Starting phenix.real_space_refine
on Thu Mar 13 21:57:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7na8_24268/03_2025/7na8_24268.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7na8_24268/03_2025/7na8_24268.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/7na8_24268/03_2025/7na8_24268.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7na8_24268/03_2025/7na8_24268.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7na8_24268/03_2025/7na8_24268.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7na8_24268/03_2025/7na8_24268.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.004 sd=   0.074
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    5687      2.51       5
     N    1502      2.21       5
     O    1636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8888
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1752
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2584
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "N"
      Number of atoms: 1784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1784
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2285
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 273}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 65
          Unusual residues: {'1KD': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.24, per 1000 atoms: 0.70
  Number of scatterers: 8888
  At special positions: 0
  Unit cell: (90.034, 122.248, 126.378, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      63     16.00
     O    1636      8.00
     N    1502      7.00
     C    5687      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 159 " - pdb=" SG  CYS N 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 116 " - pdb=" SG  CYS R 198 " distance=2.12

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.48
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 14 sheets defined
      38.7% alpha, 23.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 31
    Processing helix  chain 'A' and resid 42 through 53
      removed outlier: 3.945A  pdb=" N   LYS A  46 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   THR A  48 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.658A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 4.003A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ILE A 278 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.530A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.861A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 351
      removed outlier: 4.503A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   VAL A 332 " --> pdb=" O   GLU A 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 24
      removed outlier: 4.068A  pdb=" N   ALA B  11 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 11 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.570A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 53 through 56
      removed outlier: 4.196A  pdb=" N   GLY N  56 " --> pdb=" O   SER N  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 53 through 56'
    Processing helix  chain 'R' and resid 42 through 71
      removed outlier: 3.568A  pdb=" N   VAL R  46 " --> pdb=" O   LEU R  42 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   ALA R  48 " --> pdb=" O   ALA R  44 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU R  63 " --> pdb=" O   ALA R  59 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR R  64 " --> pdb=" O   GLY R  60 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ARG R  70 " --> pdb=" O   LEU R  66 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 72 through 75
      removed outlier: 3.570A  pdb=" N   ARG R  75 " --> pdb=" O   ARG R  72 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 72 through 75'
    Processing helix  chain 'R' and resid 78 through 101
      Proline residue:  R  97  - end of helix
      removed outlier: 3.590A  pdb=" N   VAL R 101 " --> pdb=" O   PRO R  97 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 105
      removed outlier: 3.645A  pdb=" N   GLN R 105 " --> pdb=" O   ARG R 102 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 102 through 105'
    Processing helix  chain 'R' and resid 114 through 147
      removed outlier: 3.819A  pdb=" N   LEU R 118 " --> pdb=" O   LEU R 114 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL R 122 " --> pdb=" O   LEU R 118 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLU R 124 " --> pdb=" O   GLN R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 147 through 155
    Processing helix  chain 'R' and resid 157 through 175
      removed outlier: 4.010A  pdb=" N   LYS R 161 " --> pdb=" O   LYS R 157 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU R 162 " --> pdb=" O   GLY R 158 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 181
    Processing helix  chain 'R' and resid 192 through 196
      removed outlier: 3.588A  pdb=" N   THR R 195 " --> pdb=" O   PRO R 192 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ASN R 196 " --> pdb=" O   TRP R 193 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 192 through 196'
    Processing helix  chain 'R' and resid 201 through 207
      removed outlier: 3.698A  pdb=" N   VAL R 205 " --> pdb=" O   THR R 201 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 243
      removed outlier: 3.850A  pdb=" N   TRP R 215 " --> pdb=" O   THR R 211 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   PHE R 220 " --> pdb=" O   VAL R 216 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   PHE R 221 " --> pdb=" O   SER R 217 " (cutoff:3.500A)
      Proline residue:  R 224  - end of helix
      removed outlier: 4.010A  pdb=" N   VAL R 230 " --> pdb=" O   PHE R 226 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 256 through 286
      Proline residue:  R 278  - end of helix
    Processing helix  chain 'R' and resid 296 through 319
      removed outlier: 4.122A  pdb=" N   ILE R 300 " --> pdb=" O   GLU R 296 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   TYR R 303 " --> pdb=" O   GLN R 299 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA R 316 " --> pdb=" O   PHE R 312 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 319 through 324
      removed outlier: 3.625A  pdb=" N   TYR R 323 " --> pdb=" O   ASN R 319 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ASN R 324 " --> pdb=" O   PRO R 320 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 319 through 324'
    Processing helix  chain 'R' and resid 327 through 338
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.071A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.352A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.561A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.561A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.227A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.535A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.653A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   MET B 217 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.727A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 5.973A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.698A  pdb=" N   MET N  34 " --> pdb=" O   TYR N  50 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   TYR N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12
      removed outlier: 4.241A  pdb=" N   PHE N 110 " --> pdb=" O   ARG N  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 140 through 141
      removed outlier: 3.552A  pdb=" N   ALA N 211 " --> pdb=" O   SER N 208 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'N' and resid 146 through 148
      removed outlier: 6.305A  pdb=" N   VAL N 147 " --> pdb=" O   GLU N 246 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY N 225 " --> pdb=" O   LEU N 245 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   LEU N 174 " --> pdb=" O   TYR N 190 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   TYR N 190 " --> pdb=" O   LEU N 174 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   TRP N 176 " --> pdb=" O   LEU N 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 182 through 184
      removed outlier: 3.623A  pdb=" N   ARG R 199 " --> pdb=" O   GLY R 183 " (cutoff:3.500A)

    431 hydrogen bonds defined for protein.
    1206 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: 2.74

  Time building geometry restraints manager: 2.88 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1424
        1.29 -     1.42: 2422
        1.42 -     1.56: 5143
        1.56 -     1.69: 1
        1.69 -     1.82: 90
  Bond restraints: 9080
  Sorted by residual:
  bond pdb=" N   PRO R 278 "
       pdb=" CD  PRO R 278 "
    ideal  model  delta    sigma   weight residual
    1.473  1.194  0.279 1.40e-02 5.10e+03 3.97e+02
  bond pdb=" N   PRO R  39 "
       pdb=" CD  PRO R  39 "
    ideal  model  delta    sigma   weight residual
    1.473  1.343  0.130 1.40e-02 5.10e+03 8.57e+01
  bond pdb=" CA  SER R 308 "
       pdb=" CB  SER R 308 "
    ideal  model  delta    sigma   weight residual
    1.529  1.418  0.111 1.64e-02 3.72e+03 4.55e+01
  bond pdb=" CA  ASN A 294 "
       pdb=" C   ASN A 294 "
    ideal  model  delta    sigma   weight residual
    1.527  1.602 -0.075 1.19e-02 7.06e+03 3.97e+01
  bond pdb=" C   PHE N  32 "
       pdb=" O   PHE N  32 "
    ideal  model  delta    sigma   weight residual
    1.236  1.163  0.073 1.21e-02 6.83e+03 3.64e+01
  ... (remaining 9075 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.30: 12215
        4.30 -     8.60: 74
        8.60 -    12.89: 6
       12.89 -    17.19: 1
       17.19 -    21.49: 3
  Bond angle restraints: 12299
  Sorted by residual:
  angle pdb=" N   THR A 295 "
        pdb=" CA  THR A 295 "
        pdb=" C   THR A 295 "
      ideal   model   delta    sigma   weight residual
     110.14   96.39   13.75 1.55e+00 4.16e-01 7.87e+01
  angle pdb=" C   PHE R 279 "
        pdb=" CA  PHE R 279 "
        pdb=" CB  PHE R 279 "
      ideal   model   delta    sigma   weight residual
     110.96   99.63   11.33 1.54e+00 4.22e-01 5.41e+01
  angle pdb=" C22 1KD R 401 "
        pdb=" C23 1KD R 401 "
        pdb=" C26 1KD R 401 "
      ideal   model   delta    sigma   weight residual
     109.58  131.07  -21.49 3.00e+00 1.11e-01 5.13e+01
  angle pdb=" C   LYS N 244 "
        pdb=" CA  LYS N 244 "
        pdb=" CB  LYS N 244 "
      ideal   model   delta    sigma   weight residual
     109.75   98.13   11.62 1.65e+00 3.67e-01 4.96e+01
  angle pdb=" C24 1KD R 401 "
        pdb=" C23 1KD R 401 "
        pdb=" C26 1KD R 401 "
      ideal   model   delta    sigma   weight residual
     113.62   92.66   20.96 3.00e+00 1.11e-01 4.88e+01
  ... (remaining 12294 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.74: 5132
       23.74 -    47.47: 279
       47.47 -    71.21: 33
       71.21 -    94.94: 10
       94.94 -   118.68: 3
  Dihedral angle restraints: 5457
    sinusoidal: 2204
      harmonic: 3253
  Sorted by residual:
  dihedral pdb=" CB  CYS R 116 "
           pdb=" SG  CYS R 116 "
           pdb=" SG  CYS R 198 "
           pdb=" CB  CYS R 198 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -162.31   76.31     1      1.00e+01 1.00e-02 7.33e+01
  dihedral pdb=" C   ASN R 305 "
           pdb=" N   ASN R 305 "
           pdb=" CA  ASN R 305 "
           pdb=" CB  ASN R 305 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -143.14   20.54     0      2.50e+00 1.60e-01 6.75e+01
  dihedral pdb=" C   LYS N 244 "
           pdb=" N   LYS N 244 "
           pdb=" CA  LYS N 244 "
           pdb=" CB  LYS N 244 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -104.95  -17.65     0      2.50e+00 1.60e-01 4.98e+01
  ... (remaining 5454 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.145: 1365
       0.145 -    0.289: 17
       0.289 -    0.434: 8
       0.434 -    0.579: 0
       0.579 -    0.724: 1
  Chirality restraints: 1391
  Sorted by residual:
  chirality pdb=" CA  ASN R 305 "
            pdb=" N   ASN R 305 "
            pdb=" C   ASN R 305 "
            pdb=" CB  ASN R 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.79    0.72 2.00e-01 2.50e+01 1.31e+01
  chirality pdb=" CA  PHE R 279 "
            pdb=" N   PHE R 279 "
            pdb=" C   PHE R 279 "
            pdb=" CB  PHE R 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.90   -0.39 2.00e-01 2.50e+01 3.85e+00
  chirality pdb=" CA  LEU R  42 "
            pdb=" N   LEU R  42 "
            pdb=" C   LEU R  42 "
            pdb=" CB  LEU R  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.88   -0.37 2.00e-01 2.50e+01 3.35e+00
  ... (remaining 1388 not shown)

  Planarity restraints: 1538
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R 112 "   -0.027 2.00e-02 2.50e+03   5.29e-02 2.80e+01
        pdb=" C   GLY R 112 "    0.091 2.00e-02 2.50e+03
        pdb=" O   GLY R 112 "   -0.035 2.00e-02 2.50e+03
        pdb=" N   ASP R 113 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA N 221 "   -0.018 2.00e-02 2.50e+03   3.60e-02 1.30e+01
        pdb=" C   ALA N 221 "    0.062 2.00e-02 2.50e+03
        pdb=" O   ALA N 221 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   GLU N 222 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 115 "    0.016 2.00e-02 2.50e+03   3.31e-02 1.10e+01
        pdb=" C   LEU R 115 "   -0.057 2.00e-02 2.50e+03
        pdb=" O   LEU R 115 "    0.021 2.00e-02 2.50e+03
        pdb=" N   CYS R 116 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1535 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 186
        2.67 -     3.23: 8373
        3.23 -     3.78: 13811
        3.78 -     4.34: 20368
        4.34 -     4.90: 33297
  Nonbonded interactions: 76035
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.112 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   PHE R 286 "
            pdb=" OG  SER R 287 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OG1 THR B  34 "
            pdb=" O   LEU B 300 "
     model   vdw
     2.266 3.040
  ... (remaining 76030 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:             2.630
  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:          0.440
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.610
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.279   9080  Z= 0.408
  Angle     :  0.926  21.491  12299  Z= 0.560
  Chirality :  0.060   0.724   1391
  Planarity :  0.005   0.056   1538
  Dihedral  : 15.005 118.678   3346
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.14 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.48 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.24), residues: 1102
  helix: -0.42 (0.27), residues: 385
  sheet: -0.53 (0.30), residues: 281
  loop : -0.83 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 280 
 PHE   0.023   0.002   PHE R 279 
 TYR   0.022   0.002   TYR R 284 
 ARG   0.005   0.000   ARG N 202 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 129
  time to evaluate  : 0.993 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 131
  average time/residue: 1.6022
  time to fit residues: 221.5055
Evaluate side-chains
  106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  219 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.1980
   chunk 83 optimal weight:    7.9990
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.114849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.086324 restraints weight = 14098.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.13
r_work: 0.3075 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9080  Z= 0.204
  Angle     :  0.587   6.464  12299  Z= 0.307
  Chirality :  0.043   0.139   1391
  Planarity :  0.004   0.048   1538
  Dihedral  :  7.174  75.011   1331
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.33 %
    Favored  : 89.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.25), residues: 1102
  helix:  0.64 (0.27), residues: 370
  sheet: -0.42 (0.30), residues: 268
  loop : -0.56 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 280 
 PHE   0.026   0.001   PHE R  54 
 TYR   0.020   0.001   TYR R 284 
 ARG   0.005   0.000   ARG B 197 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 1.073 
Fit side-chains
REVERT: B  214 ARG cc_start: 0.8266 (mmt180) cc_final: 0.7936 (mmt90)
REVERT: N  160 ARG cc_start: 0.8381 (ttp-110) cc_final: 0.8039 (tmm160)
REVERT: N  218 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7644 (mtm180)
  outliers start: 10
  outliers final: 4
  residues processed: 119
  average time/residue: 1.3776
  time to fit residues: 173.9638
Evaluate side-chains
  108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain N residue  218 ARG
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  219 ILE
Chi-restraints excluded: chain R residue  286 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 105 optimal weight:    0.0370
   chunk 0 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 94 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.8460

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 294 ASN
G  17 GLN
R 324 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.113944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.086409 restraints weight = 14021.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.93
r_work: 0.3066 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9080  Z= 0.202
  Angle     :  0.545   6.670  12299  Z= 0.286
  Chirality :  0.042   0.137   1391
  Planarity :  0.004   0.044   1538
  Dihedral  :  6.503  72.102   1331
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.02 %
    Favored  : 86.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.25), residues: 1102
  helix:  0.96 (0.27), residues: 370
  sheet: -0.36 (0.31), residues: 263
  loop : -0.60 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 280 
 PHE   0.011   0.001   PHE R 309 
 TYR   0.013   0.001   TYR R 313 
 ARG   0.002   0.000   ARG B 314 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 1.881 
Fit side-chains
REVERT: A  313 ARG cc_start: 0.8484 (ptp-170) cc_final: 0.8198 (ptp-110)
REVERT: A  318 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7409 (tt0)
REVERT: B  214 ARG cc_start: 0.8307 (mmt180) cc_final: 0.8003 (mmt90)
REVERT: N  160 ARG cc_start: 0.8329 (ttp-110) cc_final: 0.8041 (tmm160)
REVERT: R  303 TYR cc_start: 0.6306 (m-80) cc_final: 0.6105 (m-80)
  outliers start: 17
  outliers final: 6
  residues processed: 116
  average time/residue: 1.6040
  time to fit residues: 198.6382
Evaluate side-chains
  106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  219 ILE
Chi-restraints excluded: chain R residue  286 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 81 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0270
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 294 ASN
N 183 GLN
R 324 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.114908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.087274 restraints weight = 13857.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.98
r_work: 0.3080 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9080  Z= 0.175
  Angle     :  0.533   7.991  12299  Z= 0.279
  Chirality :  0.041   0.149   1391
  Planarity :  0.003   0.039   1538
  Dihedral  :  6.248  69.623   1331
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 14.51 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.25), residues: 1102
  helix:  1.22 (0.27), residues: 370
  sheet: -0.31 (0.31), residues: 263
  loop : -0.55 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 280 
 PHE   0.022   0.001   PHE R  54 
 TYR   0.023   0.001   TYR R 284 
 ARG   0.001   0.000   ARG B 197 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.953 
Fit side-chains
REVERT: A  271 LYS cc_start: 0.7088 (tmtt) cc_final: 0.6678 (ttpt)
REVERT: A  313 ARG cc_start: 0.8457 (ptp-170) cc_final: 0.8141 (ptp-110)
REVERT: A  318 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7319 (tt0)
REVERT: A  341 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8417 (t0)
REVERT: B  214 ARG cc_start: 0.8312 (mmt180) cc_final: 0.8044 (mmt90)
REVERT: N   93 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8751 (ttp)
REVERT: N  160 ARG cc_start: 0.8328 (ttp-110) cc_final: 0.8039 (tmm160)
REVERT: N  201 GLU cc_start: 0.8033 (tp30) cc_final: 0.7829 (tp30)
REVERT: R   87 PHE cc_start: 0.8095 (t80) cc_final: 0.7761 (t80)
  outliers start: 13
  outliers final: 6
  residues processed: 115
  average time/residue: 1.4343
  time to fit residues: 175.3003
Evaluate side-chains
  109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain N residue   93 MET
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  219 ILE
Chi-restraints excluded: chain R residue  286 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 68 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 103 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 183 GLN
R 324 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.113592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.085670 restraints weight = 13753.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 1.97
r_work: 0.3051 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9080  Z= 0.236
  Angle     :  0.556   7.295  12299  Z= 0.290
  Chirality :  0.043   0.136   1391
  Planarity :  0.004   0.037   1538
  Dihedral  :  6.405  71.550   1331
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.92 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.25), residues: 1102
  helix:  1.25 (0.27), residues: 371
  sheet: -0.29 (0.31), residues: 263
  loop : -0.52 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 280 
 PHE   0.013   0.001   PHE R 309 
 TYR   0.026   0.001   TYR A 296 
 ARG   0.001   0.000   ARG R 283 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 1.013 
Fit side-chains
REVERT: A  271 LYS cc_start: 0.7136 (tmtt) cc_final: 0.6724 (ttpt)
REVERT: A  318 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7313 (tt0)
REVERT: A  341 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8415 (t0)
REVERT: B  214 ARG cc_start: 0.8322 (mmt180) cc_final: 0.8054 (mmt90)
REVERT: N  160 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7963 (tmm160)
REVERT: N  201 GLU cc_start: 0.7991 (tp30) cc_final: 0.7790 (tp30)
  outliers start: 19
  outliers final: 11
  residues processed: 113
  average time/residue: 1.7960
  time to fit residues: 214.7489
Evaluate side-chains
  110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain N residue   76 LYS
Chi-restraints excluded: chain N residue   93 MET
Chi-restraints excluded: chain N residue  224 VAL
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue   65 MET
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  211 THR
Chi-restraints excluded: chain R residue  219 ILE
Chi-restraints excluded: chain R residue  286 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 62 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 81 optimal weight:   10.0000
   chunk 89 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 10 optimal weight:    0.2980
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 183 GLN
R 324 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.114675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.087178 restraints weight = 13847.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.92
r_work: 0.3079 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9080  Z= 0.185
  Angle     :  0.543   9.068  12299  Z= 0.281
  Chirality :  0.041   0.137   1391
  Planarity :  0.003   0.035   1538
  Dihedral  :  6.125  68.953   1331
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.96 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.25), residues: 1102
  helix:  1.42 (0.27), residues: 370
  sheet: -0.31 (0.31), residues: 265
  loop : -0.48 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 280 
 PHE   0.021   0.001   PHE R  54 
 TYR   0.024   0.001   TYR A 296 
 ARG   0.002   0.000   ARG R 283 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 1.299 
Fit side-chains
REVERT: A  271 LYS cc_start: 0.6996 (tmtt) cc_final: 0.6666 (ttpt)
REVERT: A  341 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8387 (t0)
REVERT: N   93 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8716 (ttp)
REVERT: N  144 THR cc_start: 0.7555 (m) cc_final: 0.7269 (t)
REVERT: N  160 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.7734 (mtm110)
REVERT: R   87 PHE cc_start: 0.8070 (t80) cc_final: 0.7770 (t80)
  outliers start: 15
  outliers final: 10
  residues processed: 113
  average time/residue: 1.4708
  time to fit residues: 176.4328
Evaluate side-chains
  111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   93 MET
Chi-restraints excluded: chain N residue  224 VAL
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue   65 MET
Chi-restraints excluded: chain R residue  219 ILE
Chi-restraints excluded: chain R residue  286 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 87 optimal weight:    0.4980
   chunk 19 optimal weight:    0.5980
   chunk 104 optimal weight:    0.5980
   chunk 105 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0040
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
N 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.116016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.087869 restraints weight = 13844.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 2.07
r_work: 0.3083 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9080  Z= 0.158
  Angle     :  0.522   8.121  12299  Z= 0.271
  Chirality :  0.041   0.137   1391
  Planarity :  0.003   0.033   1538
  Dihedral  :  5.855  67.166   1331
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.96 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.25), residues: 1102
  helix:  1.59 (0.28), residues: 370
  sheet: -0.27 (0.31), residues: 265
  loop : -0.44 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 280 
 PHE   0.013   0.001   PHE R 309 
 TYR   0.025   0.001   TYR R 284 
 ARG   0.007   0.000   ARG B 197 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.948 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7737 (ttm-80)
REVERT: A  271 LYS cc_start: 0.6888 (tmtt) cc_final: 0.6590 (ttpt)
REVERT: A  341 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8375 (t0)
REVERT: B  214 ARG cc_start: 0.8435 (mmt180) cc_final: 0.8115 (mmt90)
REVERT: B  217 MET cc_start: 0.7471 (ppp) cc_final: 0.7188 (ppp)
REVERT: G   46 LYS cc_start: 0.8580 (mmpt) cc_final: 0.7763 (mppt)
REVERT: N   93 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8720 (ttp)
REVERT: N  144 THR cc_start: 0.7526 (OUTLIER) cc_final: 0.7232 (t)
REVERT: N  160 ARG cc_start: 0.8285 (ttp-110) cc_final: 0.7742 (mtm110)
REVERT: R   87 PHE cc_start: 0.8006 (t80) cc_final: 0.7757 (t80)
  outliers start: 23
  outliers final: 8
  residues processed: 119
  average time/residue: 1.3632
  time to fit residues: 172.3720
Evaluate side-chains
  108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   93 MET
Chi-restraints excluded: chain N residue  144 THR
Chi-restraints excluded: chain N residue  224 VAL
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue  219 ILE
Chi-restraints excluded: chain R residue  286 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
N 183 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.114941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.086963 restraints weight = 14051.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.00
r_work: 0.3073 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9080  Z= 0.197
  Angle     :  0.547   7.812  12299  Z= 0.283
  Chirality :  0.042   0.136   1391
  Planarity :  0.003   0.036   1538
  Dihedral  :  5.968  68.583   1331
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 17.41 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.25), residues: 1102
  helix:  1.59 (0.27), residues: 370
  sheet: -0.26 (0.31), residues: 265
  loop : -0.44 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 280 
 PHE   0.013   0.001   PHE R 309 
 TYR   0.024   0.001   TYR A 296 
 ARG   0.003   0.000   ARG G  13 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.976 
Fit side-chains
REVERT: A  271 LYS cc_start: 0.6899 (tmtt) cc_final: 0.6624 (ttpt)
REVERT: A  273 LEU cc_start: 0.7510 (tp) cc_final: 0.7288 (tp)
REVERT: A  341 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8376 (t0)
REVERT: B  214 ARG cc_start: 0.8431 (mmt180) cc_final: 0.8162 (mpt180)
REVERT: B  325 MET cc_start: 0.9102 (tpp) cc_final: 0.8780 (tpp)
REVERT: G   24 ASN cc_start: 0.7674 (p0) cc_final: 0.7440 (p0)
REVERT: N   93 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8743 (ttp)
REVERT: N  144 THR cc_start: 0.7526 (OUTLIER) cc_final: 0.7210 (t)
REVERT: N  160 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.7711 (mtm110)
REVERT: R   87 PHE cc_start: 0.8032 (t80) cc_final: 0.7768 (t80)
  outliers start: 15
  outliers final: 10
  residues processed: 110
  average time/residue: 1.3784
  time to fit residues: 160.8817
Evaluate side-chains
  111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   93 MET
Chi-restraints excluded: chain N residue  144 THR
Chi-restraints excluded: chain N residue  224 VAL
Chi-restraints excluded: chain R residue   65 MET
Chi-restraints excluded: chain R residue  219 ILE
Chi-restraints excluded: chain R residue  286 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 99 optimal weight:    4.9990
   chunk 89 optimal weight:    0.4980
   chunk 77 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 82 optimal weight:   30.0000
   chunk 48 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 183 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.115108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.087118 restraints weight = 13835.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.98
r_work: 0.3077 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9080  Z= 0.192
  Angle     :  0.545   7.820  12299  Z= 0.281
  Chirality :  0.042   0.136   1391
  Planarity :  0.003   0.036   1538
  Dihedral  :  5.928  67.821   1331
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 17.41 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.25), residues: 1102
  helix:  1.58 (0.27), residues: 370
  sheet: -0.25 (0.32), residues: 265
  loop : -0.44 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 280 
 PHE   0.013   0.001   PHE R 309 
 TYR   0.025   0.001   TYR A 296 
 ARG   0.003   0.000   ARG G  13 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.968 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7916 (mtm-85) cc_final: 0.7710 (ttm-80)
REVERT: A  271 LYS cc_start: 0.6778 (tmtt) cc_final: 0.6412 (ttpt)
REVERT: A  273 LEU cc_start: 0.7512 (tp) cc_final: 0.7300 (tp)
REVERT: A  341 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8372 (t0)
REVERT: B  214 ARG cc_start: 0.8372 (mmt180) cc_final: 0.8054 (mpt180)
REVERT: G   24 ASN cc_start: 0.7689 (p0) cc_final: 0.7463 (p0)
REVERT: G   46 LYS cc_start: 0.8544 (mmpt) cc_final: 0.7778 (mppt)
REVERT: N   93 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8715 (ttp)
REVERT: N  144 THR cc_start: 0.7536 (OUTLIER) cc_final: 0.7208 (t)
REVERT: N  160 ARG cc_start: 0.8253 (ttp-110) cc_final: 0.7785 (mtm110)
REVERT: R   87 PHE cc_start: 0.8047 (t80) cc_final: 0.7773 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 110
  average time/residue: 1.3821
  time to fit residues: 161.1958
Evaluate side-chains
  115 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   93 MET
Chi-restraints excluded: chain N residue  144 THR
Chi-restraints excluded: chain N residue  224 VAL
Chi-restraints excluded: chain R residue   65 MET
Chi-restraints excluded: chain R residue  211 THR
Chi-restraints excluded: chain R residue  219 ILE
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  286 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 98 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** G  58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 183 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.114614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.086552 restraints weight = 13845.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.98
r_work: 0.3066 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9080  Z= 0.213
  Angle     :  0.568   7.650  12299  Z= 0.292
  Chirality :  0.042   0.136   1391
  Planarity :  0.003   0.036   1538
  Dihedral  :  6.006  67.871   1331
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 17.82 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.25), residues: 1102
  helix:  1.52 (0.27), residues: 370
  sheet: -0.26 (0.32), residues: 265
  loop : -0.44 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.004   0.001   HIS N  35 
 PHE   0.016   0.001   PHE R  54 
 TYR   0.028   0.001   TYR A 296 
 ARG   0.004   0.000   ARG G  13 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 1.165 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7716 (ttm-80)
REVERT: A  271 LYS cc_start: 0.6711 (tmtt) cc_final: 0.6458 (ttpt)
REVERT: A  273 LEU cc_start: 0.7533 (tp) cc_final: 0.7300 (tp)
REVERT: A  341 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8367 (t0)
REVERT: G   24 ASN cc_start: 0.7668 (p0) cc_final: 0.7447 (p0)
REVERT: N   93 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8772 (ttp)
REVERT: N  144 THR cc_start: 0.7541 (OUTLIER) cc_final: 0.7232 (t)
REVERT: N  160 ARG cc_start: 0.8254 (ttp-110) cc_final: 0.7777 (mtm110)
REVERT: R   87 PHE cc_start: 0.8061 (t80) cc_final: 0.7746 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 110
  average time/residue: 1.5748
  time to fit residues: 183.7224
Evaluate side-chains
  116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   93 MET
Chi-restraints excluded: chain N residue  144 THR
Chi-restraints excluded: chain N residue  224 VAL
Chi-restraints excluded: chain R residue   65 MET
Chi-restraints excluded: chain R residue  211 THR
Chi-restraints excluded: chain R residue  219 ILE
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  286 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 109 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0570
   chunk 91 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 88 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
G  17 GLN
** G  58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 183 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.116143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.087910 restraints weight = 13833.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 2.07
r_work: 0.3082 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9080  Z= 0.168
  Angle     :  0.544   8.357  12299  Z= 0.279
  Chirality :  0.041   0.137   1391
  Planarity :  0.003   0.036   1538
  Dihedral  :  5.764  65.950   1331
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 18.03 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.25), residues: 1102
  helix:  1.71 (0.28), residues: 363
  sheet: -0.25 (0.32), residues: 264
  loop : -0.40 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 280 
 PHE   0.013   0.001   PHE R 309 
 TYR   0.024   0.001   TYR A 296 
 ARG   0.005   0.000   ARG B 197 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7267.58 seconds
wall clock time: 127 minutes 28.39 seconds (7648.39 seconds total)