Starting phenix.real_space_refine
on Thu Jul  2 03:03:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gnr_51478/07_2026/9gnr_51478.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gnr_51478/07_2026/9gnr_51478.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gnr_51478/07_2026/9gnr_51478.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gnr_51478/07_2026/9gnr_51478.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gnr_51478/07_2026/9gnr_51478.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gnr_51478/07_2026/9gnr_51478.cif"
  }
  resolution = 2.92
  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=   0.002 sd=   0.028
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: 6
    Type Number    sf(0)   Gaussians
     Ni      2      6.56       5
     P       1      5.49       5
     S      30      5.16       5
     C    3788      2.51       5
     N    1048      2.21       5
     O    1185      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6054
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 777
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'CXM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 952
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 117}
    Chain: "C"
      Number of atoms: 4318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4318
          Classifications: {'peptide': 570}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 541}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 5
          Ad-hoc single atom residues: {' NI': 2}
          Unusual residues: {'2PA': 1}
          Classifications: {'undetermined': 1}
          Chain breaks: 2
  Residues with excluded nonbonded symmetry interactions: 27
    residue:
      pdb=" N   LYS A   8 " occ=0.70
      ... (7 atoms not shown)
      pdb=" NZ  LYS A   8 " occ=0.70
    residue:
      pdb=" N   GLN A  12 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NE2 GLN A  12 " occ=0.50
    residue:
      pdb=" N   LYS A  29 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS A  29 " occ=0.50
    residue:
      pdb=" N   MET A  44 " occ=0.70
      ... (6 atoms not shown)
      pdb=" CE  MET A  44 " occ=0.70
    residue:
      pdb=" N   MET A  70 " occ=0.70
      ... (6 atoms not shown)
      pdb=" CE  MET A  70 " occ=0.70
    residue:
      pdb=" N   ARG B  13 " occ=0.70
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  13 " occ=0.70
    residue:
      pdb=" N   GLY B  17 " occ=0.50
      ... (2 atoms not shown)
      pdb=" O   GLY B  17 " occ=0.50
    residue:
      pdb=" N   SER B  33 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER B  33 " occ=0.50
    residue:
      pdb=" N   GLU B  54 " occ=0.50
      ... (7 atoms not shown)
      pdb=" OE2 GLU B  54 " occ=0.50
    residue:
      pdb=" N   GLU B 111 " occ=0.70
      ... (7 atoms not shown)
      pdb=" OE2 GLU B 111 " occ=0.70
    residue:
      pdb=" N   MET C   1 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CE  MET C   1 " occ=0.50
    residue:
      pdb=" N   ARG C   5 " occ=0.50
      ... (9 atoms not shown)
      pdb=" NH2 ARG C   5 " occ=0.50
    ... (remaining 15 not shown)
  Time building chain proxies: 1.68, per 1000 atoms: 0.28
  Number of scatterers: 6054
  At special positions: 0
  Unit cell: (114.126, 78.565, 81.046, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ni      2     28.00
     S      30     16.00
     P       1     15.00
     O    1185      8.00
     N    1048      7.00
     C    3788      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: 0.56
  Conformation dependent library (CDL) restraints added in 226.6 milliseconds
  

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1416

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 11 sheets defined
      35.0% alpha, 21.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 26
      removed outlier: 3.515A  pdb=" N   LYS A   8 " --> pdb=" O   ASN A   4 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLN A  12 " --> pdb=" O   LYS A   8 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A  13 " --> pdb=" O   GLU A   9 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ARG A  26 " --> pdb=" O   LYS A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 50
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 65 through 69
      removed outlier: 3.575A  pdb=" N   VAL A  69 " --> pdb=" O   ARG A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 77
    Processing helix  chain 'B' and resid 47 through 51
      removed outlier: 3.736A  pdb=" N   VAL B  51 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 63
      removed outlier: 3.674A  pdb=" N   ILE B  63 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 120
    Processing helix  chain 'C' and resid 5 through 12
    Processing helix  chain 'C' and resid 144 through 151
      removed outlier: 3.737A  pdb=" N   VAL C 148 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 171
    Processing helix  chain 'C' and resid 176 through 187
    Processing helix  chain 'C' and resid 188 through 190
      No H-bonds generated for 'chain 'C' and resid 188 through 190'
    Processing helix  chain 'C' and resid 204 through 215
      removed outlier: 4.153A  pdb=" N   ILE C 208 " --> pdb=" O   SER C 204 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLN C 211 " --> pdb=" O   PRO C 207 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE C 212 " --> pdb=" O   ILE C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 243
    Processing helix  chain 'C' and resid 258 through 267
    Processing helix  chain 'C' and resid 286 through 293
    Processing helix  chain 'C' and resid 308 through 318
      removed outlier: 4.400A  pdb=" N   ILE C 312 " --> pdb=" O   THR C 308 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   ASP C 313 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU C 316 " --> pdb=" O   ILE C 312 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   ASP C 317 " --> pdb=" O   ASP C 313 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   MET C 318 " --> pdb=" O   GLU C 314 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 319 through 322
    Processing helix  chain 'C' and resid 329 through 340
    Processing helix  chain 'C' and resid 341 through 354
      removed outlier: 3.583A  pdb=" N   ILE C 350 " --> pdb=" O   ALA C 346 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 372 through 389
    Processing helix  chain 'C' and resid 399 through 408
    Processing helix  chain 'C' and resid 412 through 418
    Processing helix  chain 'C' and resid 480 through 484
      removed outlier: 6.769A  pdb=" N   GLY C 484 " --> pdb=" O   GLY C 481 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 485 through 490
      removed outlier: 3.764A  pdb=" N   ASP C 489 " --> pdb=" O   ASP C 485 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 496 through 503
    Processing helix  chain 'C' and resid 503 through 509
    Processing helix  chain 'C' and resid 524 through 528
    Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 86
    Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 13
    Processing sheet with id=AA3, first strand: chain 'B' and resid 18 through 20
    Processing sheet with id=AA4, first strand: chain 'B' and resid 55 through 56
    Processing sheet with id=AA5, first strand: chain 'B' and resid 40 through 43
    Processing sheet with id=AA6, first strand: chain 'B' and resid 95 through 96
    Processing sheet with id=AA7, first strand: chain 'C' and resid 93 through 98
      removed outlier: 5.091A  pdb=" N   ILE C  94 " --> pdb=" O   LYS C  90 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   LYS C  90 " --> pdb=" O   ILE C  94 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY C  96 " --> pdb=" O   GLY C  88 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   TYR C  83 " --> pdb=" O   LEU C  75 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   LEU C  75 " --> pdb=" O   TYR C  83 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   ALA C  85 " --> pdb=" O   ASN C  73 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  85 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   LEU C  70 " --> pdb=" O   ILE C 122 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 93 through 98
      removed outlier: 5.091A  pdb=" N   ILE C  94 " --> pdb=" O   LYS C  90 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   LYS C  90 " --> pdb=" O   ILE C  94 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY C  96 " --> pdb=" O   GLY C  88 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   TYR C  83 " --> pdb=" O   LEU C  75 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   LEU C  75 " --> pdb=" O   TYR C  83 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   ALA C  85 " --> pdb=" O   ASN C  73 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  85 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ALA C 131 " --> pdb=" O   LEU C  77 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   LYS C 452 " --> pdb=" O   ILE C 456 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   ILE C 456 " --> pdb=" O   LYS C 452 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 133 through 139
      removed outlier: 6.649A  pdb=" N   GLY C 133 " --> pdb=" O   THR C 156 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   PHE C 158 " --> pdb=" O   GLY C 133 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ASP C 135 " --> pdb=" O   PHE C 158 " (cutoff:3.500A)
      removed outlier: 8.343A  pdb=" N   GLY C 160 " --> pdb=" O   ASP C 135 " (cutoff:3.500A)
      removed outlier: 9.065A  pdb=" N   HIS C 137 " --> pdb=" O   GLY C 160 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY C 218 " --> pdb=" O   ILE C 196 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   VAL C 246 " --> pdb=" O   HIS C 272 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ILE C 271 " --> pdb=" O   LEU C 297 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 133 through 139
      removed outlier: 6.649A  pdb=" N   GLY C 133 " --> pdb=" O   THR C 156 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   PHE C 158 " --> pdb=" O   GLY C 133 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ASP C 135 " --> pdb=" O   PHE C 158 " (cutoff:3.500A)
      removed outlier: 8.343A  pdb=" N   GLY C 160 " --> pdb=" O   ASP C 135 " (cutoff:3.500A)
      removed outlier: 9.065A  pdb=" N   HIS C 137 " --> pdb=" O   GLY C 160 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   ILE C 196 " --> pdb=" O   PHE C 494 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 537 through 539

    234 hydrogen bonds defined for protein.
    627 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: 1.12

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2069
        1.34 -     1.46: 1058
        1.46 -     1.58: 2970
        1.58 -     1.69: 0
        1.69 -     1.81: 59
  Bond restraints: 6156
  Sorted by residual:
  bond pdb=" NZ  KCX C 220 "
       pdb=" CX  KCX C 220 "
    ideal  model  delta    sigma   weight residual
    1.411  1.331  0.080 2.00e-02 2.50e+03 1.61e+01
  bond pdb=" CE  KCX C 220 "
       pdb=" NZ  KCX C 220 "
    ideal  model  delta    sigma   weight residual
    1.442  1.492 -0.050 2.00e-02 2.50e+03 6.19e+00
  bond pdb=" SD  CXM A   1 "
       pdb=" CE  CXM A   1 "
    ideal  model  delta    sigma   weight residual
    1.808  1.763  0.045 2.00e-02 2.50e+03 4.99e+00
  bond pdb=" C   CXM A   1 "
       pdb=" O   CXM A   1 "
    ideal  model  delta    sigma   weight residual
    1.231  1.270 -0.039 2.00e-02 2.50e+03 3.78e+00
  bond pdb=" CA  CXM A   1 "
       pdb=" C   CXM A   1 "
    ideal  model  delta    sigma   weight residual
    1.525  1.563 -0.038 2.10e-02 2.27e+03 3.20e+00
  ... (remaining 6151 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.11: 8223
        2.11 -     4.22: 87
        4.22 -     6.33: 17
        6.33 -     8.44: 6
        8.44 -    10.55: 1
  Bond angle restraints: 8334
  Sorted by residual:
  angle pdb=" CB  LYS C   2 "
        pdb=" CG  LYS C   2 "
        pdb=" CD  LYS C   2 "
      ideal   model   delta    sigma   weight residual
     111.30  121.85  -10.55 2.30e+00 1.89e-01 2.10e+01
  angle pdb=" N   ASP C 363 "
        pdb=" CA  ASP C 363 "
        pdb=" C   ASP C 363 "
      ideal   model   delta    sigma   weight residual
     111.28  106.16    5.12 1.35e+00 5.49e-01 1.44e+01
  angle pdb=" CA  GLN C 501 "
        pdb=" CB  GLN C 501 "
        pdb=" CG  GLN C 501 "
      ideal   model   delta    sigma   weight residual
     114.10  121.52   -7.42 2.00e+00 2.50e-01 1.38e+01
  angle pdb=" CA  GLN B 115 "
        pdb=" CB  GLN B 115 "
        pdb=" CG  GLN B 115 "
      ideal   model   delta    sigma   weight residual
     114.10  121.40   -7.30 2.00e+00 2.50e-01 1.33e+01
  angle pdb=" CB  GLN B 115 "
        pdb=" CG  GLN B 115 "
        pdb=" CD  GLN B 115 "
      ideal   model   delta    sigma   weight residual
     112.60  118.45   -5.85 1.70e+00 3.46e-01 1.18e+01
  ... (remaining 8329 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 3122
       17.37 -    34.74: 426
       34.74 -    52.11: 120
       52.11 -    69.49: 32
       69.49 -    86.86: 12
  Dihedral angle restraints: 3712
    sinusoidal: 1489
      harmonic: 2223
  Sorted by residual:
  dihedral pdb=" CA  ASP C 363 "
           pdb=" C   ASP C 363 "
           pdb=" N   ALA C 364 "
           pdb=" CA  ALA C 364 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.40  -24.60     0      5.00e+00 4.00e-02 2.42e+01
  dihedral pdb=" CA  TRP C 438 "
           pdb=" C   TRP C 438 "
           pdb=" N   GLU C 439 "
           pdb=" CA  GLU C 439 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.83   18.17     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  MET C 563 "
           pdb=" C   MET C 563 "
           pdb=" N   ALA C 564 "
           pdb=" CA  ALA C 564 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.35  -17.65     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 3709 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 574
       0.032 -    0.064: 216
       0.064 -    0.096: 92
       0.096 -    0.128: 53
       0.128 -    0.160: 6
  Chirality restraints: 941
  Sorted by residual:
  chirality pdb=" CG  LEU B 114 "
            pdb=" CB  LEU B 114 "
            pdb=" CD1 LEU B 114 "
            pdb=" CD2 LEU B 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CA  ASN C 302 "
            pdb=" N   ASN C 302 "
            pdb=" C   ASN C 302 "
            pdb=" CB  ASN C 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.36e-01
  chirality pdb=" CA  ILE C  97 "
            pdb=" N   ILE C  97 "
            pdb=" C   ILE C  97 "
            pdb=" CB  ILE C  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.65e-01
  ... (remaining 938 not shown)

  Planarity restraints: 1100
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 284 "    0.035 5.00e-02 4.00e+02   5.20e-02 4.32e+00
        pdb=" N   PRO C 285 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO C 285 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 285 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A  34 "    0.007 2.00e-02 2.50e+03   1.46e-02 2.14e+00
        pdb=" CD  GLU A  34 "   -0.025 2.00e-02 2.50e+03
        pdb=" OE1 GLU A  34 "    0.009 2.00e-02 2.50e+03
        pdb=" OE2 GLU A  34 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A  32 "   -0.022 5.00e-02 4.00e+02   3.36e-02 1.80e+00
        pdb=" N   PRO A  33 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A  33 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  33 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1097 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 77
        2.54 -     3.13: 4633
        3.13 -     3.72: 9742
        3.72 -     4.31: 14240
        4.31 -     4.90: 23690
  Nonbonded interactions: 52382
  Sorted by model distance:
  nonbonded pdb=" OQ1 KCX C 220 "
            pdb="NI    NI C 601 "
     model   vdw
     1.955 2.920
  nonbonded pdb=" NE2 HIS C 275 "
            pdb="NI    NI C 601 "
     model   vdw
     1.956 3.000
  nonbonded pdb=" NE2 HIS C 139 "
            pdb="NI    NI C 602 "
     model   vdw
     1.959 3.000
  nonbonded pdb=" OQ2 KCX C 220 "
            pdb="NI    NI C 602 "
     model   vdw
     1.988 2.920
  nonbonded pdb="NI    NI C 601 "
            pdb=" O1  2PA C 603 "
     model   vdw
     2.005 2.920
  ... (remaining 52377 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.98
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.860
  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:             0.020
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.280
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  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:10.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8787
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      :  0.003   0.080   6156  Z= 0.143
  Angle     :  0.586  10.551   8334  Z= 0.300
  Chirality :  0.045   0.160    941
  Planarity :  0.004   0.052   1100
  Dihedral  : 18.053  86.858   2296
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.58 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 28.04 %
    Favored  : 66.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.42 (0.30), residues: 782
  helix:  1.19 (0.37), residues: 208
  sheet:  0.50 (0.48), residues: 105
  loop : -0.13 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 449 
 TYR   0.017   0.001   TYR A  32 
 PHE   0.004   0.001   PHE C 442 
 TRP   0.016   0.001   TRP C 438 
 HIS   0.007   0.001   HIS C 137 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 ( 6156)
  covalent geometry    : angle       0.58642 /  0.30 ( 8334)
  hydrogen bonds       : bond        0.16325 / 11.89 (  222)
  hydrogen bonds       : angle       6.83061 /  5.19 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 98
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: B   76 ARG cc_start: 0.9128 (ttm-80) cc_final: 0.8853 (ttm-80)
REVERT: C  320 MET cc_start: 0.5546 (mmt) cc_final: 0.5084 (tmt)
  outliers start: 32
  outliers final: 27
  residues processed: 123
  average time/residue: 0.5140
  time to fit residues: 66.5033
Evaluate side-chains
  113 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue   71 LEU
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  147 ASP
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  186 SER
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  299 SER
Chi-restraints excluded: chain C residue  314 GLU
Chi-restraints excluded: chain C residue  467 SER
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  516 THR
Chi-restraints excluded: chain C residue  551 GLU
Chi-restraints excluded: chain C residue  552 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   overall best weight:    2.1784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  22 ASN
B  68 ASN
B 104 ASN
** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 142 ASN
C 245 GLN
C 293 HIS
C 315 HIS
C 387 GLN
C 418 GLN
** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 522 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.113434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.092389 restraints weight = 9061.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 1.84
r_work: 0.2997 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (12 function evaluations)
r_final: 0.2833
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8915
moved from start:          0.1029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6156  Z= 0.175
  Angle     :  0.569   7.552   8334  Z= 0.295
  Chirality :  0.047   0.184    941
  Planarity :  0.004   0.051   1100
  Dihedral  :  7.463  58.311    891
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.96 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 24.92 %
    Favored  : 70.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.50 (0.31), residues: 782
  helix:  1.09 (0.36), residues: 224
  sheet:  0.89 (0.48), residues: 95
  loop : -0.11 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 566 
 TYR   0.013   0.001   TYR B   6 
 PHE   0.007   0.001   PHE B  48 
 TRP   0.013   0.001   TRP C 438 
 HIS   0.004   0.001   HIS C 249 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.18 ( 6156)
  covalent geometry    : angle       0.56886 /  0.29 ( 8334)
  hydrogen bonds       : bond        0.04341 /  3.07 (  222)
  hydrogen bonds       : angle       4.99275 /  3.67 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 94
  time to evaluate  : 0.169 
Fit side-chains
REVERT: C  320 MET cc_start: 0.5751 (mmt) cc_final: 0.5131 (tmt)
REVERT: C  547 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8466 (ttpp)
  outliers start: 32
  outliers final: 12
  residues processed: 114
  average time/residue: 0.5711
  time to fit residues: 67.9809
Evaluate side-chains
  97 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  360 MET
Chi-restraints excluded: chain C residue  551 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 16 optimal weight:    8.9990
   chunk 32 optimal weight:    0.6980
   chunk 73 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 7 optimal weight:    0.0470
   chunk 35 optimal weight:    6.9990
   chunk 47 optimal weight:    9.9990
   chunk 52 optimal weight:    0.0570
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.5600

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 137 HIS ** 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 = 0.3363 r_free = 0.3363 target = 0.110440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.089413 restraints weight = 8920.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 1.80
r_work: 0.2944 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2833
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.2831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8901
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6156  Z= 0.140
  Angle     :  0.549   7.821   8334  Z= 0.280
  Chirality :  0.046   0.207    941
  Planarity :  0.004   0.053   1100
  Dihedral  :  6.171  56.572    867
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.45 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 25.23 %
    Favored  : 70.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 (0.30), residues: 782
  helix:  1.04 (0.35), residues: 231
  sheet:  0.90 (0.47), residues: 95
  loop : -0.17 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 305 
 TYR   0.009   0.001   TYR B   6 
 PHE   0.006   0.001   PHE B  48 
 TRP   0.013   0.001   TRP C 438 
 HIS   0.004   0.001   HIS C 249 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 ( 6156)
  covalent geometry    : angle       0.54931 /  0.28 ( 8334)
  hydrogen bonds       : bond        0.03673 /  2.58 (  222)
  hydrogen bonds       : angle       4.69824 /  3.43 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 89
  time to evaluate  : 0.228 
Fit side-chains
REVERT: B   31 ARG cc_start: 0.8410 (mtp-110) cc_final: 0.7341 (mtp-110)
REVERT: C  320 MET cc_start: 0.5625 (mmt) cc_final: 0.5023 (tmt)
REVERT: C  386 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7901 (mttt)
  outliers start: 27
  outliers final: 9
  residues processed: 107
  average time/residue: 0.5403
  time to fit residues: 60.6015
Evaluate side-chains
  94 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  386 LYS
Chi-restraints excluded: chain C residue  498 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0870
   chunk 39 optimal weight:    0.8980
   chunk 30 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 10 optimal weight:    0.0050
   chunk 68 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 61 optimal weight:    9.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.5772

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 137 HIS ** 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 = 0.3397 r_free = 0.3397 target = 0.112540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.091917 restraints weight = 9037.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 1.80
r_work: 0.2994 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.2880
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8863
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6156  Z= 0.102
  Angle     :  0.523   7.625   8334  Z= 0.267
  Chirality :  0.045   0.229    941
  Planarity :  0.004   0.055   1100
  Dihedral  :  5.110  42.704    859
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.07 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 26.17 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.58 (0.31), residues: 782
  helix:  1.18 (0.35), residues: 232
  sheet:  1.00 (0.48), residues: 95
  loop : -0.11 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  94 
 TYR   0.007   0.001   TYR C  79 
 PHE   0.004   0.001   PHE B  57 
 TRP   0.014   0.001   TRP C 438 
 HIS   0.004   0.001   HIS C 249 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00226 /  0.10 ( 6156)
  covalent geometry    : angle       0.52274 /  0.27 ( 8334)
  hydrogen bonds       : bond        0.03140 /  2.20 (  222)
  hydrogen bonds       : angle       4.45920 /  3.23 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.235 
Fit side-chains
REVERT: B   28 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8736 (p)
REVERT: B   31 ARG cc_start: 0.8399 (mtp-110) cc_final: 0.8019 (mtp180)
REVERT: B   81 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6966 (pp20)
REVERT: B   83 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6501 (mmm)
REVERT: C   78 ASP cc_start: 0.8389 (t0) cc_final: 0.8143 (t0)
REVERT: C  320 MET cc_start: 0.5568 (mmt) cc_final: 0.4988 (tmt)
REVERT: C  386 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7933 (mttt)
REVERT: C  470 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.8108 (p)
  outliers start: 22
  outliers final: 9
  residues processed: 105
  average time/residue: 0.5182
  time to fit residues: 57.2367
Evaluate side-chains
  95 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  315 HIS
Chi-restraints excluded: chain C residue  386 LYS
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  552 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    0.1980
   chunk 25 optimal weight:    7.9990
   chunk 16 optimal weight:    0.7980
   chunk 73 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 35 optimal weight:    9.9990
   chunk 57 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    1.3582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 315 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.110471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.089607 restraints weight = 9104.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 1.81
r_work: 0.2967 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8882
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6156  Z= 0.130
  Angle     :  0.545   8.577   8334  Z= 0.275
  Chirality :  0.046   0.232    941
  Planarity :  0.004   0.060   1100
  Dihedral  :  4.958  43.813    859
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.45 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 26.32 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.60 (0.31), residues: 782
  helix:  1.21 (0.35), residues: 232
  sheet:  0.81 (0.47), residues: 96
  loop : -0.06 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  94 
 TYR   0.006   0.001   TYR C  79 
 PHE   0.006   0.001   PHE B  48 
 TRP   0.011   0.001   TRP C 438 
 HIS   0.007   0.001   HIS C 222 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.13 ( 6156)
  covalent geometry    : angle       0.54486 /  0.27 ( 8334)
  hydrogen bonds       : bond        0.03312 /  2.34 (  222)
  hydrogen bonds       : angle       4.43647 /  3.21 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 0.228 
Fit side-chains
REVERT: B   28 THR cc_start: 0.9076 (m) cc_final: 0.8778 (p)
REVERT: C    2 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8570 (mmmt)
REVERT: C  320 MET cc_start: 0.5573 (mmt) cc_final: 0.5343 (mmm)
  outliers start: 21
  outliers final: 9
  residues processed: 100
  average time/residue: 0.4699
  time to fit residues: 49.4021
Evaluate side-chains
  88 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  552 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 21 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 315 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.109686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.088811 restraints weight = 9036.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 1.79
r_work: 0.2955 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2843
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8896
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6156  Z= 0.144
  Angle     :  0.543   7.126   8334  Z= 0.278
  Chirality :  0.046   0.232    941
  Planarity :  0.004   0.054   1100
  Dihedral  :  4.851  45.551    857
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.84 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 26.95 %
    Favored  : 70.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.53 (0.31), residues: 782
  helix:  1.11 (0.35), residues: 232
  sheet:  0.76 (0.46), residues: 96
  loop : -0.07 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  94 
 TYR   0.006   0.001   TYR B   6 
 PHE   0.006   0.001   PHE B  48 
 TRP   0.011   0.001   TRP C 438 
 HIS   0.005   0.001   HIS C 222 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.14 ( 6156)
  covalent geometry    : angle       0.54250 /  0.28 ( 8334)
  hydrogen bonds       : bond        0.03443 /  2.43 (  222)
  hydrogen bonds       : angle       4.45586 /  3.22 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.177 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8431 (mt)
REVERT: B   28 THR cc_start: 0.9079 (m) cc_final: 0.8808 (p)
REVERT: B   31 ARG cc_start: 0.8537 (mtp180) cc_final: 0.8282 (mmm160)
REVERT: C    2 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8584 (mmmt)
REVERT: C  320 MET cc_start: 0.5618 (mmt) cc_final: 0.5392 (mmm)
  outliers start: 18
  outliers final: 9
  residues processed: 97
  average time/residue: 0.4785
  time to fit residues: 48.7232
Evaluate side-chains
  92 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  552 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 73 optimal weight:    7.9990
   chunk 26 optimal weight:    0.3980
   chunk 22 optimal weight:    5.9990
   chunk 61 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 44 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   overall best weight:    2.2788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 315 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.110307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.089610 restraints weight = 9088.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 1.77
r_work: 0.2973 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2863
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2863
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8988
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6156  Z= 0.178
  Angle     :  0.590   8.485   8334  Z= 0.300
  Chirality :  0.048   0.257    941
  Planarity :  0.004   0.063   1100
  Dihedral  :  4.934  45.973    857
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.84 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 26.64 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.44 (0.31), residues: 782
  helix:  1.00 (0.35), residues: 231
  sheet:  0.68 (0.46), residues: 96
  loop : -0.10 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  94 
 TYR   0.009   0.001   TYR B   6 
 PHE   0.008   0.001   PHE B  48 
 TRP   0.011   0.001   TRP C 438 
 HIS   0.004   0.001   HIS C 249 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00427 /  0.18 ( 6156)
  covalent geometry    : angle       0.58951 /  0.30 ( 8334)
  hydrogen bonds       : bond        0.03674 /  2.60 (  222)
  hydrogen bonds       : angle       4.52350 /  3.26 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.204 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8612 (mt)
REVERT: B   28 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8881 (p)
REVERT: B   83 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6580 (mmm)
REVERT: B  112 LEU cc_start: 0.8975 (tm) cc_final: 0.8699 (tm)
REVERT: C    2 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8624 (mmmt)
REVERT: C  367 MET cc_start: 0.8656 (ptm) cc_final: 0.8295 (ptt)
  outliers start: 17
  outliers final: 8
  residues processed: 94
  average time/residue: 0.4758
  time to fit residues: 46.9364
Evaluate side-chains
  91 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  516 THR
Chi-restraints excluded: chain C residue  552 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 47 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   chunk 73 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 12 optimal weight:   10.0000
   chunk 68 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 315 HIS
C 324 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.111162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.090641 restraints weight = 9076.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 1.77
r_work: 0.2986 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2876
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2876
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8968
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6156  Z= 0.139
  Angle     :  0.586   8.738   8334  Z= 0.298
  Chirality :  0.047   0.309    941
  Planarity :  0.005   0.060   1100
  Dihedral  :  4.680  36.224    856
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.84 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 27.73 %
    Favored  : 69.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.43 (0.30), residues: 782
  helix:  0.96 (0.35), residues: 231
  sheet:  0.74 (0.46), residues: 96
  loop : -0.10 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 116 
 TYR   0.007   0.001   TYR B   6 
 PHE   0.006   0.001   PHE B  48 
 TRP   0.013   0.001   TRP C 438 
 HIS   0.012   0.001   HIS C 324 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 ( 6156)
  covalent geometry    : angle       0.58633 /  0.30 ( 8334)
  hydrogen bonds       : bond        0.03449 /  2.43 (  222)
  hydrogen bonds       : angle       4.49216 /  3.24 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: B    7 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8645 (mt)
REVERT: B   28 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8898 (p)
REVERT: B   31 ARG cc_start: 0.8308 (mmm160) cc_final: 0.8056 (mmm-85)
REVERT: C    2 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8605 (mmmt)
REVERT: C  367 MET cc_start: 0.8552 (ptm) cc_final: 0.8298 (ptt)
  outliers start: 15
  outliers final: 8
  residues processed: 94
  average time/residue: 0.4960
  time to fit residues: 49.0638
Evaluate side-chains
  93 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  320 MET
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  552 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0670
   chunk 66 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0980
   chunk 72 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.8120

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 315 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.114136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.093915 restraints weight = 9065.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 1.76
r_work: 0.3056 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2948
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8972
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6156  Z= 0.110
  Angle     :  0.564   9.548   8334  Z= 0.288
  Chirality :  0.046   0.312    941
  Planarity :  0.004   0.066   1100
  Dihedral  :  4.412  21.206    856
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.96 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 27.57 %
    Favored  : 70.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 (0.31), residues: 782
  helix:  1.09 (0.35), residues: 231
  sheet:  0.82 (0.47), residues: 96
  loop : -0.05 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 116 
 TYR   0.007   0.001   TYR C  79 
 PHE   0.004   0.001   PHE C 442 
 TRP   0.015   0.001   TRP C 438 
 HIS   0.006   0.001   HIS C 324 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.11 ( 6156)
  covalent geometry    : angle       0.56446 /  0.29 ( 8334)
  hydrogen bonds       : bond        0.03111 /  2.20 (  222)
  hydrogen bonds       : angle       4.35743 /  3.12 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.240 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8627 (mt)
REVERT: C    2 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8567 (mmmt)
REVERT: C  367 MET cc_start: 0.8573 (ptm) cc_final: 0.8352 (ptt)
REVERT: C  385 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8283 (tttt)
REVERT: C  470 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8155 (p)
  outliers start: 15
  outliers final: 5
  residues processed: 98
  average time/residue: 0.5237
  time to fit residues: 53.9408
Evaluate side-chains
  93 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  385 LYS
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  552 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 61 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 315 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.112234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.091889 restraints weight = 9135.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 1.76
r_work: 0.3023 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2911
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2911 r_free = 0.2911    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2911 r_free = 0.2911    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2911
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9006
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6156  Z= 0.165
  Angle     :  0.601   9.230   8334  Z= 0.307
  Chirality :  0.047   0.303    941
  Planarity :  0.005   0.069   1100
  Dihedral  :  4.565  25.229    856
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.84 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 28.04 %
    Favored  : 70.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.46 (0.31), residues: 782
  helix:  0.99 (0.35), residues: 231
  sheet:  0.73 (0.46), residues: 96
  loop : -0.08 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  31 
 TYR   0.008   0.001   TYR B   6 
 PHE   0.008   0.001   PHE B  48 
 TRP   0.011   0.001   TRP C 438 
 HIS   0.007   0.001   HIS C 222 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.17 ( 6156)
  covalent geometry    : angle       0.60137 /  0.31 ( 8334)
  hydrogen bonds       : bond        0.03556 /  2.52 (  222)
  hydrogen bonds       : angle       4.47223 /  3.20 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.223 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8692 (mt)
REVERT: C    2 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8591 (mmmt)
REVERT: C  367 MET cc_start: 0.8622 (ptm) cc_final: 0.8417 (ptt)
REVERT: C  385 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8253 (tttt)
  outliers start: 11
  outliers final: 6
  residues processed: 94
  average time/residue: 0.5146
  time to fit residues: 50.7229
Evaluate side-chains
  92 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  385 LYS
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  552 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 72 optimal weight:    0.0000
   chunk 44 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    7.9990
   chunk 52 optimal weight:    0.2980
   chunk 63 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 315 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.114098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.093835 restraints weight = 8875.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 1.75
r_work: 0.3038 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2937
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8941
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   6156  Z= 0.108
  Angle     :  0.566   9.198   8334  Z= 0.290
  Chirality :  0.046   0.294    941
  Planarity :  0.005   0.068   1100
  Dihedral  :  4.369  22.337    856
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.07 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 28.35 %
    Favored  : 69.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.62 (0.31), residues: 782
  helix:  1.13 (0.35), residues: 235
  sheet:  0.83 (0.47), residues: 96
  loop : -0.00 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  31 
 TYR   0.007   0.001   TYR C  79 
 PHE   0.004   0.001   PHE C 442 
 TRP   0.015   0.001   TRP C 438 
 HIS   0.006   0.001   HIS C 222 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 6156)
  covalent geometry    : angle       0.56617 /  0.29 ( 8334)
  hydrogen bonds       : bond        0.03070 /  2.18 (  222)
  hydrogen bonds       : angle       4.33421 /  3.09 (  627)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2102.70 seconds
wall clock time: 36 minutes 39.55 seconds (2199.55 seconds total)