0.05405 (  588)
  hydrogen bonds       : angle       3.53012 ( 1728)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A   37 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8984 (mp)
REVERT: A   61 LYS cc_start: 0.8652 (mmtt) cc_final: 0.8303 (mtmm)
REVERT: B   37 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.9001 (mp)
REVERT: B   61 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8201 (mtmm)
REVERT: B   65 LYS cc_start: 0.8848 (ptmt) cc_final: 0.8611 (pttt)
  outliers start: 20
  outliers final: 17
  residues processed: 126
  average time/residue: 0.0896
  time to fit residues: 16.6452
Evaluate side-chains
  126 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   86 MET
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  293 TRP
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  293 TRP
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0170
   chunk 20 optimal weight:    4.9990
   chunk 99 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0470
   chunk 13 optimal weight:    0.0070
   chunk 65 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 113 optimal weight:    0.4980
   overall best weight:    0.2734

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 312 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.136220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.107745 restraints weight = 13965.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 1.87
r_work: 0.3036 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10104  Z= 0.098
  Angle     :  0.428   6.476  13642  Z= 0.223
  Chirality :  0.038   0.128   1532
  Planarity :  0.003   0.041   1732
  Dihedral  :  3.007  11.321   1318
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.38 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.70 (0.25), residues: 1200
  helix:  3.58 (0.20), residues: 632
  sheet: -1.08 (0.42), residues: 136
  loop :  0.01 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 357 
 TYR   0.008   0.001   TYR A 153 
 PHE   0.016   0.001   PHE A 470 
 TRP   0.007   0.001   TRP A 619 
 HIS   0.003   0.000   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00190 (10104)
  covalent geometry    : angle       0.42814 (13642)
  hydrogen bonds       : bond        0.04534 (  588)
  hydrogen bonds       : angle       3.28243 ( 1728)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A   59 LEU cc_start: 0.8597 (mp) cc_final: 0.8264 (tt)
REVERT: A   61 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8342 (mtmm)
REVERT: A  337 GLU cc_start: 0.8557 (tt0) cc_final: 0.8239 (mm-30)
REVERT: A  439 MET cc_start: 0.8903 (tpt) cc_final: 0.8702 (mmm)
REVERT: A  459 HIS cc_start: 0.7039 (t70) cc_final: 0.6665 (t70)
REVERT: B   56 PHE cc_start: 0.8205 (m-10) cc_final: 0.7895 (m-80)
REVERT: B   61 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8173 (mtmm)
REVERT: B   65 LYS cc_start: 0.8829 (ptmt) cc_final: 0.8601 (pttt)
REVERT: B  523 ASP cc_start: 0.8033 (t70) cc_final: 0.7734 (t0)
REVERT: B  561 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8081 (tm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 131
  average time/residue: 0.0941
  time to fit residues: 17.9622
Evaluate side-chains
  112 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain B residue  293 TRP
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0980
   chunk 94 optimal weight:    7.9990
   chunk 109 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 79 optimal weight:    0.0040
   chunk 19 optimal weight:    0.3980
   chunk 75 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.4592

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.135338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.106523 restraints weight = 13812.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 1.90
r_work: 0.3004 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.3540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10104  Z= 0.104
  Angle     :  0.448   8.070  13642  Z= 0.233
  Chirality :  0.039   0.178   1532
  Planarity :  0.003   0.039   1732
  Dihedral  :  2.985  13.887   1318
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 12.30 %
    Favored  : 87.07 %
  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:  2.80 (0.25), residues: 1200
  helix:  3.63 (0.20), residues: 630
  sheet: -1.02 (0.41), residues: 136
  loop :  0.11 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 357 
 TYR   0.007   0.001   TYR B 153 
 PHE   0.017   0.001   PHE A 470 
 TRP   0.009   0.001   TRP A 259 
 HIS   0.002   0.000   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 (10104)
  covalent geometry    : angle       0.44810 (13642)
  hydrogen bonds       : bond        0.04703 (  588)
  hydrogen bonds       : angle       3.33270 ( 1728)

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 111
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A   59 LEU cc_start: 0.8587 (mp) cc_final: 0.8263 (tt)
REVERT: A   61 LYS cc_start: 0.8663 (mmtt) cc_final: 0.8345 (mtmm)
REVERT: A  260 SER cc_start: 0.8363 (t) cc_final: 0.8082 (m)
REVERT: A  337 GLU cc_start: 0.8557 (tt0) cc_final: 0.8235 (mm-30)
REVERT: A  459 HIS cc_start: 0.7182 (t70) cc_final: 0.6682 (t70)
REVERT: A  512 GLN cc_start: 0.6584 (tt0) cc_final: 0.6312 (tp-100)
REVERT: B   61 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8161 (mtmm)
REVERT: B   65 LYS cc_start: 0.8821 (ptmt) cc_final: 0.8605 (pttt)
REVERT: B  559 MET cc_start: 0.9219 (mtm) cc_final: 0.9008 (mtm)
  outliers start: 7
  outliers final: 6
  residues processed: 116
  average time/residue: 0.0952
  time to fit residues: 16.1277
Evaluate side-chains
  113 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  293 TRP
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain B residue  293 TRP
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0870
   chunk 110 optimal weight:    1.9990
   chunk 100 optimal weight:    0.3980
   chunk 93 optimal weight:    0.5980
   chunk 82 optimal weight:    4.9990
   chunk 116 optimal weight:    0.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.5760

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.134567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.105653 restraints weight = 13994.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 1.89
r_work: 0.2993 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  10104  Z= 0.108
  Angle     :  0.450   7.942  13642  Z= 0.233
  Chirality :  0.039   0.129   1532
  Planarity :  0.003   0.037   1732
  Dihedral  :  3.006  13.905   1318
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 12.30 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.89 (0.25), residues: 1200
  helix:  3.68 (0.19), residues: 630
  sheet: -1.03 (0.41), residues: 136
  loop :  0.22 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 627 
 TYR   0.008   0.001   TYR A 153 
 PHE   0.015   0.001   PHE A 470 
 TRP   0.007   0.001   TRP A 619 
 HIS   0.002   0.000   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (10104)
  covalent geometry    : angle       0.44991 (13642)
  hydrogen bonds       : bond        0.04831 (  588)
  hydrogen bonds       : angle       3.35159 ( 1728)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2506.93 seconds
wall clock time: 43 minutes 34.77 seconds (2614.77 seconds total)