Starting phenix.real_space_refine
on Wed Mar  4 01:15:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f4h_31452/03_2026/7f4h_31452.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f4h_31452/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f4h_31452/03_2026/7f4h_31452.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f4h_31452/03_2026/7f4h_31452.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f4h_31452/03_2026/7f4h_31452.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f4h_31452/03_2026/7f4h_31452.cif"
  }
  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-5986/lib/python3.9/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}
          Modifications used: {'PEPT-D': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 5}
    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: 2.13, per 1000 atoms: 0.22
  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: 0.70
  Conformation dependent library (CDL) restraints added in 471.2 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: 0.27
  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: 0.89 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  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
  bond pdb=" N   PHE A 345 "
       pdb=" CA  PHE A 345 "
    ideal  model  delta    sigma   weight residual
    1.458  1.483 -0.025 1.26e-02 6.30e+03 3.79e+00
  ... (remaining 10043 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 12268
        1.67 -     3.34: 1236
        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: 5561
       17.79 -    35.58: 345
       35.58 -    53.37: 43
       53.37 -    71.16: 14
       71.16 -    88.95: 11
  Dihedral angle restraints: 5974
    sinusoidal: 2309
      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 5971 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:             0.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.630
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:7.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
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= 0.626
  Chirality :  0.064   0.281   1550
  Planarity :  0.011   0.153   1729
  Dihedral  : 12.813  88.946   3594
  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
  covalent geometry    : bond        0.00974 (10048)
  covalent geometry    : angle       1.04171 (13614)
  SS BOND              : bond        0.00876 (    5)
  SS BOND              : angle       1.76937 (   10)
  hydrogen bonds       : bond        0.15825 (  537)
  hydrogen bonds       : angle       7.18560 ( 1485)
  link_TRANS           : bond        0.00580 (    1)
  link_TRANS           : angle       1.32519 (    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  : 0.374 
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: 0.6873 (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: 0.7571 (m-40)
REVERT: R  262 THR cc_start: 0.8466 (m) cc_final: 0.8192 (p)
REVERT: S  218 ARG cc_start: 0.8158 (mtm-85) cc_final: 0.7955 (ptp-110)
REVERT: S  223 ASP cc_start: 0.8515 (m-30) cc_final: 0.8235 (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: 0.6716
  time to fit residues: 203.7236
Evaluate side-chains
  179 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 178
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9990
   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:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 117 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
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
S  13 GLN
S 171 ASN
S 179 GLN
S 183 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.097296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.070658 restraints weight = 17568.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 2.73
r_work: 0.2880 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10054  Z= 0.160
  Angle     :  0.660   7.445  13627  Z= 0.354
  Chirality :  0.044   0.260   1550
  Planarity :  0.005   0.038   1729
  Dihedral  :  5.865  50.898   1383
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 12.32 %
    Favored  : 85.14 %
  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:  0.56 (0.23), residues: 1240
  helix:  1.74 (0.25), residues: 408
  sheet: -0.57 (0.27), residues: 304
  loop : -0.00 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 356 
 TYR   0.016   0.001   TYR N  32 
 PHE   0.022   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
  covalent geometry    : bond        0.00350 (10048)
  covalent geometry    : angle       0.65996 (13614)
  SS BOND              : bond        0.00220 (    5)
  SS BOND              : angle       1.10047 (   10)
  hydrogen bonds       : bond        0.04364 (  537)
  hydrogen bonds       : angle       5.50695 ( 1485)
  link_TRANS           : bond        0.00080 (    1)
  link_TRANS           : angle       0.65320 (    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
  227 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 200
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8471 (ttm110) cc_final: 0.8078 (ptp-110)
REVERT: G   21 MET cc_start: 0.8723 (mmm) cc_final: 0.8457 (mtp)
REVERT: G   22 GLU cc_start: 0.7606 (tt0) cc_final: 0.7348 (mt-10)
REVERT: G   26 ASP cc_start: 0.8650 (p0) cc_final: 0.8412 (p0)
REVERT: G   38 MET cc_start: 0.8211 (ptp) cc_final: 0.7688 (ttm)
REVERT: G   42 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8034 (mm-30)
REVERT: A   27 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8143 (mt-10)
REVERT: N   33 LYS cc_start: 0.8564 (ttmt) cc_final: 0.7831 (tttt)
REVERT: N   39 GLN cc_start: 0.9181 (tt0) cc_final: 0.8792 (tt0)
REVERT: N   53 GLN cc_start: 0.8170 (pm20) cc_final: 0.7614 (pm20)
REVERT: N   73 ASP cc_start: 0.8225 (t0) cc_final: 0.7182 (t0)
REVERT: N   76 LYS cc_start: 0.9333 (mtpt) cc_final: 0.8706 (mtmm)
REVERT: N  120 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8585 (mm-40)
REVERT: B   10 GLU cc_start: 0.8552 (tp30) cc_final: 0.7942 (tp30)
REVERT: B  217 MET cc_start: 0.8878 (ptp) cc_final: 0.8106 (pmm)
REVERT: B  262 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.8018 (mtp)
REVERT: B  275 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8497 (p)
REVERT: B  325 MET cc_start: 0.8745 (mmt) cc_final: 0.8431 (mmm)
REVERT: R   73 MET cc_start: 0.8353 (ppp) cc_final: 0.8124 (ppp)
REVERT: R  114 GLN cc_start: 0.7418 (tm-30) cc_final: 0.7216 (tm-30)
REVERT: R  117 ASP cc_start: 0.7639 (t70) cc_final: 0.7426 (t0)
REVERT: R  148 TYR cc_start: 0.8632 (m-80) cc_final: 0.8422 (m-80)
REVERT: R  226 LYS cc_start: 0.7290 (mmmt) cc_final: 0.7065 (mmmt)
REVERT: R  238 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8259 (tptm)
REVERT: R  278 LYS cc_start: 0.9217 (mmpt) cc_final: 0.8698 (mmpt)
REVERT: R  303 GLN cc_start: 0.8741 (mp10) cc_final: 0.8203 (mm110)
REVERT: S   73 ASP cc_start: 0.7810 (t0) cc_final: 0.7096 (t0)
REVERT: S  174 LEU cc_start: 0.8903 (tp) cc_final: 0.8614 (tm)
REVERT: S  186 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8564 (pt0)
REVERT: S  223 ASP cc_start: 0.8656 (m-30) cc_final: 0.8385 (m-30)
REVERT: S  244 LYS cc_start: 0.8684 (tttm) cc_final: 0.8429 (ttmm)
REVERT: S  246 GLU cc_start: 0.8164 (mp0) cc_final: 0.7621 (mp0)
  outliers start: 27
  outliers final: 4
  residues processed: 216
  average time/residue: 0.6532
  time to fit residues: 149.8738
Evaluate side-chains
  184 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 176
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 LEU
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  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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 93 optimal weight:    7.9990
   chunk 118 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
G  24 ASN
A  35 GLN
A 279 ASN
A 292 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 118 ASN
** R 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 183 GLN
S 194 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.095958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.069134 restraints weight = 17410.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 2.72
r_work: 0.2853 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2697 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10054  Z= 0.156
  Angle     :  0.591   7.146  13627  Z= 0.316
  Chirality :  0.043   0.269   1550
  Planarity :  0.004   0.037   1729
  Dihedral  :  5.259  43.590   1381
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.39 %
    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:  0.77 (0.24), residues: 1240
  helix:  1.94 (0.25), residues: 407
  sheet: -0.62 (0.28), residues: 312
  loop :  0.24 (0.28), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG S 202 
 TYR   0.012   0.001   TYR N  32 
 PHE   0.018   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
  covalent geometry    : bond        0.00347 (10048)
  covalent geometry    : angle       0.59065 (13614)
  SS BOND              : bond        0.00185 (    5)
  SS BOND              : angle       0.95715 (   10)
  hydrogen bonds       : bond        0.03962 (  537)
  hydrogen bonds       : angle       5.20816 ( 1485)
  link_TRANS           : bond        0.00072 (    1)
  link_TRANS           : angle       0.59505 (    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
  214 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 192
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   21 MET cc_start: 0.8743 (mmm) cc_final: 0.8202 (mtp)
REVERT: G   22 GLU cc_start: 0.7512 (tt0) cc_final: 0.7300 (mt-10)
REVERT: G   26 ASP cc_start: 0.8673 (p0) cc_final: 0.8287 (p0)
REVERT: G   29 LYS cc_start: 0.8786 (mptm) cc_final: 0.8542 (tppt)
REVERT: G   38 MET cc_start: 0.8143 (ptp) cc_final: 0.7629 (ttm)
REVERT: G   42 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8177 (mm-30)
REVERT: A   27 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8133 (mt-10)
REVERT: N   33 LYS cc_start: 0.8586 (ttmt) cc_final: 0.7918 (tttt)
REVERT: N   39 GLN cc_start: 0.9220 (tt0) cc_final: 0.8905 (tt0)
REVERT: N   46 GLU cc_start: 0.8562 (tt0) cc_final: 0.8182 (pt0)
REVERT: N   53 GLN cc_start: 0.8250 (pm20) cc_final: 0.7742 (pm20)
REVERT: N   67 ARG cc_start: 0.8360 (mtm110) cc_final: 0.8116 (mtm-85)
REVERT: N   73 ASP cc_start: 0.8300 (t0) cc_final: 0.7511 (t0)
REVERT: N   86 LEU cc_start: 0.9259 (mp) cc_final: 0.8914 (mm)
REVERT: N  120 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8465 (mm-40)
REVERT: B   10 GLU cc_start: 0.8810 (tp30) cc_final: 0.8214 (tp30)
REVERT: B   59 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8708 (m-80)
REVERT: B   61 MET cc_start: 0.8934 (ptm) cc_final: 0.8702 (ppp)
REVERT: B  217 MET cc_start: 0.8909 (ptp) cc_final: 0.8248 (pmm)
REVERT: B  258 ASP cc_start: 0.8697 (t0) cc_final: 0.7778 (t0)
REVERT: B  262 MET cc_start: 0.8005 (mtp) cc_final: 0.7764 (mtp)
REVERT: B  275 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8502 (p)
REVERT: B  325 MET cc_start: 0.8846 (mmt) cc_final: 0.8536 (mmm)
REVERT: R  114 GLN cc_start: 0.7439 (tm-30) cc_final: 0.7154 (tm-30)
REVERT: R  117 ASP cc_start: 0.7653 (t70) cc_final: 0.7445 (t0)
REVERT: R  148 TYR cc_start: 0.8705 (m-80) cc_final: 0.8445 (m-80)
REVERT: R  307 ARG cc_start: 0.7774 (tpm170) cc_final: 0.7527 (tpm170)
REVERT: S   73 ASP cc_start: 0.7955 (t0) cc_final: 0.7313 (t0)
REVERT: S   90 ASP cc_start: 0.8963 (m-30) cc_final: 0.8732 (m-30)
REVERT: S  186 GLN cc_start: 0.8818 (pt0) cc_final: 0.8567 (pt0)
REVERT: S  218 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7810 (mtm-85)
REVERT: S  220 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8027 (mp0)
REVERT: S  223 ASP cc_start: 0.8680 (m-30) cc_final: 0.7478 (m-30)
REVERT: S  246 GLU cc_start: 0.8180 (mp0) cc_final: 0.7623 (mp0)
  outliers start: 22
  outliers final: 5
  residues processed: 207
  average time/residue: 0.6454
  time to fit residues: 141.6841
Evaluate side-chains
  194 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 186
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  284 LEU
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  218 ARG
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:    4.9990
   chunk 111 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 25 optimal weight:    7.9990
   chunk 84 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 121 optimal weight:    4.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
G  24 ASN
A 292 ASN
N  84 ASN
B  75 GLN
B 340 ASN
R  56 ASN
R  91 ASN
** R 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S  77 ASN
S 183 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.091833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.064914 restraints weight = 17919.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.2925 rms_B_bonded: 2.68
r_work: 0.2755 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2601 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  10054  Z= 0.264
  Angle     :  0.638   7.018  13627  Z= 0.337
  Chirality :  0.045   0.243   1550
  Planarity :  0.004   0.037   1729
  Dihedral  :  5.312  39.319   1381
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.52 %
    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:  0.76 (0.24), residues: 1240
  helix:  1.95 (0.24), residues: 407
  sheet: -0.72 (0.27), residues: 314
  loop :  0.30 (0.29), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  13 
 TYR   0.013   0.002   TYR S 173 
 PHE   0.023   0.002   PHE R 147 
 TRP   0.018   0.002   TRP A 234 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 (10048)
  covalent geometry    : angle       0.63760 (13614)
  SS BOND              : bond        0.00169 (    5)
  SS BOND              : angle       1.30125 (   10)
  hydrogen bonds       : bond        0.04064 (  537)
  hydrogen bonds       : angle       5.21585 ( 1485)
  link_TRANS           : bond        0.00216 (    1)
  link_TRANS           : angle       0.76041 (    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
  218 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 185
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8587 (ttm110) cc_final: 0.8060 (ptp-110)
REVERT: G   17 GLU cc_start: 0.8905 (tp30) cc_final: 0.8639 (tp30)
REVERT: G   21 MET cc_start: 0.8769 (mmm) cc_final: 0.8287 (mtp)
REVERT: G   26 ASP cc_start: 0.8743 (p0) cc_final: 0.8360 (p0)
REVERT: G   38 MET cc_start: 0.8295 (ptp) cc_final: 0.7787 (ttm)
REVERT: G   42 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8243 (mm-30)
REVERT: A   58 LYS cc_start: 0.8610 (mmmm) cc_final: 0.8306 (tmmt)
REVERT: N    3 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7786 (pt0)
REVERT: N   33 LYS cc_start: 0.8506 (ttmt) cc_final: 0.7820 (tttt)
REVERT: N   39 GLN cc_start: 0.9298 (tt0) cc_final: 0.8989 (tt0)
REVERT: N   46 GLU cc_start: 0.8582 (tt0) cc_final: 0.8087 (pt0)
REVERT: N   53 GLN cc_start: 0.8357 (pm20) cc_final: 0.7839 (pm20)
REVERT: N   86 LEU cc_start: 0.9406 (mp) cc_final: 0.9201 (mm)
REVERT: N  120 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8556 (mm-40)
REVERT: B   10 GLU cc_start: 0.8856 (tp30) cc_final: 0.8008 (tp30)
REVERT: B   13 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8482 (pp30)
REVERT: B  217 MET cc_start: 0.8967 (ptp) cc_final: 0.8313 (pmm)
REVERT: B  254 ASP cc_start: 0.7999 (t0) cc_final: 0.7635 (t70)
REVERT: B  258 ASP cc_start: 0.8781 (t0) cc_final: 0.7963 (t0)
REVERT: B  275 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8567 (p)
REVERT: B  325 MET cc_start: 0.8876 (mmt) cc_final: 0.8575 (mmm)
REVERT: R  114 GLN cc_start: 0.7450 (tm-30) cc_final: 0.7140 (tm-30)
REVERT: R  117 ASP cc_start: 0.7647 (t70) cc_final: 0.7381 (t0)
REVERT: R  226 LYS cc_start: 0.7312 (mmmt) cc_final: 0.7109 (mmmt)
REVERT: R  307 ARG cc_start: 0.7873 (tpm170) cc_final: 0.7450 (tpm170)
REVERT: S   19 LYS cc_start: 0.8848 (tttp) cc_final: 0.8597 (tttm)
REVERT: S   46 GLU cc_start: 0.8977 (tt0) cc_final: 0.8686 (pt0)
REVERT: S   73 ASP cc_start: 0.7832 (t0) cc_final: 0.7135 (t0)
REVERT: S   77 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8451 (m110)
REVERT: S   90 ASP cc_start: 0.9025 (m-30) cc_final: 0.8742 (m-30)
REVERT: S   93 MET cc_start: 0.9071 (ttt) cc_final: 0.8714 (ttp)
REVERT: S  186 GLN cc_start: 0.8816 (pt0) cc_final: 0.8544 (pt0)
REVERT: S  218 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7744 (ptp-110)
REVERT: S  220 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8086 (mp0)
REVERT: S  223 ASP cc_start: 0.8671 (m-30) cc_final: 0.7411 (m-30)
REVERT: S  244 LYS cc_start: 0.8662 (ttmm) cc_final: 0.8447 (ttmm)
REVERT: S  246 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7608 (mp0)
REVERT: F    6 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.7391 (t-90)
  outliers start: 33
  outliers final: 13
  residues processed: 204
  average time/residue: 0.6412
  time to fit residues: 138.9468
Evaluate side-chains
  190 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 172
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
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  369 THR
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  245 SER
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  244 THR
Chi-restraints excluded: chain R residue  276 ILE
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain S residue   77 ASN
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0770
   chunk 35 optimal weight:    0.9990
   chunk 87 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 103 optimal weight:    0.7980
   overall best weight:    1.3744

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

Flipped N/Q/H residues before XYZ refinement:
G  24 ASN
A 279 ASN
N   1 GLN
N  35 ASN
N  84 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 115 GLN
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 = 0.3470 r_free = 0.3470 target = 0.093927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.066666 restraints weight = 17520.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 2.73
r_work: 0.2796 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2642 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10054  Z= 0.169
  Angle     :  0.592   7.071  13627  Z= 0.312
  Chirality :  0.042   0.220   1550
  Planarity :  0.004   0.039   1729
  Dihedral  :  5.106  38.491   1381
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 16.84 %
    Favored  : 80.34 %
  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:  0.80 (0.24), residues: 1240
  helix:  2.05 (0.24), residues: 407
  sheet: -0.79 (0.27), residues: 322
  loop :  0.36 (0.29), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 151 
 TYR   0.012   0.001   TYR N  32 
 PHE   0.015   0.002   PHE R 147 
 TRP   0.013   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (10048)
  covalent geometry    : angle       0.59135 (13614)
  SS BOND              : bond        0.00488 (    5)
  SS BOND              : angle       1.22876 (   10)
  hydrogen bonds       : bond        0.03743 (  537)
  hydrogen bonds       : angle       5.12335 ( 1485)
  link_TRANS           : bond        0.00060 (    1)
  link_TRANS           : angle       0.52678 (    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
  209 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 179
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   26 ASP cc_start: 0.8782 (p0) cc_final: 0.8417 (p0)
REVERT: G   29 LYS cc_start: 0.8797 (mptm) cc_final: 0.8567 (tppt)
REVERT: G   38 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7802 (ttm)
REVERT: G   42 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8236 (mm-30)
REVERT: A   58 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8323 (tmmt)
REVERT: A  305 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8954 (mppt)
REVERT: N   33 LYS cc_start: 0.8502 (ttmt) cc_final: 0.7825 (tttt)
REVERT: N   39 GLN cc_start: 0.9321 (tt0) cc_final: 0.9000 (tt0)
REVERT: N   46 GLU cc_start: 0.8603 (tt0) cc_final: 0.8076 (pt0)
REVERT: N   53 GLN cc_start: 0.8297 (pm20) cc_final: 0.7823 (pm20)
REVERT: N  120 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8529 (mm-40)
REVERT: B   10 GLU cc_start: 0.8861 (tp30) cc_final: 0.8077 (tp30)
REVERT: B   13 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8469 (pp30)
REVERT: B   59 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8695 (m-80)
REVERT: B   61 MET cc_start: 0.9268 (ppp) cc_final: 0.9056 (ppp)
REVERT: B  170 ASP cc_start: 0.8171 (p0) cc_final: 0.7914 (p0)
REVERT: B  172 GLU cc_start: 0.7833 (pm20) cc_final: 0.7414 (pm20)
REVERT: B  217 MET cc_start: 0.8998 (ptp) cc_final: 0.8282 (pmm)
REVERT: B  258 ASP cc_start: 0.8753 (t0) cc_final: 0.8011 (t0)
REVERT: B  275 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8538 (p)
REVERT: B  325 MET cc_start: 0.8890 (mmt) cc_final: 0.8602 (mmm)
REVERT: R  114 GLN cc_start: 0.7368 (tm-30) cc_final: 0.7079 (tm-30)
REVERT: R  117 ASP cc_start: 0.7696 (t70) cc_final: 0.7435 (t0)
REVERT: R  226 LYS cc_start: 0.7323 (mmmt) cc_final: 0.6873 (mmmt)
REVERT: S   46 GLU cc_start: 0.8964 (tt0) cc_final: 0.8667 (pt0)
REVERT: S   73 ASP cc_start: 0.7916 (t0) cc_final: 0.7323 (t0)
REVERT: S   83 MET cc_start: 0.9188 (mtm) cc_final: 0.8871 (ptm)
REVERT: S   90 ASP cc_start: 0.9030 (m-30) cc_final: 0.8722 (m-30)
REVERT: S   93 MET cc_start: 0.9051 (ttt) cc_final: 0.8699 (ttp)
REVERT: S  186 GLN cc_start: 0.8805 (pt0) cc_final: 0.8581 (pt0)
REVERT: S  218 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7701 (ptp-110)
REVERT: S  220 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8092 (mp0)
REVERT: S  223 ASP cc_start: 0.8685 (m-30) cc_final: 0.7524 (m-30)
REVERT: S  246 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7646 (mp0)
REVERT: F    6 HIS cc_start: 0.8434 (OUTLIER) cc_final: 0.7320 (t-90)
  outliers start: 30
  outliers final: 12
  residues processed: 199
  average time/residue: 0.6721
  time to fit residues: 141.8108
Evaluate side-chains
  197 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 179
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
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  266 LEU
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  234 PHE
Chi-restraints excluded: chain B residue  245 SER
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  218 ARG
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:    1.9990
   chunk 79 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 120 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.9588

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

Flipped N/Q/H residues before XYZ refinement:
G  24 ASN
A 279 ASN
A 292 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 = 0.3489 r_free = 0.3489 target = 0.094916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.067949 restraints weight = 17759.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 2.75
r_work: 0.2828 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2675 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.3890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10054  Z= 0.141
  Angle     :  0.581   9.538  13627  Z= 0.304
  Chirality :  0.042   0.215   1550
  Planarity :  0.004   0.040   1729
  Dihedral  :  4.865  34.919   1381
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.69 %
    Favored  : 79.96 %
  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:  0.91 (0.24), residues: 1240
  helix:  2.23 (0.24), residues: 405
  sheet: -0.67 (0.27), residues: 333
  loop :  0.31 (0.30), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG G  13 
 TYR   0.012   0.001   TYR N  32 
 PHE   0.014   0.001   PHE R  45 
 TRP   0.012   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (10048)
  covalent geometry    : angle       0.58060 (13614)
  SS BOND              : bond        0.00143 (    5)
  SS BOND              : angle       1.00011 (   10)
  hydrogen bonds       : bond        0.03595 (  537)
  hydrogen bonds       : angle       4.99967 ( 1485)
  link_TRANS           : bond        0.00052 (    1)
  link_TRANS           : angle       0.40441 (    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
  202 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 177
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8629 (ttm110) cc_final: 0.8081 (ptp-110)
REVERT: G   26 ASP cc_start: 0.8805 (p0) cc_final: 0.8447 (p0)
REVERT: G   29 LYS cc_start: 0.8797 (mptm) cc_final: 0.8558 (tppt)
REVERT: G   38 MET cc_start: 0.8222 (ptp) cc_final: 0.7817 (ttm)
REVERT: G   42 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8212 (mm-30)
REVERT: A   58 LYS cc_start: 0.8566 (mmmm) cc_final: 0.8338 (tmmt)
REVERT: A  305 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8945 (mppt)
REVERT: N   33 LYS cc_start: 0.8472 (ttmt) cc_final: 0.7813 (tttt)
REVERT: N   46 GLU cc_start: 0.8618 (tt0) cc_final: 0.8031 (pt0)
REVERT: N   53 GLN cc_start: 0.8288 (pm20) cc_final: 0.7770 (pm20)
REVERT: N  120 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8501 (mm-40)
REVERT: B   10 GLU cc_start: 0.8876 (tp30) cc_final: 0.8102 (tp30)
REVERT: B   13 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8306 (pp30)
REVERT: B   59 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.8640 (m-80)
REVERT: B  188 MET cc_start: 0.8793 (mmm) cc_final: 0.8397 (mmm)
REVERT: B  217 MET cc_start: 0.9049 (ptp) cc_final: 0.8303 (pmm)
REVERT: B  258 ASP cc_start: 0.8763 (t0) cc_final: 0.8035 (t0)
REVERT: B  325 MET cc_start: 0.8900 (mmt) cc_final: 0.8616 (mmm)
REVERT: R  114 GLN cc_start: 0.7475 (tm-30) cc_final: 0.7165 (tm-30)
REVERT: R  226 LYS cc_start: 0.7377 (mmmt) cc_final: 0.7080 (mmmt)
REVERT: S   46 GLU cc_start: 0.8944 (tt0) cc_final: 0.8647 (pt0)
REVERT: S   73 ASP cc_start: 0.7921 (t0) cc_final: 0.7306 (t0)
REVERT: S   90 ASP cc_start: 0.9038 (m-30) cc_final: 0.8729 (m-30)
REVERT: S  218 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7788 (ptp-110)
REVERT: S  220 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8206 (mp0)
REVERT: S  223 ASP cc_start: 0.8551 (m-30) cc_final: 0.7574 (m-30)
REVERT: S  246 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7649 (mp0)
REVERT: F    6 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.7431 (t-90)
  outliers start: 25
  outliers final: 14
  residues processed: 192
  average time/residue: 0.6582
  time to fit residues: 133.7216
Evaluate side-chains
  184 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 A residue  305 LYS
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  277 SER
Chi-restraints excluded: chain R residue   40 ILE
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  244 THR
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 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:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 43 optimal weight:   10.0000
   chunk 85 optimal weight:    3.9990
   chunk 28 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 88 optimal weight:    2.9990
   chunk 120 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
S 186 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.093278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.065998 restraints weight = 17757.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 2.75
r_work: 0.2788 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2634 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.3954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  10054  Z= 0.202
  Angle     :  0.599   7.737  13627  Z= 0.314
  Chirality :  0.043   0.203   1550
  Planarity :  0.004   0.041   1729
  Dihedral  :  4.835  22.262   1381
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 18.44 %
    Favored  : 78.83 %
  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:  0.90 (0.24), residues: 1240
  helix:  2.23 (0.24), residues: 406
  sheet: -0.78 (0.27), residues: 322
  loop :  0.35 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG G  13 
 TYR   0.014   0.001   TYR S 173 
 PHE   0.017   0.002   PHE R 147 
 TRP   0.014   0.002   TRP A 234 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (10048)
  covalent geometry    : angle       0.59875 (13614)
  SS BOND              : bond        0.00167 (    5)
  SS BOND              : angle       1.13357 (   10)
  hydrogen bonds       : bond        0.03708 (  537)
  hydrogen bonds       : angle       5.04149 ( 1485)
  link_TRANS           : bond        0.00137 (    1)
  link_TRANS           : angle       0.60967 (    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
  203 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 174
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8572 (ttm110) cc_final: 0.8066 (ptp-110)
REVERT: G   21 MET cc_start: 0.8654 (mmm) cc_final: 0.8161 (mtp)
REVERT: G   26 ASP cc_start: 0.8798 (p0) cc_final: 0.8446 (p0)
REVERT: G   29 LYS cc_start: 0.8800 (mptm) cc_final: 0.8564 (tppt)
REVERT: G   38 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7804 (ttm)
REVERT: G   42 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8227 (mm-30)
REVERT: A   58 LYS cc_start: 0.8563 (mmmm) cc_final: 0.8299 (tmmt)
REVERT: A  305 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8954 (mppt)
REVERT: N   33 LYS cc_start: 0.8541 (ttmt) cc_final: 0.7875 (tttt)
REVERT: N   46 GLU cc_start: 0.8560 (tt0) cc_final: 0.7999 (pt0)
REVERT: N   53 GLN cc_start: 0.8343 (pm20) cc_final: 0.7804 (pm20)
REVERT: N  120 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8484 (mm-40)
REVERT: B   10 GLU cc_start: 0.8872 (tp30) cc_final: 0.8112 (tp30)
REVERT: B   13 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8340 (pp30)
REVERT: B   59 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8644 (m-80)
REVERT: B  217 MET cc_start: 0.9037 (ptp) cc_final: 0.8391 (pmm)
REVERT: B  254 ASP cc_start: 0.7981 (t70) cc_final: 0.7470 (t70)
REVERT: B  258 ASP cc_start: 0.8812 (t0) cc_final: 0.8052 (t0)
REVERT: B  275 SER cc_start: 0.9093 (m) cc_final: 0.8832 (p)
REVERT: B  325 MET cc_start: 0.8938 (mmt) cc_final: 0.8647 (mmm)
REVERT: R   55 GLU cc_start: 0.8878 (tt0) cc_final: 0.8517 (tt0)
REVERT: R  114 GLN cc_start: 0.7499 (tm-30) cc_final: 0.7180 (tm-30)
REVERT: S   46 GLU cc_start: 0.8969 (tt0) cc_final: 0.8655 (pt0)
REVERT: S   73 ASP cc_start: 0.7844 (t0) cc_final: 0.7183 (t0)
REVERT: S   90 ASP cc_start: 0.9063 (m-30) cc_final: 0.8742 (m-30)
REVERT: S  218 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7756 (ptp-110)
REVERT: S  220 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8264 (mp0)
REVERT: S  223 ASP cc_start: 0.8373 (m-30) cc_final: 0.7238 (m-30)
REVERT: F    6 HIS cc_start: 0.8401 (OUTLIER) cc_final: 0.7449 (t-90)
  outliers start: 29
  outliers final: 16
  residues processed: 190
  average time/residue: 0.6311
  time to fit residues: 127.2222
Evaluate side-chains
  190 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
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  234 PHE
Chi-restraints excluded: chain B residue  245 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  183 TYR
Chi-restraints excluded: chain R residue  244 THR
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 S residue  218 ARG
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:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0040
   chunk 84 optimal weight:    0.9990
   chunk 65 optimal weight:    0.3980
   chunk 76 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
A 384 GLN
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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.095801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.069057 restraints weight = 17729.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 2.75
r_work: 0.2853 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.4086

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= 0.126
  Angle     :  0.580   8.540  13627  Z= 0.304
  Chirality :  0.041   0.211   1550
  Planarity :  0.004   0.041   1729
  Dihedral  :  4.600  20.540   1381
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.38 %
    Favored  : 78.46 %
  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:  1.00 (0.24), residues: 1240
  helix:  2.32 (0.24), residues: 407
  sheet: -0.61 (0.27), residues: 331
  loop :  0.33 (0.30), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG N 105 
 TYR   0.011   0.001   TYR N  32 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.010   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10048)
  covalent geometry    : angle       0.58008 (13614)
  SS BOND              : bond        0.00284 (    5)
  SS BOND              : angle       0.72470 (   10)
  hydrogen bonds       : bond        0.03473 (  537)
  hydrogen bonds       : angle       4.91595 ( 1485)
  link_TRANS           : bond        0.00000 (    1)
  link_TRANS           : angle       0.30927 (    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
  195 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 172
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8622 (ttm110) cc_final: 0.7898 (ptp-110)
REVERT: G   26 ASP cc_start: 0.8824 (p0) cc_final: 0.8491 (p0)
REVERT: G   29 LYS cc_start: 0.8788 (mptm) cc_final: 0.8416 (tppt)
REVERT: G   38 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7684 (ttm)
REVERT: G   42 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8270 (mm-30)
REVERT: A   58 LYS cc_start: 0.8566 (mmmm) cc_final: 0.8312 (tmmt)
REVERT: N   13 GLN cc_start: 0.8512 (tp40) cc_final: 0.8191 (mp10)
REVERT: N   33 LYS cc_start: 0.8466 (ttmt) cc_final: 0.7818 (tttt)
REVERT: N   46 GLU cc_start: 0.8533 (tt0) cc_final: 0.8012 (pt0)
REVERT: N   53 GLN cc_start: 0.8280 (pm20) cc_final: 0.7805 (pm20)
REVERT: N  105 ARG cc_start: 0.8522 (mtm-85) cc_final: 0.8243 (mpp80)
REVERT: N  120 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8453 (mm-40)
REVERT: B   10 GLU cc_start: 0.8927 (tp30) cc_final: 0.8177 (tp30)
REVERT: B   13 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8349 (pp30)
REVERT: B   59 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8411 (m-80)
REVERT: B  217 MET cc_start: 0.9081 (ptp) cc_final: 0.8425 (pmm)
REVERT: B  258 ASP cc_start: 0.8775 (t0) cc_final: 0.8026 (t0)
REVERT: B  275 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8724 (p)
REVERT: B  325 MET cc_start: 0.8888 (mmt) cc_final: 0.8606 (mmm)
REVERT: R   55 GLU cc_start: 0.8747 (tt0) cc_final: 0.8360 (tt0)
REVERT: R   67 ARG cc_start: 0.7876 (mtt90) cc_final: 0.7595 (mtm180)
REVERT: R  114 GLN cc_start: 0.7557 (tm-30) cc_final: 0.7260 (tm-30)
REVERT: S   19 LYS cc_start: 0.8751 (tttm) cc_final: 0.8414 (tppt)
REVERT: S   46 GLU cc_start: 0.8949 (tt0) cc_final: 0.8678 (pt0)
REVERT: S   52 SER cc_start: 0.9307 (t) cc_final: 0.8865 (p)
REVERT: S   73 ASP cc_start: 0.7883 (t0) cc_final: 0.7264 (t0)
REVERT: S   83 MET cc_start: 0.9139 (mtm) cc_final: 0.8834 (ptm)
REVERT: S   90 ASP cc_start: 0.9045 (m-30) cc_final: 0.8750 (m-30)
REVERT: S  186 GLN cc_start: 0.8799 (pt0) cc_final: 0.8540 (pt0)
REVERT: S  218 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7748 (ptp-110)
REVERT: S  220 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8300 (mp0)
REVERT: S  223 ASP cc_start: 0.8229 (m-30) cc_final: 0.7400 (m-30)
REVERT: F    6 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.7534 (t-90)
  outliers start: 23
  outliers final: 13
  residues processed: 185
  average time/residue: 0.6641
  time to fit residues: 130.4644
Evaluate side-chains
  183 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 165
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   46 LYS
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   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
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  162 SER
Chi-restraints excluded: chain S residue  218 ARG
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:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 30 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 109 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 82 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 115 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3504 r_free = 0.3504 target = 0.095604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.068615 restraints weight = 17616.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 2.76
r_work: 0.2844 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2690 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.4216

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= 0.139
  Angle     :  0.596   9.688  13627  Z= 0.312
  Chirality :  0.041   0.207   1550
  Planarity :  0.004   0.041   1729
  Dihedral  :  4.552  22.300   1381
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 19.76 %
    Favored  : 77.99 %
  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:  1.05 (0.24), residues: 1240
  helix:  2.41 (0.24), residues: 407
  sheet: -0.57 (0.27), residues: 331
  loop :  0.30 (0.30), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG N 105 
 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
  covalent geometry    : bond        0.00310 (10048)
  covalent geometry    : angle       0.59595 (13614)
  SS BOND              : bond        0.00118 (    5)
  SS BOND              : angle       0.92549 (   10)
  hydrogen bonds       : bond        0.03475 (  537)
  hydrogen bonds       : angle       4.89011 ( 1485)
  link_TRANS           : bond        0.00042 (    1)
  link_TRANS           : angle       0.46411 (    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
  197 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 173
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8420 (ttm110) cc_final: 0.7973 (ptp-110)
REVERT: G   22 GLU cc_start: 0.8065 (tp30) cc_final: 0.7737 (tp30)
REVERT: G   26 ASP cc_start: 0.8796 (p0) cc_final: 0.8492 (p0)
REVERT: G   29 LYS cc_start: 0.8778 (mptm) cc_final: 0.8410 (tppt)
REVERT: G   38 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7801 (ttm)
REVERT: G   42 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8316 (mm-30)
REVERT: A   58 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8328 (tmmt)
REVERT: A  305 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8938 (mppt)
REVERT: A  356 ARG cc_start: 0.8363 (mtm110) cc_final: 0.8047 (mtm110)
REVERT: N   33 LYS cc_start: 0.8475 (ttmt) cc_final: 0.7814 (tttt)
REVERT: N   46 GLU cc_start: 0.8578 (tt0) cc_final: 0.8097 (pt0)
REVERT: N   53 GLN cc_start: 0.8273 (pm20) cc_final: 0.7777 (pm20)
REVERT: N  105 ARG cc_start: 0.8530 (mtm-85) cc_final: 0.8272 (mpp80)
REVERT: N  120 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8452 (mm-40)
REVERT: B   10 GLU cc_start: 0.8959 (tp30) cc_final: 0.8281 (tp30)
REVERT: B   13 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8435 (pp30)
REVERT: B   23 LYS cc_start: 0.8684 (tptp) cc_final: 0.8451 (tptp)
REVERT: B   59 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8371 (m-80)
REVERT: B   61 MET cc_start: 0.9215 (ppp) cc_final: 0.8998 (ppp)
REVERT: B  172 GLU cc_start: 0.7864 (pm20) cc_final: 0.7505 (pm20)
REVERT: B  217 MET cc_start: 0.9078 (ptp) cc_final: 0.8408 (pmm)
REVERT: B  258 ASP cc_start: 0.8791 (t0) cc_final: 0.8030 (t0)
REVERT: B  275 SER cc_start: 0.8986 (OUTLIER) cc_final: 0.8734 (p)
REVERT: B  325 MET cc_start: 0.8894 (mmt) cc_final: 0.8615 (mmm)
REVERT: R   55 GLU cc_start: 0.8770 (tt0) cc_final: 0.8359 (tt0)
REVERT: R   67 ARG cc_start: 0.7881 (mtt90) cc_final: 0.7646 (mtm180)
REVERT: R   73 MET cc_start: 0.8566 (ppp) cc_final: 0.8265 (pp-130)
REVERT: R  114 GLN cc_start: 0.7529 (tm-30) cc_final: 0.7275 (tm-30)
REVERT: S   19 LYS cc_start: 0.8746 (tttm) cc_final: 0.8399 (tppt)
REVERT: S   46 GLU cc_start: 0.8966 (tt0) cc_final: 0.8693 (pt0)
REVERT: S   52 SER cc_start: 0.9296 (t) cc_final: 0.8808 (p)
REVERT: S   73 ASP cc_start: 0.7865 (t0) cc_final: 0.7242 (t0)
REVERT: S   90 ASP cc_start: 0.9046 (m-30) cc_final: 0.8744 (m-30)
REVERT: S  218 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7762 (ptp-110)
REVERT: S  223 ASP cc_start: 0.8244 (m-30) cc_final: 0.7255 (m-30)
REVERT: F    6 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.7547 (t-90)
REVERT: F   11 LYS cc_start: 0.9365 (mmmm) cc_final: 0.9051 (mmpt)
  outliers start: 24
  outliers final: 12
  residues processed: 187
  average time/residue: 0.6590
  time to fit residues: 130.7810
Evaluate side-chains
  183 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 165
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   38 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   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
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  158 LEU
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 S residue  218 ARG
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:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 114 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 119 optimal weight:    5.9990
   chunk 121 optimal weight:    0.0870
   chunk 90 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    2.0166

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

Flipped N/Q/H residues before XYZ refinement:
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
S 186 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.093189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.066026 restraints weight = 17673.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 2.73
r_work: 0.2791 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2636 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.4200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10054  Z= 0.208
  Angle     :  0.642   9.853  13627  Z= 0.335
  Chirality :  0.043   0.218   1550
  Planarity :  0.004   0.040   1729
  Dihedral  :  4.750  22.593   1381
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 20.51 %
    Favored  : 77.61 %
  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:  1.03 (0.24), residues: 1240
  helix:  2.43 (0.24), residues: 404
  sheet: -0.64 (0.27), residues: 331
  loop :  0.33 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG N  19 
 TYR   0.015   0.001   TYR N  32 
 PHE   0.016   0.002   PHE R 147 
 TRP   0.013   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (10048)
  covalent geometry    : angle       0.64106 (13614)
  SS BOND              : bond        0.00205 (    5)
  SS BOND              : angle       1.17164 (   10)
  hydrogen bonds       : bond        0.03638 (  537)
  hydrogen bonds       : angle       4.98086 ( 1485)
  link_TRANS           : bond        0.00138 (    1)
  link_TRANS           : angle       0.51729 (    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
  185 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 165
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8613 (ttm110) cc_final: 0.7914 (ptp-110)
REVERT: G   22 GLU cc_start: 0.8057 (tp30) cc_final: 0.7734 (tp30)
REVERT: G   26 ASP cc_start: 0.8723 (p0) cc_final: 0.8416 (p0)
REVERT: G   29 LYS cc_start: 0.8795 (mptm) cc_final: 0.8428 (tppt)
REVERT: G   38 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7831 (ttm)
REVERT: G   42 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8347 (mm-30)
REVERT: A   58 LYS cc_start: 0.8553 (mmmm) cc_final: 0.8335 (tmmt)
REVERT: A  305 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8906 (mppt)
REVERT: A  317 ARG cc_start: 0.8839 (mtm-85) cc_final: 0.8023 (mtm-85)
REVERT: N   13 GLN cc_start: 0.8400 (tp40) cc_final: 0.8079 (mp10)
REVERT: N   33 LYS cc_start: 0.8552 (ttmt) cc_final: 0.7853 (tttt)
REVERT: N   46 GLU cc_start: 0.8593 (tt0) cc_final: 0.8149 (pt0)
REVERT: N   53 GLN cc_start: 0.8381 (pm20) cc_final: 0.7878 (pm20)
REVERT: N  105 ARG cc_start: 0.8561 (mtm-85) cc_final: 0.8240 (mpp80)
REVERT: N  120 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8558 (mm-40)
REVERT: B   10 GLU cc_start: 0.8981 (tp30) cc_final: 0.8268 (tp30)
REVERT: B   13 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8393 (pp30)
REVERT: B   23 LYS cc_start: 0.8739 (tptp) cc_final: 0.8515 (tptp)
REVERT: B   59 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8551 (m-80)
REVERT: B  217 MET cc_start: 0.9088 (ptp) cc_final: 0.8416 (pmm)
REVERT: B  254 ASP cc_start: 0.8030 (t70) cc_final: 0.7488 (t70)
REVERT: B  258 ASP cc_start: 0.8825 (t0) cc_final: 0.8005 (t0)
REVERT: B  325 MET cc_start: 0.8950 (mmt) cc_final: 0.8667 (mmm)
REVERT: R   55 GLU cc_start: 0.8799 (tt0) cc_final: 0.8415 (tt0)
REVERT: R   67 ARG cc_start: 0.7941 (mtt90) cc_final: 0.7703 (mtm180)
REVERT: R   73 MET cc_start: 0.8575 (ppp) cc_final: 0.8221 (pp-130)
REVERT: R  114 GLN cc_start: 0.7527 (tm-30) cc_final: 0.7277 (tm-30)
REVERT: R  199 MET cc_start: 0.7890 (tpp) cc_final: 0.7432 (tpp)
REVERT: S   46 GLU cc_start: 0.8974 (tt0) cc_final: 0.8676 (pt0)
REVERT: S   73 ASP cc_start: 0.7868 (t0) cc_final: 0.7237 (t0)
REVERT: S   83 MET cc_start: 0.9105 (mtm) cc_final: 0.8811 (ptm)
REVERT: S   89 GLU cc_start: 0.8516 (mp0) cc_final: 0.8171 (mp0)
REVERT: S   90 ASP cc_start: 0.9078 (m-30) cc_final: 0.8721 (m-30)
REVERT: F    6 HIS cc_start: 0.8381 (OUTLIER) cc_final: 0.7594 (t-90)
  outliers start: 20
  outliers final: 13
  residues processed: 178
  average time/residue: 0.6563
  time to fit residues: 124.0977
Evaluate side-chains
  179 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   38 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   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
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  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  305 LEU
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:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 96 optimal weight:    8.9990
   chunk 76 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9990
   chunk 100 optimal weight:    3.9990
   chunk 103 optimal weight:    0.6980
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.092727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.066095 restraints weight = 17788.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 2.69
r_work: 0.2792 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2637 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.4257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10054  Z= 0.202
  Angle     :  0.634   9.527  13627  Z= 0.332
  Chirality :  0.043   0.209   1550
  Planarity :  0.004   0.040   1729
  Dihedral  :  4.794  23.064   1381
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 20.60 %
    Favored  : 77.33 %
  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:  1.01 (0.24), residues: 1240
  helix:  2.40 (0.24), residues: 404
  sheet: -0.68 (0.27), residues: 331
  loop :  0.35 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG N  19 
 TYR   0.015   0.001   TYR N  32 
 PHE   0.016   0.002   PHE R 147 
 TRP   0.012   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 (10048)
  covalent geometry    : angle       0.63358 (13614)
  SS BOND              : bond        0.00202 (    5)
  SS BOND              : angle       1.10703 (   10)
  hydrogen bonds       : bond        0.03615 (  537)
  hydrogen bonds       : angle       5.00738 ( 1485)
  link_TRANS           : bond        0.00151 (    1)
  link_TRANS           : angle       0.62604 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4434.19 seconds
wall clock time: 76 minutes 6.88 seconds (4566.88 seconds total)