Starting phenix.real_space_refine
on Thu Jul  2 18:53:16 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7f4h_31452/07_2026/7f4h_31452.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f4h_31452/07_2026/7f4h_31452.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f4h_31452/07_2026/7f4h_31452.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f4h_31452/07_2026/7f4h_31452.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7f4h_31452/07_2026/7f4h_31452.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7f4h_31452/07_2026/7f4h_31452.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f4h_31452/07_2026/7f4h_31452.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f4h_31452/07_2026/7f4h_31452.map"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      65      5.16       5
     C    6249      2.51       5
     N    1708      2.21       5
     O    1826      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 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: 9849
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "G"
      Number of atoms: 427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 427
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "A"
      Number of atoms: 1942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1942
          Classifications: {'peptide': 234}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 963
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2590
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 25
    Chain: "R"
      Number of atoms: 2054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2054
          Classifications: {'peptide': 267}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 6, 'TRANS': 260}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "S"
      Number of atoms: 1771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1771
          Classifications: {'peptide': 230}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 38
          Classifications: {'peptide': 5}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 4}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1, 'NLE:plan-1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "F"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 63
          Classifications: {'peptide': 7}
          Link IDs: {'PTRANS': 1, 'TRANS': 5}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'DPN:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.80, per 1000 atoms: 0.18
  Number of scatterers: 9849
  At special positions: 0
  Unit cell: (117.04, 97.185, 129.58, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      65     16.00
     O    1826      8.00
     N    1708      7.00
     C    6249      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 267 " - pdb=" SG  CYS R 273 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " DPN F   7 " - " HIS F   6 "
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 266.2 milliseconds
  

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DPN F   7 "
  Number of C-beta restraints generated:  2362

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 15 sheets defined
      37.0% alpha, 24.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'A' and resid 13 through 39
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 252 through 279
      removed outlier: 3.906A  pdb=" N   GLN A 267 " --> pdb=" O   TYR A 253 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.935A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 4.006A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'R' and resid 41 through 66
    Processing helix  chain 'R' and resid 67 through 70
    Processing helix  chain 'R' and resid 71 through 103
    Processing helix  chain 'R' and resid 109 through 148
      removed outlier: 3.612A  pdb=" N   LEU R 116 " --> pdb=" O   VAL R 112 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 151 through 156
    Processing helix  chain 'R' and resid 157 through 182
    Processing helix  chain 'R' and resid 185 through 226
      removed outlier: 3.691A  pdb=" N   LEU R 189 " --> pdb=" O   HIS R 185 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 238 through 267
      Proline residue:  R 256  - end of helix
      removed outlier: 3.656A  pdb=" N   VAL R 265 " --> pdb=" O   LEU R 261 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 278
      removed outlier: 3.640A  pdb=" N   ILE R 276 " --> pdb=" O   THR R 272 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 279 through 299
      Proline residue:  R 295  - end of helix
    Processing helix  chain 'R' and resid 302 through 311
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.929A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
    Processing helix  chain 'S' and resid 220 through 224
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.282A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.059A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AA3, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.659A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 51
      removed outlier: 3.622A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.624A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.844A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.973A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.924A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.672A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.585A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.757A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.686A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.082A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.082A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.639A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.828A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)

    541 hydrogen bonds defined for protein.
    1485 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: 1.63

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.20 -     1.34: 2961
        1.34 -     1.47: 2757
        1.47 -     1.61: 4239
        1.61 -     1.74: 0
        1.74 -     1.88: 91
  Bond restraints: 10048
  Sorted by residual:
  bond pdb=" N   GLY B 341 "
       pdb=" CA  GLY B 341 "
    ideal  model  delta    sigma   weight residual
    1.449  1.496 -0.047 1.45e-02 4.76e+03 1.04e+01
  bond pdb=" CB  THR S  78 "
       pdb=" OG1 THR S  78 "
    ideal  model  delta    sigma   weight residual
    1.433  1.398  0.035 1.60e-02 3.91e+03 4.90e+00
  bond pdb=" CB  CYS B 166 "
       pdb=" SG  CYS B 166 "
    ideal  model  delta    sigma   weight residual
    1.808  1.880 -0.072 3.30e-02 9.18e+02 4.78e+00
  bond pdb=" CB  DPN F   7 "
       pdb=" CG  DPN F   7 "
    ideal  model  delta    sigma   weight residual
    1.501  1.544 -0.043 2.00e-02 2.50e+03 4.52e+00
  bond pdb=" CB  LYS R 310 "
       pdb=" CG  LYS R 310 "
    ideal  model  delta    sigma   weight residual
    1.520  1.579 -0.059 3.00e-02 1.11e+03 3.81e+00
  ... (remaining 10043 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 12267
        1.67 -     3.34: 1237
        3.34 -     5.02: 91
        5.02 -     6.69: 14
        6.69 -     8.36: 5
  Bond angle restraints: 13614
  Sorted by residual:
  angle pdb=" O   ASN B 340 "
        pdb=" C   ASN B 340 "
        pdb=" N   GLY B 341 "
      ideal   model   delta    sigma   weight residual
     122.72  115.74    6.98 1.33e+00 5.65e-01 2.75e+01
  angle pdb=" C   ARG S 191 "
        pdb=" N   MET S 192 "
        pdb=" CA  MET S 192 "
      ideal   model   delta    sigma   weight residual
     121.54  129.28   -7.74 1.91e+00 2.74e-01 1.64e+01
  angle pdb=" C   THR N  28 "
        pdb=" N   PHE N  29 "
        pdb=" CA  PHE N  29 "
      ideal   model   delta    sigma   weight residual
     120.82  126.35   -5.53 1.50e+00 4.44e-01 1.36e+01
  angle pdb=" N   GLY B 141 "
        pdb=" CA  GLY B 141 "
        pdb=" C   GLY B 141 "
      ideal   model   delta    sigma   weight residual
     113.18  121.54   -8.36 2.37e+00 1.78e-01 1.24e+01
  angle pdb=" CA  ASP B  76 "
        pdb=" CB  ASP B  76 "
        pdb=" CG  ASP B  76 "
      ideal   model   delta    sigma   weight residual
     112.60  115.89   -3.29 1.00e+00 1.00e+00 1.08e+01
  ... (remaining 13609 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 5560
       17.79 -    35.58: 345
       35.58 -    53.37: 43
       53.37 -    71.16: 14
       71.16 -    88.95: 11
  Dihedral angle restraints: 5973
    sinusoidal: 2308
      harmonic: 3665
  Sorted by residual:
  dihedral pdb=" CA  THR S 172 "
           pdb=" C   THR S 172 "
           pdb=" N   TYR S 173 "
           pdb=" CA  TYR S 173 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.30   29.70     0      5.00e+00 4.00e-02 3.53e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.34   29.66     0      5.00e+00 4.00e-02 3.52e+01
  dihedral pdb=" CA  PHE A 238 "
           pdb=" C   PHE A 238 "
           pdb=" N   ASN A 239 "
           pdb=" CA  ASN A 239 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.26   28.74     0      5.00e+00 4.00e-02 3.30e+01
  ... (remaining 5970 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1018
       0.056 -    0.112: 389
       0.112 -    0.168: 124
       0.168 -    0.224: 16
       0.224 -    0.281: 3
  Chirality restraints: 1550
  Sorted by residual:
  chirality pdb=" CA  TYR S 173 "
            pdb=" N   TYR S 173 "
            pdb=" C   TYR S 173 "
            pdb=" CB  TYR S 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" CA  MET S 192 "
            pdb=" N   MET S 192 "
            pdb=" C   MET S 192 "
            pdb=" CB  MET S 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.78e+00
  chirality pdb=" CG  LEU A 270 "
            pdb=" CB  LEU A 270 "
            pdb=" CD1 LEU A 270 "
            pdb=" CD2 LEU A 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.82    0.24 2.00e-01 2.50e+01 1.38e+00
  ... (remaining 1547 not shown)

  Planarity restraints: 1730
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 340 "   -0.046 2.00e-02 2.50e+03   8.94e-02 8.00e+01
        pdb=" C   ASN B 340 "    0.155 2.00e-02 2.50e+03
        pdb=" O   ASN B 340 "   -0.058 2.00e-02 2.50e+03
        pdb=" N   GLY B 341 "   -0.051 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG N  72 "   -0.341 9.50e-02 1.11e+02   1.53e-01 1.55e+01
        pdb=" NE  ARG N  72 "    0.027 2.00e-02 2.50e+03
        pdb=" CZ  ARG N  72 "   -0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG N  72 "    0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG N  72 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR S 173 "   -0.017 2.00e-02 2.50e+03   2.73e-02 1.49e+01
        pdb=" CG  TYR S 173 "    0.008 2.00e-02 2.50e+03
        pdb=" CD1 TYR S 173 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR S 173 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR S 173 "    0.040 2.00e-02 2.50e+03
        pdb=" CE2 TYR S 173 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR S 173 "    0.030 2.00e-02 2.50e+03
        pdb=" OH  TYR S 173 "   -0.048 2.00e-02 2.50e+03
  ... (remaining 1727 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1779
        2.78 -     3.31: 9987
        3.31 -     3.84: 17680
        3.84 -     4.37: 21596
        4.37 -     4.90: 36052
  Nonbonded interactions: 87094
  Sorted by model distance:
  nonbonded pdb=" O   DPN F   7 "
            pdb="CA    CA R 501 "
     model   vdw
     2.253 2.510
  nonbonded pdb=" OD1 ASP R 121 "
            pdb="CA    CA R 501 "
     model   vdw
     2.255 2.510
  nonbonded pdb=" OE2 GLU A 314 "
            pdb=" NZ  LYS N  65 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" OD2 ASP R 121 "
            pdb="CA    CA R 501 "
     model   vdw
     2.298 2.510
  nonbonded pdb=" OE2 GLU A 344 "
            pdb=" NH1 ARG A 347 "
     model   vdw
     2.303 3.120
  ... (remaining 87089 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.570
  Find NCS groups from input model:        0.060
  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:7.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.072  10054  Z= 0.522
  Angle     :  1.043   8.359  13627  Z= 0.625
  Chirality :  0.064   0.281   1550
  Planarity :  0.011   0.153   1729
  Dihedral  : 12.815  88.946   3593
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 (0.22), residues: 1240
  helix:  0.04 (0.22), residues: 404
  sheet: -0.43 (0.29), residues: 285
  loop : -0.52 (0.26), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.027   0.005   ARG A 385 
 TYR   0.048   0.009   TYR S 173 
 PHE   0.035   0.008   PHE N  68 
 TRP   0.044   0.010   TRP A 281 
 HIS   0.020   0.006   HIS R 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00973 /  0.52 (10048)
  covalent geometry    : angle       1.04188 /  0.63 (13614)
  SS BOND              : bond        0.00876 /  0.52 (    5)
  SS BOND              : angle       1.76937 /  1.04 (   10)
  hydrogen bonds       : bond        0.15825 / 10.78 (  537)
  hydrogen bonds       : angle       7.18560 /  5.06 ( 1485)
  link_TRANS           : bond        0.00580 /  0.31 (    1)
  link_TRANS           : angle       1.32519 /  0.51 (    3)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 287
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: N   33 LYS cc_start: 0.8573 (ttmt) cc_final: 0.7917 (tttt)
REVERT: N   39 GLN cc_start: 0.8754 (tt0) cc_final: 0.8296 (tt0)
REVERT: N   53 GLN cc_start: 0.8504 (pm20) cc_final: 0.8091 (pm20)
REVERT: B    6 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8888 (tm-30)
REVERT: B  259 GLN cc_start: 0.7109 (mt0) cc_final: 0.6874 (mt0)
REVERT: B  292 PHE cc_start: 0.8777 (m-10) cc_final: 0.8463 (m-10)
REVERT: B  325 MET cc_start: 0.8337 (mmt) cc_final: 0.7789 (mmm)
REVERT: R   68 ASN cc_start: 0.7906 (m-40) cc_final: 0.7630 (m-40)
REVERT: R  262 THR cc_start: 0.8466 (m) cc_final: 0.8192 (p)
REVERT: S  223 ASP cc_start: 0.8515 (m-30) cc_final: 0.8280 (m-30)
REVERT: S  244 LYS cc_start: 0.9083 (tttm) cc_final: 0.8811 (ttmm)
  outliers start: 0
  outliers final: 1
  residues processed: 287
  average time/residue: 0.5825
  time to fit residues: 177.2218
Evaluate side-chains
  178 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 117 optimal weight:    0.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  24 ASN
A 267 GLN
A 271 ASN
A 292 ASN
A 294 GLN
N  74 ASN
B 175 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 115 GLN
R 118 ASN
S  13 GLN
S 171 ASN
S 179 GLN
S 183 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.097013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.070488 restraints weight = 17626.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 2.72
r_work: 0.2874 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10054  Z= 0.159
  Angle     :  0.659   6.886  13627  Z= 0.354
  Chirality :  0.044   0.250   1550
  Planarity :  0.005   0.037   1729
  Dihedral  :  5.769  30.975   1382
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 12.32 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.57 (0.23), residues: 1240
  helix:  1.75 (0.25), residues: 408
  sheet: -0.54 (0.27), residues: 310
  loop :  0.01 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 356 
 TYR   0.016   0.001   TYR N  32 
 PHE   0.021   0.002   PHE R  45 
 TRP   0.019   0.002   TRP B 339 
 HIS   0.004   0.001   HIS A 357 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.16 (10048)
  covalent geometry    : angle       0.65878 /  0.35 (13614)
  SS BOND              : bond        0.00218 /  0.16 (    5)
  SS BOND              : angle       1.11407 /  0.64 (   10)
  hydrogen bonds       : bond        0.04479 /  3.06 (  537)
  hydrogen bonds       : angle       5.52324 /  3.86 ( 1485)
  link_TRANS           : bond        0.00076 /  0.04 (    1)
  link_TRANS           : angle       0.57643 /  0.22 (    3)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 198
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8478 (ttm110) cc_final: 0.8124 (ptp-170)
REVERT: G   21 MET cc_start: 0.8723 (mmm) cc_final: 0.8425 (mtp)
REVERT: G   26 ASP cc_start: 0.8642 (p0) cc_final: 0.8403 (p0)
REVERT: G   38 MET cc_start: 0.8211 (ptp) cc_final: 0.7641 (ttm)
REVERT: G   42 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8035 (mm-30)
REVERT: A   27 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8151 (mt-10)
REVERT: N   33 LYS cc_start: 0.8569 (ttmt) cc_final: 0.7847 (tttt)
REVERT: N   39 GLN cc_start: 0.9194 (tt0) cc_final: 0.8802 (tt0)
REVERT: N   53 GLN cc_start: 0.8176 (pm20) cc_final: 0.7626 (pm20)
REVERT: N   73 ASP cc_start: 0.8225 (t0) cc_final: 0.7293 (t0)
REVERT: N   76 LYS cc_start: 0.9331 (mtpt) cc_final: 0.8803 (mtmm)
REVERT: N  120 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8587 (mm-40)
REVERT: B   10 GLU cc_start: 0.8568 (tp30) cc_final: 0.7968 (tp30)
REVERT: B   13 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8825 (tm-30)
REVERT: B  262 MET cc_start: 0.8111 (mtp) cc_final: 0.7800 (mtp)
REVERT: B  275 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8497 (p)
REVERT: B  325 MET cc_start: 0.8739 (mmt) cc_final: 0.8428 (mmm)
REVERT: R   73 MET cc_start: 0.8367 (ppp) cc_final: 0.8141 (ppp)
REVERT: R  148 TYR cc_start: 0.8633 (m-80) cc_final: 0.8419 (m-80)
REVERT: R  226 LYS cc_start: 0.7270 (mmmt) cc_final: 0.7067 (mmmt)
REVERT: R  238 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8260 (tptm)
REVERT: R  278 LYS cc_start: 0.9212 (mmpt) cc_final: 0.8693 (mmpt)
REVERT: R  303 GLN cc_start: 0.8735 (mp10) cc_final: 0.8141 (mm110)
REVERT: S   73 ASP cc_start: 0.7821 (t0) cc_final: 0.7116 (t0)
REVERT: S  174 LEU cc_start: 0.8898 (tp) cc_final: 0.8623 (tm)
REVERT: S  186 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8570 (pt0)
REVERT: S  218 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8111 (mtm110)
REVERT: S  220 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8222 (mp0)
REVERT: S  223 ASP cc_start: 0.8695 (m-30) cc_final: 0.7976 (m-30)
REVERT: S  244 LYS cc_start: 0.8726 (tttm) cc_final: 0.8481 (ttmm)
REVERT: S  246 GLU cc_start: 0.8162 (mp0) cc_final: 0.7623 (mp0)
  outliers start: 26
  outliers final: 4
  residues processed: 212
  average time/residue: 0.5168
  time to fit residues: 116.5247
Evaluate side-chains
  182 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 174
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue  238 LYS
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain S residue  186 GLN
Chi-restraints excluded: chain S residue  218 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9980
   chunk 118 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   overall best weight:    1.7784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  24 ASN
A  35 GLN
A 279 ASN
A 292 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  91 ASN
S  39 GLN
S  77 ASN
S 183 GLN
S 194 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.094258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.067182 restraints weight = 17496.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 2.71
r_work: 0.2808 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2651 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10054  Z= 0.193
  Angle     :  0.607   7.132  13627  Z= 0.324
  Chirality :  0.043   0.242   1550
  Planarity :  0.004   0.039   1729
  Dihedral  :  5.278  24.543   1380
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 13.83 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.74 (0.24), residues: 1240
  helix:  1.94 (0.25), residues: 407
  sheet: -0.62 (0.28), residues: 313
  loop :  0.20 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG N  19 
 TYR   0.014   0.001   TYR S 173 
 PHE   0.021   0.002   PHE R 147 
 TRP   0.017   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A 357 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00433 /  0.19 (10048)
  covalent geometry    : angle       0.60627 /  0.32 (13614)
  SS BOND              : bond        0.00233 /  0.16 (    5)
  SS BOND              : angle       1.15014 /  0.64 (   10)
  hydrogen bonds       : bond        0.04098 /  2.80 (  537)
  hydrogen bonds       : angle       5.24786 /  3.65 ( 1485)
  link_TRANS           : bond        0.00115 /  0.06 (    1)
  link_TRANS           : angle       0.61902 /  0.24 (    3)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 189
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   21 MET cc_start: 0.8741 (mmm) cc_final: 0.8272 (mtp)
REVERT: G   26 ASP cc_start: 0.8668 (p0) cc_final: 0.8280 (p0)
REVERT: G   38 MET cc_start: 0.8223 (ptp) cc_final: 0.7656 (ttm)
REVERT: G   42 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8205 (mm-30)
REVERT: A   27 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8240 (mt-10)
REVERT: N   13 GLN cc_start: 0.8694 (mp10) cc_final: 0.8472 (tp40)
REVERT: N   33 LYS cc_start: 0.8606 (ttmt) cc_final: 0.7928 (tttt)
REVERT: N   39 GLN cc_start: 0.9240 (tt0) cc_final: 0.8931 (tt0)
REVERT: N   46 GLU cc_start: 0.8536 (tt0) cc_final: 0.8150 (pt0)
REVERT: N   53 GLN cc_start: 0.8274 (pm20) cc_final: 0.7768 (pm20)
REVERT: N   73 ASP cc_start: 0.8289 (t0) cc_final: 0.7460 (t0)
REVERT: N   86 LEU cc_start: 0.9368 (mp) cc_final: 0.9112 (mm)
REVERT: N  120 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8620 (mm-40)
REVERT: B   10 GLU cc_start: 0.8819 (tp30) cc_final: 0.8098 (tp30)
REVERT: B   13 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8790 (tm-30)
REVERT: B   59 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.8703 (m-80)
REVERT: B  217 MET cc_start: 0.8897 (ptp) cc_final: 0.8216 (pmm)
REVERT: B  258 ASP cc_start: 0.8728 (t0) cc_final: 0.7884 (t0)
REVERT: B  262 MET cc_start: 0.8214 (mtp) cc_final: 0.7861 (mtp)
REVERT: B  275 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8509 (p)
REVERT: B  325 MET cc_start: 0.8870 (mmt) cc_final: 0.8541 (mmm)
REVERT: R  114 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7295 (tm-30)
REVERT: R  238 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8285 (tptm)
REVERT: R  307 ARG cc_start: 0.7817 (tpm170) cc_final: 0.7442 (tpm170)
REVERT: S   73 ASP cc_start: 0.7912 (t0) cc_final: 0.7227 (t0)
REVERT: S   77 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8426 (m110)
REVERT: S   90 ASP cc_start: 0.8938 (m-30) cc_final: 0.8678 (m-30)
REVERT: S  186 GLN cc_start: 0.8793 (pt0) cc_final: 0.8532 (pt0)
REVERT: S  218 ARG cc_start: 0.8644 (ptp-110) cc_final: 0.7697 (mtm-85)
REVERT: S  220 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8042 (mp0)
REVERT: S  223 ASP cc_start: 0.8697 (m-30) cc_final: 0.7707 (m-30)
REVERT: S  246 GLU cc_start: 0.8187 (mp0) cc_final: 0.7611 (mp0)
  outliers start: 28
  outliers final: 10
  residues processed: 208
  average time/residue: 0.6776
  time to fit residues: 149.8301
Evaluate side-chains
  194 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 180
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue   40 ILE
Chi-restraints excluded: chain R residue   62 THR
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  238 LYS
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain S residue   77 ASN
Chi-restraints excluded: chain S residue  162 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 8 optimal weight:    0.8980
   chunk 111 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 121 optimal weight:    3.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 292 ASN
N  84 ASN
B  75 GLN
B 340 ASN
** R 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  39 GLN
S 183 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.094341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.067241 restraints weight = 17755.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 2.75
r_work: 0.2806 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2651 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.3454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10054  Z= 0.175
  Angle     :  0.592   6.604  13627  Z= 0.313
  Chirality :  0.043   0.233   1550
  Planarity :  0.004   0.037   1729
  Dihedral  :  5.077  22.471   1380
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.56 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.79 (0.24), residues: 1240
  helix:  1.98 (0.24), residues: 407
  sheet: -0.67 (0.27), residues: 307
  loop :  0.26 (0.28), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G  13 
 TYR   0.012   0.001   TYR S 173 
 PHE   0.017   0.002   PHE R 147 
 TRP   0.014   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.17 (10048)
  covalent geometry    : angle       0.59124 /  0.31 (13614)
  SS BOND              : bond        0.00131 /  0.09 (    5)
  SS BOND              : angle       0.98375 /  0.56 (   10)
  hydrogen bonds       : bond        0.03838 /  2.63 (  537)
  hydrogen bonds       : angle       5.13723 /  3.57 ( 1485)
  link_TRANS           : bond        0.00111 /  0.06 (    1)
  link_TRANS           : angle       0.57602 /  0.23 (    3)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 184
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8578 (ttm110) cc_final: 0.8232 (ttm110)
REVERT: G   21 MET cc_start: 0.8699 (mmm) cc_final: 0.8416 (mtp)
REVERT: G   26 ASP cc_start: 0.8721 (p0) cc_final: 0.8345 (p0)
REVERT: G   38 MET cc_start: 0.8256 (ptp) cc_final: 0.7700 (ttm)
REVERT: G   42 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8196 (mm-30)
REVERT: A   58 LYS cc_start: 0.8594 (mmmm) cc_final: 0.8231 (pptt)
REVERT: N    3 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7758 (pt0)
REVERT: N   13 GLN cc_start: 0.8716 (mp10) cc_final: 0.8490 (tp40)
REVERT: N   33 LYS cc_start: 0.8551 (ttmt) cc_final: 0.7886 (tttt)
REVERT: N   39 GLN cc_start: 0.9263 (tt0) cc_final: 0.8992 (tt0)
REVERT: N   45 LEU cc_start: 0.8736 (mt) cc_final: 0.8240 (tt)
REVERT: N   46 GLU cc_start: 0.8531 (tt0) cc_final: 0.8082 (pt0)
REVERT: N   53 GLN cc_start: 0.8283 (pm20) cc_final: 0.7796 (pm20)
REVERT: N   73 ASP cc_start: 0.8316 (t0) cc_final: 0.7463 (t0)
REVERT: N   86 LEU cc_start: 0.9355 (mp) cc_final: 0.9144 (mm)
REVERT: N  120 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8574 (mm-40)
REVERT: B   10 GLU cc_start: 0.8892 (tp30) cc_final: 0.8272 (tp30)
REVERT: B   13 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8820 (tm-30)
REVERT: B   44 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8257 (mp10)
REVERT: B   59 TYR cc_start: 0.9010 (OUTLIER) cc_final: 0.8657 (m-80)
REVERT: B  188 MET cc_start: 0.8903 (mmm) cc_final: 0.8527 (mmm)
REVERT: B  217 MET cc_start: 0.8971 (ptp) cc_final: 0.8318 (pmm)
REVERT: B  258 ASP cc_start: 0.8774 (t0) cc_final: 0.7945 (t0)
REVERT: B  262 MET cc_start: 0.8177 (mtp) cc_final: 0.7537 (mtp)
REVERT: B  275 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8536 (p)
REVERT: B  325 MET cc_start: 0.8832 (mmt) cc_final: 0.8520 (mmm)
REVERT: R  114 GLN cc_start: 0.7422 (tm-30) cc_final: 0.7112 (tm-30)
REVERT: R  238 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8447 (tttm)
REVERT: S   46 GLU cc_start: 0.8922 (tt0) cc_final: 0.8684 (pt0)
REVERT: S   73 ASP cc_start: 0.7953 (t0) cc_final: 0.7296 (t0)
REVERT: S   83 MET cc_start: 0.9085 (mtm) cc_final: 0.8854 (ptm)
REVERT: S   90 ASP cc_start: 0.8991 (m-30) cc_final: 0.8709 (m-30)
REVERT: S   93 MET cc_start: 0.9072 (ttt) cc_final: 0.8713 (ttp)
REVERT: S  186 GLN cc_start: 0.8821 (pt0) cc_final: 0.8586 (pt0)
REVERT: S  220 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8120 (mp0)
REVERT: S  223 ASP cc_start: 0.8648 (m-30) cc_final: 0.7515 (m-30)
REVERT: S  244 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8379 (ttmm)
REVERT: S  246 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7666 (mp0)
REVERT: F    6 HIS cc_start: 0.8152 (OUTLIER) cc_final: 0.7401 (t-90)
  outliers start: 22
  outliers final: 9
  residues processed: 200
  average time/residue: 0.6668
  time to fit residues: 141.7763
Evaluate side-chains
  199 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 184
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue   40 ILE
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  238 LYS
Chi-restraints excluded: chain R residue  276 ILE
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain F residue    6 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 10 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 101 optimal weight:   10.0000
   chunk 42 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 103 optimal weight:    0.8980
   overall best weight:    1.7586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 292 ASN
N   1 GLN
N  35 ASN
N  84 ASN
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 225 HIS
** R 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.093739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.066500 restraints weight = 17546.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 2.73
r_work: 0.2795 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2640 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.3693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10054  Z= 0.189
  Angle     :  0.596   7.292  13627  Z= 0.313
  Chirality :  0.043   0.212   1550
  Planarity :  0.004   0.038   1729
  Dihedral  :  4.967  22.399   1380
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 16.37 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.84 (0.24), residues: 1240
  helix:  2.01 (0.25), residues: 407
  sheet: -0.70 (0.27), residues: 312
  loop :  0.37 (0.29), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 151 
 TYR   0.014   0.001   TYR N  32 
 PHE   0.017   0.002   PHE R 147 
 TRP   0.015   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00424 /  0.19 (10048)
  covalent geometry    : angle       0.59501 /  0.31 (13614)
  SS BOND              : bond        0.00371 /  0.20 (    5)
  SS BOND              : angle       1.18069 /  0.67 (   10)
  hydrogen bonds       : bond        0.03766 /  2.57 (  537)
  hydrogen bonds       : angle       5.11586 /  3.56 ( 1485)
  link_TRANS           : bond        0.00121 /  0.06 (    1)
  link_TRANS           : angle       0.53714 /  0.21 (    3)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 181
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   21 MET cc_start: 0.8705 (mmm) cc_final: 0.8252 (mtp)
REVERT: G   26 ASP cc_start: 0.8754 (p0) cc_final: 0.8392 (p0)
REVERT: G   38 MET cc_start: 0.8285 (ptp) cc_final: 0.7791 (ttm)
REVERT: G   42 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8233 (mm-30)
REVERT: A   58 LYS cc_start: 0.8572 (mmmm) cc_final: 0.8317 (tmmt)
REVERT: A  305 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8954 (mppt)
REVERT: N   13 GLN cc_start: 0.8914 (mp10) cc_final: 0.8652 (tp40)
REVERT: N   33 LYS cc_start: 0.8519 (ttmt) cc_final: 0.7834 (tttt)
REVERT: N   39 GLN cc_start: 0.9291 (tt0) cc_final: 0.9076 (tt0)
REVERT: N   46 GLU cc_start: 0.8560 (tt0) cc_final: 0.8101 (pt0)
REVERT: N   53 GLN cc_start: 0.8301 (pm20) cc_final: 0.7831 (pm20)
REVERT: N   67 ARG cc_start: 0.8422 (mtm110) cc_final: 0.8045 (mtm-85)
REVERT: N   84 ASN cc_start: 0.8496 (m-40) cc_final: 0.8285 (m110)
REVERT: N  120 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8555 (mm-40)
REVERT: B   10 GLU cc_start: 0.8915 (tp30) cc_final: 0.8281 (tp30)
REVERT: B   13 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8780 (tm-30)
REVERT: B   59 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.8641 (m-80)
REVERT: B  170 ASP cc_start: 0.8181 (p0) cc_final: 0.7914 (p0)
REVERT: B  172 GLU cc_start: 0.7835 (pm20) cc_final: 0.7430 (pm20)
REVERT: B  188 MET cc_start: 0.8878 (mmm) cc_final: 0.8480 (mmm)
REVERT: B  217 MET cc_start: 0.9009 (ptp) cc_final: 0.8359 (pmm)
REVERT: B  258 ASP cc_start: 0.8772 (t0) cc_final: 0.7997 (t0)
REVERT: B  262 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7518 (mtp)
REVERT: B  275 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8719 (m)
REVERT: B  322 ASP cc_start: 0.8727 (m-30) cc_final: 0.8465 (m-30)
REVERT: B  325 MET cc_start: 0.8885 (mmt) cc_final: 0.8595 (mmm)
REVERT: R  114 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7247 (tm-30)
REVERT: R  307 ARG cc_start: 0.7835 (tpm170) cc_final: 0.7574 (tpm170)
REVERT: S   46 GLU cc_start: 0.8971 (tt0) cc_final: 0.8682 (pt0)
REVERT: S   73 ASP cc_start: 0.7895 (t0) cc_final: 0.7177 (t0)
REVERT: S   90 ASP cc_start: 0.9026 (m-30) cc_final: 0.8727 (m-30)
REVERT: S  220 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8069 (mp0)
REVERT: S  223 ASP cc_start: 0.8679 (m-30) cc_final: 0.7106 (m-30)
REVERT: S  246 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7623 (mp0)
REVERT: F    6 HIS cc_start: 0.8402 (OUTLIER) cc_final: 0.7463 (t-90)
  outliers start: 33
  outliers final: 15
  residues processed: 204
  average time/residue: 0.6164
  time to fit residues: 133.8856
Evaluate side-chains
  198 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 178
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  305 LYS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue   40 ILE
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  276 ILE
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain S residue  113 GLN
Chi-restraints excluded: chain F residue    6 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 115 optimal weight:    0.8980
   chunk 87 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 120 optimal weight:   10.0000
   chunk 11 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 279 ASN
A 292 ASN
A 384 GLN
N   1 GLN
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 225 HIS
** R 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.095510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.068481 restraints weight = 17754.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 2.76
r_work: 0.2841 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2685 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.3840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10054  Z= 0.135
  Angle     :  0.580   8.885  13627  Z= 0.304
  Chirality :  0.042   0.220   1550
  Planarity :  0.004   0.039   1729
  Dihedral  :  4.773  21.332   1380
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.40 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.94 (0.24), residues: 1240
  helix:  2.21 (0.24), residues: 405
  sheet: -0.60 (0.27), residues: 333
  loop :  0.35 (0.30), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG G  13 
 TYR   0.012   0.001   TYR N  32 
 PHE   0.014   0.002   PHE A 212 
 TRP   0.011   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 362 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.14 (10048)
  covalent geometry    : angle       0.57954 /  0.30 (13614)
  SS BOND              : bond        0.00117 /  0.07 (    5)
  SS BOND              : angle       0.99327 /  0.56 (   10)
  hydrogen bonds       : bond        0.03566 /  2.44 (  537)
  hydrogen bonds       : angle       4.98781 /  3.47 ( 1485)
  link_TRANS           : bond        0.00062 /  0.03 (    1)
  link_TRANS           : angle       0.33560 /  0.13 (    3)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 182
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8383 (ttm110) cc_final: 0.7917 (ptp-110)
REVERT: G   21 MET cc_start: 0.8693 (mmm) cc_final: 0.8421 (mtp)
REVERT: G   26 ASP cc_start: 0.8792 (p0) cc_final: 0.8440 (p0)
REVERT: G   38 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7806 (ttm)
REVERT: G   42 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8253 (mm-30)
REVERT: A   58 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8323 (tmmt)
REVERT: N   33 LYS cc_start: 0.8482 (ttmt) cc_final: 0.7833 (tttt)
REVERT: N   39 GLN cc_start: 0.9249 (tt0) cc_final: 0.9037 (tt0)
REVERT: N   46 GLU cc_start: 0.8559 (tt0) cc_final: 0.8080 (pt0)
REVERT: N   53 GLN cc_start: 0.8263 (pm20) cc_final: 0.7752 (pm20)
REVERT: N   67 ARG cc_start: 0.8434 (mtm110) cc_final: 0.8102 (mtm-85)
REVERT: N   83 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8609 (mtm)
REVERT: N   86 LEU cc_start: 0.9317 (mm) cc_final: 0.8983 (mm)
REVERT: N  120 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8506 (mm-40)
REVERT: B   10 GLU cc_start: 0.8945 (tp30) cc_final: 0.8306 (tp30)
REVERT: B   13 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8837 (tm-30)
REVERT: B   59 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8613 (m-80)
REVERT: B  146 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8276 (mm)
REVERT: B  170 ASP cc_start: 0.8245 (p0) cc_final: 0.7927 (p0)
REVERT: B  172 GLU cc_start: 0.7895 (pm20) cc_final: 0.7480 (pm20)
REVERT: B  188 MET cc_start: 0.8746 (mmm) cc_final: 0.8429 (mmm)
REVERT: B  217 MET cc_start: 0.9060 (ptp) cc_final: 0.8406 (pmm)
REVERT: B  258 ASP cc_start: 0.8773 (t0) cc_final: 0.7982 (t0)
REVERT: B  262 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7396 (mtp)
REVERT: B  325 MET cc_start: 0.8891 (mmt) cc_final: 0.8612 (mmm)
REVERT: R  114 GLN cc_start: 0.7494 (tm-30) cc_final: 0.7139 (tm-30)
REVERT: S   19 LYS cc_start: 0.8756 (tttm) cc_final: 0.8460 (tppt)
REVERT: S   46 GLU cc_start: 0.8984 (tt0) cc_final: 0.8704 (pt0)
REVERT: S   73 ASP cc_start: 0.7931 (t0) cc_final: 0.7341 (t0)
REVERT: S   83 MET cc_start: 0.9173 (mtm) cc_final: 0.8838 (ptm)
REVERT: S   90 ASP cc_start: 0.9032 (m-30) cc_final: 0.8719 (m-30)
REVERT: S  186 GLN cc_start: 0.8803 (pt0) cc_final: 0.8592 (pt0)
REVERT: S  218 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7837 (ptp-110)
REVERT: S  223 ASP cc_start: 0.8508 (m-30) cc_final: 0.7542 (m-30)
REVERT: F    6 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.7365 (t-90)
  outliers start: 29
  outliers final: 16
  residues processed: 200
  average time/residue: 0.6052
  time to fit residues: 128.7604
Evaluate side-chains
  204 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 181
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue   40 ILE
Chi-restraints excluded: chain R residue   83 SER
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  276 ILE
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  308 THR
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  218 ARG
Chi-restraints excluded: chain F residue    6 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 117 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 85 optimal weight:    3.9990
   chunk 28 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0870
   chunk 88 optimal weight:    4.9990
   chunk 120 optimal weight:    7.9990
   chunk 82 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    1.5964

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 279 ASN
A 292 ASN
N   1 GLN
N  84 ASN
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  91 ASN
R 225 HIS
** R 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.094084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.066915 restraints weight = 17803.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 2.74
r_work: 0.2809 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2654 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.3964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10054  Z= 0.178
  Angle     :  0.591   7.678  13627  Z= 0.310
  Chirality :  0.042   0.196   1550
  Planarity :  0.004   0.039   1729
  Dihedral  :  4.762  21.781   1380
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 17.69 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.97 (0.24), residues: 1240
  helix:  2.24 (0.24), residues: 405
  sheet: -0.59 (0.27), residues: 333
  loop :  0.36 (0.30), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G  13 
 TYR   0.012   0.001   TYR S 173 
 PHE   0.016   0.002   PHE R 147 
 TRP   0.014   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 362 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.18 (10048)
  covalent geometry    : angle       0.59068 /  0.31 (13614)
  SS BOND              : bond        0.00189 /  0.11 (    5)
  SS BOND              : angle       1.19246 /  0.68 (   10)
  hydrogen bonds       : bond        0.03654 /  2.49 (  537)
  hydrogen bonds       : angle       4.99145 /  3.46 ( 1485)
  link_TRANS           : bond        0.00113 /  0.06 (    1)
  link_TRANS           : angle       0.49560 /  0.19 (    3)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 176
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   21 MET cc_start: 0.8693 (mmm) cc_final: 0.8280 (mtp)
REVERT: G   22 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7653 (tp30)
REVERT: G   26 ASP cc_start: 0.8782 (p0) cc_final: 0.8423 (p0)
REVERT: G   38 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7804 (ttm)
REVERT: G   42 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8274 (mm-30)
REVERT: A   58 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8315 (tmmt)
REVERT: A  305 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8944 (mppt)
REVERT: N   33 LYS cc_start: 0.8516 (ttmt) cc_final: 0.7862 (tttt)
REVERT: N   46 GLU cc_start: 0.8594 (tt0) cc_final: 0.8088 (pt0)
REVERT: N   53 GLN cc_start: 0.8344 (pm20) cc_final: 0.7825 (pm20)
REVERT: N   67 ARG cc_start: 0.8432 (mtm110) cc_final: 0.8153 (mtm-85)
REVERT: N   86 LEU cc_start: 0.9340 (mm) cc_final: 0.8999 (mm)
REVERT: N  120 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8466 (mm-40)
REVERT: B   10 GLU cc_start: 0.8966 (tp30) cc_final: 0.8346 (tp30)
REVERT: B   13 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8806 (tm-30)
REVERT: B   59 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8636 (m-80)
REVERT: B  188 MET cc_start: 0.8779 (mmm) cc_final: 0.8412 (mmm)
REVERT: B  217 MET cc_start: 0.9078 (ptp) cc_final: 0.8428 (pmm)
REVERT: B  258 ASP cc_start: 0.8782 (t0) cc_final: 0.8029 (t0)
REVERT: B  262 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7449 (mtp)
REVERT: B  275 SER cc_start: 0.9030 (m) cc_final: 0.8765 (p)
REVERT: B  325 MET cc_start: 0.8929 (mmt) cc_final: 0.8638 (mmm)
REVERT: R   55 GLU cc_start: 0.8913 (tt0) cc_final: 0.8560 (tt0)
REVERT: R  114 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7359 (tm-30)
REVERT: R  226 LYS cc_start: 0.7303 (mmmt) cc_final: 0.6910 (mmmt)
REVERT: S   46 GLU cc_start: 0.9002 (tt0) cc_final: 0.8688 (pt0)
REVERT: S   73 ASP cc_start: 0.7873 (t0) cc_final: 0.7247 (t0)
REVERT: S   90 ASP cc_start: 0.9048 (m-30) cc_final: 0.8739 (m-30)
REVERT: S  186 GLN cc_start: 0.8801 (pt0) cc_final: 0.8565 (pt0)
REVERT: S  223 ASP cc_start: 0.8298 (m-30) cc_final: 0.8036 (m-30)
REVERT: F    6 HIS cc_start: 0.8429 (OUTLIER) cc_final: 0.7479 (t-90)
  outliers start: 32
  outliers final: 19
  residues processed: 194
  average time/residue: 0.5637
  time to fit residues: 116.3376
Evaluate side-chains
  203 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 179
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  305 LYS
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue   40 ILE
Chi-restraints excluded: chain R residue   83 SER
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  183 TYR
Chi-restraints excluded: chain R residue  276 ILE
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  308 THR
Chi-restraints excluded: chain R residue  311 GLU
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain F residue    6 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0010
   chunk 84 optimal weight:    0.3980
   chunk 65 optimal weight:    1.9990
   chunk 76 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.6788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 279 ASN
A 292 ASN
N   1 GLN
N  84 ASN
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 225 HIS
** R 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.095992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.069207 restraints weight = 17781.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 2.76
r_work: 0.2856 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2702 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.4073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10054  Z= 0.129
  Angle     :  0.584   8.403  13627  Z= 0.307
  Chirality :  0.041   0.227   1550
  Planarity :  0.004   0.043   1729
  Dihedral  :  4.614  22.758   1380
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 19.00 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.24), residues: 1240
  helix:  2.36 (0.24), residues: 405
  sheet: -0.54 (0.27), residues: 331
  loop :  0.33 (0.30), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG G  13 
 TYR   0.011   0.001   TYR N  32 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.011   0.001   TRP A 234 
 HIS   0.002   0.001   HIS A 362 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.13 (10048)
  covalent geometry    : angle       0.58398 /  0.31 (13614)
  SS BOND              : bond        0.00119 /  0.08 (    5)
  SS BOND              : angle       0.81252 /  0.46 (   10)
  hydrogen bonds       : bond        0.03446 /  2.35 (  537)
  hydrogen bonds       : angle       4.88837 /  3.40 ( 1485)
  link_TRANS           : bond        0.00021 /  0.01 (    1)
  link_TRANS           : angle       0.33888 /  0.13 (    3)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 180
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8540 (ttm110) cc_final: 0.7920 (mtt-85)
REVERT: G   21 MET cc_start: 0.8688 (mmm) cc_final: 0.8426 (mtp)
REVERT: G   26 ASP cc_start: 0.8802 (p0) cc_final: 0.8458 (p0)
REVERT: G   38 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7704 (ttm)
REVERT: G   42 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8294 (mm-30)
REVERT: A   58 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8316 (tmmt)
REVERT: N   33 LYS cc_start: 0.8486 (ttmt) cc_final: 0.7823 (tttt)
REVERT: N   46 GLU cc_start: 0.8546 (tt0) cc_final: 0.8031 (pt0)
REVERT: N   53 GLN cc_start: 0.8278 (pm20) cc_final: 0.7800 (pm20)
REVERT: N   67 ARG cc_start: 0.8321 (mtm110) cc_final: 0.8091 (mtm-85)
REVERT: N   86 LEU cc_start: 0.9398 (mm) cc_final: 0.9133 (mm)
REVERT: N  105 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8232 (mpp80)
REVERT: N  120 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8491 (mm-40)
REVERT: B   10 GLU cc_start: 0.8989 (tp30) cc_final: 0.8406 (tp30)
REVERT: B   13 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8836 (tm-30)
REVERT: B   44 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8336 (mp10)
REVERT: B   59 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8543 (m-80)
REVERT: B  217 MET cc_start: 0.9089 (ptp) cc_final: 0.8484 (pmm)
REVERT: B  258 ASP cc_start: 0.8785 (t0) cc_final: 0.7994 (t0)
REVERT: B  262 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7406 (mtp)
REVERT: B  275 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8700 (p)
REVERT: B  325 MET cc_start: 0.8885 (mmt) cc_final: 0.8607 (mmm)
REVERT: R   55 GLU cc_start: 0.8794 (tt0) cc_final: 0.8435 (tt0)
REVERT: R   67 ARG cc_start: 0.7934 (mtt90) cc_final: 0.7646 (mtm180)
REVERT: R  114 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7346 (tm-30)
REVERT: R  226 LYS cc_start: 0.7297 (mmmt) cc_final: 0.7062 (mmmt)
REVERT: S   19 LYS cc_start: 0.8726 (tttm) cc_final: 0.8336 (tppt)
REVERT: S   46 GLU cc_start: 0.8998 (tt0) cc_final: 0.8720 (pt0)
REVERT: S   52 SER cc_start: 0.9303 (t) cc_final: 0.8832 (p)
REVERT: S   73 ASP cc_start: 0.7878 (t0) cc_final: 0.7279 (t0)
REVERT: S   83 MET cc_start: 0.9166 (mtm) cc_final: 0.8833 (ptm)
REVERT: S   90 ASP cc_start: 0.9035 (m-30) cc_final: 0.8748 (m-30)
REVERT: S  223 ASP cc_start: 0.8192 (m-30) cc_final: 0.7862 (m-30)
REVERT: F    6 HIS cc_start: 0.8417 (OUTLIER) cc_final: 0.7543 (t-90)
  outliers start: 24
  outliers final: 15
  residues processed: 195
  average time/residue: 0.5938
  time to fit residues: 123.1682
Evaluate side-chains
  198 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 177
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue   40 ILE
Chi-restraints excluded: chain R residue   83 SER
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  276 ILE
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  308 THR
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain F residue    6 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 58 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 115 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 279 ASN
A 292 ASN
N   1 GLN
N  84 ASN
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 225 HIS
** R 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 186 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.095697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.068797 restraints weight = 17676.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 2.75
r_work: 0.2850 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2695 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.4173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10054  Z= 0.141
  Angle     :  0.592   8.984  13627  Z= 0.310
  Chirality :  0.041   0.197   1550
  Planarity :  0.004   0.040   1729
  Dihedral  :  4.566  21.600   1380
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 19.76 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.24), residues: 1240
  helix:  2.42 (0.24), residues: 406
  sheet: -0.51 (0.27), residues: 331
  loop :  0.34 (0.29), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG G  13 
 TYR   0.012   0.001   TYR N  32 
 PHE   0.012   0.001   PHE R 147 
 TRP   0.011   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 357 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.14 (10048)
  covalent geometry    : angle       0.59195 /  0.31 (13614)
  SS BOND              : bond        0.00157 /  0.11 (    5)
  SS BOND              : angle       0.82526 /  0.47 (   10)
  hydrogen bonds       : bond        0.03456 /  2.35 (  537)
  hydrogen bonds       : angle       4.86064 /  3.37 ( 1485)
  link_TRANS           : bond        0.00085 /  0.04 (    1)
  link_TRANS           : angle       0.41650 /  0.16 (    3)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 173
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7799 (ptp-110)
REVERT: G   21 MET cc_start: 0.8645 (mmm) cc_final: 0.8196 (mtp)
REVERT: G   26 ASP cc_start: 0.8791 (p0) cc_final: 0.8449 (p0)
REVERT: G   38 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7784 (ttm)
REVERT: G   42 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8313 (mm-30)
REVERT: A   58 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8331 (tmmt)
REVERT: A  305 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8933 (mppt)
REVERT: A  356 ARG cc_start: 0.8384 (mtm110) cc_final: 0.8049 (mtm110)
REVERT: N   33 LYS cc_start: 0.8483 (ttmt) cc_final: 0.7826 (tttt)
REVERT: N   46 GLU cc_start: 0.8543 (tt0) cc_final: 0.8057 (pt0)
REVERT: N   53 GLN cc_start: 0.8268 (pm20) cc_final: 0.7780 (pm20)
REVERT: N   67 ARG cc_start: 0.8304 (mtm110) cc_final: 0.8103 (mtm-85)
REVERT: N  105 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.8254 (mpp80)
REVERT: N  120 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8466 (mm-40)
REVERT: B   10 GLU cc_start: 0.8984 (tp30) cc_final: 0.8396 (tp30)
REVERT: B   13 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8885 (tm-30)
REVERT: B   23 LYS cc_start: 0.8712 (tptp) cc_final: 0.8475 (tptp)
REVERT: B   44 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8343 (mp10)
REVERT: B   59 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8481 (m-80)
REVERT: B  170 ASP cc_start: 0.8252 (p0) cc_final: 0.8020 (p0)
REVERT: B  172 GLU cc_start: 0.7817 (pm20) cc_final: 0.7441 (pm20)
REVERT: B  217 MET cc_start: 0.9079 (ptp) cc_final: 0.8453 (pmm)
REVERT: B  258 ASP cc_start: 0.8786 (t0) cc_final: 0.7930 (t0)
REVERT: B  262 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7354 (mtp)
REVERT: B  275 SER cc_start: 0.8995 (m) cc_final: 0.8715 (p)
REVERT: B  325 MET cc_start: 0.8894 (mmt) cc_final: 0.8617 (mmm)
REVERT: R   55 GLU cc_start: 0.8726 (tt0) cc_final: 0.8381 (tt0)
REVERT: R  114 GLN cc_start: 0.7527 (tm-30) cc_final: 0.7307 (tm-30)
REVERT: S   19 LYS cc_start: 0.8714 (tttm) cc_final: 0.8362 (tppt)
REVERT: S   46 GLU cc_start: 0.9030 (tt0) cc_final: 0.8758 (pt0)
REVERT: S   73 ASP cc_start: 0.7867 (t0) cc_final: 0.7266 (t0)
REVERT: S   90 ASP cc_start: 0.9041 (m-30) cc_final: 0.8748 (m-30)
REVERT: S  186 GLN cc_start: 0.8829 (pt0) cc_final: 0.8613 (pt0)
REVERT: F    6 HIS cc_start: 0.8378 (OUTLIER) cc_final: 0.7552 (t-90)
REVERT: F   11 LYS cc_start: 0.9364 (mmmm) cc_final: 0.9062 (mmpt)
  outliers start: 26
  outliers final: 14
  residues processed: 190
  average time/residue: 0.6103
  time to fit residues: 123.2883
Evaluate side-chains
  186 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 166
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  305 LYS
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue   40 ILE
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  183 TYR
Chi-restraints excluded: chain R residue  276 ILE
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain F residue    6 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 114 optimal weight:    5.9990
   chunk 88 optimal weight:    2.9990
   chunk 119 optimal weight:    6.9990
   chunk 121 optimal weight:    4.9990
   chunk 90 optimal weight:    7.9990
   chunk 9 optimal weight:    0.1980
   chunk 14 optimal weight:    0.8980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 220 HIS
A 279 ASN
A 292 ASN
N   1 GLN
N  82 GLN
N  84 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 225 HIS
R 301 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.095148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.068264 restraints weight = 17643.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 2.74
r_work: 0.2837 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.4214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10054  Z= 0.154
  Angle     :  0.606   9.265  13627  Z= 0.317
  Chirality :  0.042   0.229   1550
  Planarity :  0.004   0.040   1729
  Dihedral  :  4.581  21.635   1380
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 20.23 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.24), residues: 1240
  helix:  2.45 (0.24), residues: 407
  sheet: -0.50 (0.27), residues: 331
  loop :  0.37 (0.30), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG G  13 
 TYR   0.013   0.001   TYR N  32 
 PHE   0.013   0.001   PHE R 147 
 TRP   0.011   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 357 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 (10048)
  covalent geometry    : angle       0.60612 /  0.32 (13614)
  SS BOND              : bond        0.00164 /  0.11 (    5)
  SS BOND              : angle       0.94820 /  0.54 (   10)
  hydrogen bonds       : bond        0.03479 /  2.37 (  537)
  hydrogen bonds       : angle       4.85382 /  3.36 ( 1485)
  link_TRANS           : bond        0.00069 /  0.04 (    1)
  link_TRANS           : angle       0.37869 /  0.15 (    3)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8511 (ttm110) cc_final: 0.7924 (mtt-85)
REVERT: G   21 MET cc_start: 0.8629 (mmm) cc_final: 0.8387 (mtp)
REVERT: G   26 ASP cc_start: 0.8786 (p0) cc_final: 0.8473 (p0)
REVERT: G   38 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7804 (ttm)
REVERT: G   42 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8365 (mm-30)
REVERT: A   58 LYS cc_start: 0.8545 (mmmm) cc_final: 0.8321 (tmmt)
REVERT: A  305 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8962 (mppt)
REVERT: A  317 ARG cc_start: 0.8832 (mtm-85) cc_final: 0.8017 (mtm-85)
REVERT: N   33 LYS cc_start: 0.8505 (ttmt) cc_final: 0.7829 (tttt)
REVERT: N   46 GLU cc_start: 0.8533 (tt0) cc_final: 0.8112 (pt0)
REVERT: N   53 GLN cc_start: 0.8314 (pm20) cc_final: 0.7835 (pm20)
REVERT: N   67 ARG cc_start: 0.8305 (mtm110) cc_final: 0.8095 (mtm-85)
REVERT: N  105 ARG cc_start: 0.8518 (mtm-85) cc_final: 0.8277 (mpp80)
REVERT: N  120 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8475 (mm-40)
REVERT: B   10 GLU cc_start: 0.8987 (tp30) cc_final: 0.8417 (tp30)
REVERT: B   13 GLN cc_start: 0.9144 (tm-30) cc_final: 0.8890 (tm-30)
REVERT: B   23 LYS cc_start: 0.8769 (tptp) cc_final: 0.8534 (tptp)
REVERT: B   37 ILE cc_start: 0.7851 (mt) cc_final: 0.7577 (mm)
REVERT: B   44 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8346 (mp10)
REVERT: B   59 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.8225 (m-80)
REVERT: B  170 ASP cc_start: 0.8255 (p0) cc_final: 0.8016 (p0)
REVERT: B  217 MET cc_start: 0.9107 (ptp) cc_final: 0.8490 (pmm)
REVERT: B  254 ASP cc_start: 0.7997 (t70) cc_final: 0.7463 (t70)
REVERT: B  258 ASP cc_start: 0.8780 (t0) cc_final: 0.8048 (t0)
REVERT: B  262 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7390 (mtp)
REVERT: B  325 MET cc_start: 0.8910 (mmt) cc_final: 0.8627 (mmm)
REVERT: R   55 GLU cc_start: 0.8686 (tt0) cc_final: 0.8291 (tt0)
REVERT: R   67 ARG cc_start: 0.7875 (mtt90) cc_final: 0.7638 (mtm180)
REVERT: R  114 GLN cc_start: 0.7446 (tm-30) cc_final: 0.7228 (tm-30)
REVERT: S   19 LYS cc_start: 0.8743 (tttm) cc_final: 0.8376 (tppt)
REVERT: S   46 GLU cc_start: 0.9029 (tt0) cc_final: 0.8729 (pt0)
REVERT: S   73 ASP cc_start: 0.7876 (t0) cc_final: 0.7268 (t0)
REVERT: S   83 MET cc_start: 0.9056 (mtm) cc_final: 0.8761 (ptm)
REVERT: S   90 ASP cc_start: 0.9053 (m-30) cc_final: 0.8718 (m-30)
REVERT: S  186 GLN cc_start: 0.8859 (pt0) cc_final: 0.8647 (pt0)
REVERT: F    6 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.7569 (t-90)
  outliers start: 22
  outliers final: 14
  residues processed: 185
  average time/residue: 0.5919
  time to fit residues: 116.5522
Evaluate side-chains
  187 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 167
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  305 LYS
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   40 ILE
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  276 ILE
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain F residue    6 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 15 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 93 optimal weight:    9.9990
   chunk 96 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   overall best weight:    1.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 279 ASN
A 292 ASN
N   1 GLN
N  84 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 225 HIS
R 301 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.094394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.067256 restraints weight = 17801.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.75
r_work: 0.2814 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2658 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.4243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10054  Z= 0.177
  Angle     :  0.622   9.250  13627  Z= 0.325
  Chirality :  0.042   0.205   1550
  Planarity :  0.004   0.040   1729
  Dihedral  :  4.635  21.992   1380
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 20.32 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.24), residues: 1240
  helix:  2.45 (0.24), residues: 406
  sheet: -0.52 (0.27), residues: 331
  loop :  0.36 (0.29), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG G  13 
 TYR   0.013   0.001   TYR S 173 
 PHE   0.015   0.002   PHE R 147 
 TRP   0.012   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 357 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.18 (10048)
  covalent geometry    : angle       0.62206 /  0.33 (13614)
  SS BOND              : bond        0.00164 /  0.10 (    5)
  SS BOND              : angle       1.02868 /  0.59 (   10)
  hydrogen bonds       : bond        0.03536 /  2.41 (  537)
  hydrogen bonds       : angle       4.89699 /  3.38 ( 1485)
  link_TRANS           : bond        0.00113 /  0.06 (    1)
  link_TRANS           : angle       0.45493 /  0.17 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4033.89 seconds
wall clock time: 69 minutes 29.47 seconds (4169.47 seconds total)