Starting phenix.real_space_refine
on Fri Nov 15 11:12:10 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lll_23425/11_2024/7lll_23425.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lll_23425/11_2024/7lll_23425.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lll_23425/11_2024/7lll_23425.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lll_23425/11_2024/7lll_23425.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lll_23425/11_2024/7lll_23425.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lll_23425/11_2024/7lll_23425.cif"
  }
  resolution = 3.7
  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=  -0.000 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: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5670      2.51       5
     N    1555      2.21       5
     O    1659      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 8940
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1928
          Classifications: {'peptide': 233}
          Link IDs: {'PTRANS': 6, 'TRANS': 226}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2615
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "P"
      Number of atoms: 231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 231
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
    Chain: "R"
      Number of atoms: 2749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2749
          Classifications: {'peptide': 366}
          Incomplete info: {'truncation_to_alanine': 73}
          Link IDs: {'PTRANS': 13, 'TRANS': 352}
          Chain breaks: 4
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 313
          Unresolved non-hydrogen angles: 414
          Unresolved non-hydrogen dihedrals: 281
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 6, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 210
  Time building chain proxies: 5.43, per 1000 atoms: 0.61
  Number of scatterers: 8940
  At special positions: 0
  Unit cell: (87.87, 103.53, 174, 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      56     16.00
     O    1659      8.00
     N    1555      7.00
     C    5670      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, 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=2.03
    Simple disulfide: pdb=" SG  CYS R  46 " - pdb=" SG  CYS R  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  62 " - pdb=" SG  CYS R 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " distance=2.05

  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: 2.24
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2172

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 13 sheets defined
      38.1% alpha, 13.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 23
      removed outlier: 3.772A  pdb=" N   ARG A  20 " --> pdb=" O   GLU A  16 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ALA A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 33
      removed outlier: 3.601A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN A  31 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 278
      removed outlier: 3.785A  pdb=" N   LYS A 271 " --> pdb=" O   GLN A 267 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   LEU A 272 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   SER A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.659A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.785A  pdb=" N   PHE A 315 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 312 through 316'
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.655A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASP A 343 " --> pdb=" O   TYR A 339 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 375
      removed outlier: 3.705A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 380
    Processing helix  chain 'A' and resid 380 through 391
      removed outlier: 3.833A  pdb=" N   MET A 386 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ARG A 389 " --> pdb=" O   ARG A 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 23
      removed outlier: 4.258A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASP B  20 " --> pdb=" O   ASN B  16 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA B  21 " --> pdb=" O   GLN B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.699A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 21
      removed outlier: 3.854A  pdb=" N   GLN G  11 " --> pdb=" O   ALA G   7 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 33
    Processing helix  chain 'G' and resid 34 through 44
      removed outlier: 4.228A  pdb=" N   GLU G  42 " --> pdb=" O   MET G  38 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.815A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 4.182A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 28
      removed outlier: 4.144A  pdb=" N   SER P   8 " --> pdb=" O   GLY P   4 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   MET P  14 " --> pdb=" O   LEU P  10 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ALA P  18 " --> pdb=" O   MET P  14 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL P  19 " --> pdb=" O   GLU P  15 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ARG P  20 " --> pdb=" O   GLU P  16 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   TRP P  25 " --> pdb=" O   LEU P  21 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LEU P  26 " --> pdb=" O   PHE P  22 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LYS P  27 " --> pdb=" O   ILE P  23 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ASN P  28 " --> pdb=" O   GLU P  24 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 31 through 53
      removed outlier: 3.720A  pdb=" N   VAL R  36 " --> pdb=" O   LEU R  32 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLN R  37 " --> pdb=" O   TRP R  33 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   CYS R  46 " --> pdb=" O   TYR R  42 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ARG R  48 " --> pdb=" O   ARG R  44 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   SER R  49 " --> pdb=" O   GLN R  45 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 89 through 93
    Processing helix  chain 'R' and resid 139 through 149
      removed outlier: 4.164A  pdb=" N   TYR R 145 " --> pdb=" O   LEU R 141 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ILE R 146 " --> pdb=" O   LEU R 142 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ILE R 147 " --> pdb=" O   PHE R 143 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 150 through 169
      removed outlier: 3.801A  pdb=" N   LEU R 154 " --> pdb=" O   VAL R 150 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE R 156 " --> pdb=" O   TYR R 152 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   SER R 157 " --> pdb=" O   ALA R 153 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   LEU R 159 " --> pdb=" O   SER R 155 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL R 160 " --> pdb=" O   PHE R 156 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   SER R 163 " --> pdb=" O   LEU R 159 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU R 166 " --> pdb=" O   ALA R 162 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   LEU R 167 " --> pdb=" O   SER R 163 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   PHE R 169 " --> pdb=" O   ILE R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 204
      removed outlier: 3.822A  pdb=" N   HIS R 180 " --> pdb=" O   ARG R 176 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ASN R 182 " --> pdb=" O   TYR R 178 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU R 189 " --> pdb=" O   ALA R 185 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU R 192 " --> pdb=" O   ILE R 188 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE R 196 " --> pdb=" O   LEU R 192 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   LYS R 197 " --> pdb=" O   SER R 193 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASP R 198 " --> pdb=" O   VAL R 194 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA R 199 " --> pdb=" O   PHE R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 223 through 228
      removed outlier: 4.235A  pdb=" N   ARG R 227 " --> pdb=" O   SER R 223 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 228 through 237
      removed outlier: 3.983A  pdb=" N   GLN R 234 " --> pdb=" O   PHE R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 244 through 251
    Processing helix  chain 'R' and resid 264 through 268
    Processing helix  chain 'R' and resid 269 through 274
      removed outlier: 3.500A  pdb=" N   TRP R 274 " --> pdb=" O   VAL R 270 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 276 through 280
    Processing helix  chain 'R' and resid 281 through 291
      removed outlier: 3.603A  pdb=" N   VAL R 287 " --> pdb=" O   PRO R 283 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR R 289 " --> pdb=" O   GLY R 285 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR R 291 " --> pdb=" O   VAL R 287 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 294 through 298
      removed outlier: 3.817A  pdb=" N   THR R 298 " --> pdb=" O   GLY R 295 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 308
    Processing helix  chain 'R' and resid 310 through 329
      removed outlier: 3.509A  pdb=" N   PHE R 315 " --> pdb=" O   LEU R 311 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU R 322 " --> pdb=" O   GLY R 318 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ILE R 323 " --> pdb=" O   VAL R 319 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   PHE R 324 " --> pdb=" O   ASN R 320 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 330 through 338
      removed outlier: 3.765A  pdb=" N   LEU R 335 " --> pdb=" O   VAL R 331 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA R 337 " --> pdb=" O   SER R 333 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 345 through 361
      removed outlier: 3.866A  pdb=" N   THR R 355 " --> pdb=" O   LYS R 351 " (cutoff:3.500A)
      Proline residue:  R 358  - end of helix
    Processing helix  chain 'R' and resid 362 through 367
    Processing helix  chain 'R' and resid 378 through 391
      removed outlier: 3.839A  pdb=" N   THR R 386 " --> pdb=" O   ILE R 382 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   SER R 389 " --> pdb=" O   PHE R 385 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 393 through 404
      removed outlier: 3.538A  pdb=" N   PHE R 404 " --> pdb=" O   ILE R 400 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 406 through 419
      removed outlier: 3.693A  pdb=" N   ARG R 414 " --> pdb=" O   GLN R 410 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ARG R 419 " --> pdb=" O   LYS R 415 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 3.815A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   HIS A  41 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A  44 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE A 245 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.526A  pdb=" N   TYR B  59 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.640A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA B 113 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.663A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.029A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.638A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.841A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 295 through 297
      removed outlier: 6.655A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 320
      removed outlier: 4.077A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA B 328 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR B 329 " --> pdb=" O   LYS B 337 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
    Processing sheet with id=AB2, first strand: chain 'N' and resid 45 through 51
      removed outlier: 6.708A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL N  93 " --> pdb=" O   GLN N  39 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   THR N 122 " --> pdb=" O   TYR N  94 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 70 through 73
      removed outlier: 3.770A  pdb=" N   SER N  71 " --> pdb=" O   TYR N  80 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 80 through 81
      removed outlier: 4.039A  pdb=" N   VAL R  81 " --> pdb=" O   ARG R 102 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   ARG R 102 " --> pdb=" O   VAL R  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4

    269 hydrogen bonds defined for protein.
    753 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: 2.25

  Time building geometry restraints manager: 2.57 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2357
        1.33 -     1.45: 1817
        1.45 -     1.58: 4870
        1.58 -     1.70: 0
        1.70 -     1.82: 76
  Bond restraints: 9120
  Sorted by residual:
  bond pdb=" N   VAL R 370 "
       pdb=" CA  VAL R 370 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.033 8.60e-03 1.35e+04 1.47e+01
  bond pdb=" C   TRP R  72 "
       pdb=" N   PRO R  73 "
    ideal  model  delta    sigma   weight residual
    1.332  1.377 -0.045 1.26e-02 6.30e+03 1.30e+01
  bond pdb=" C   LEU R 311 "
       pdb=" N   PRO R 312 "
    ideal  model  delta    sigma   weight residual
    1.335  1.382 -0.046 1.36e-02 5.41e+03 1.17e+01
  bond pdb=" N   LEU R 359 "
       pdb=" CA  LEU R 359 "
    ideal  model  delta    sigma   weight residual
    1.458  1.500 -0.043 1.27e-02 6.20e+03 1.14e+01
  bond pdb=" N   GLU R 294 "
       pdb=" CA  GLU R 294 "
    ideal  model  delta    sigma   weight residual
    1.455  1.494 -0.038 1.23e-02 6.61e+03 9.75e+00
  ... (remaining 9115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 11989
        2.37 -     4.73: 339
        4.73 -     7.10: 26
        7.10 -     9.46: 4
        9.46 -    11.83: 1
  Bond angle restraints: 12359
  Sorted by residual:
  angle pdb=" N   VAL R 370 "
        pdb=" CA  VAL R 370 "
        pdb=" C   VAL R 370 "
      ideal   model   delta    sigma   weight residual
     113.71  107.88    5.83 9.50e-01 1.11e+00 3.77e+01
  angle pdb=" N   PRO R 358 "
        pdb=" CA  PRO R 358 "
        pdb=" C   PRO R 358 "
      ideal   model   delta    sigma   weight residual
     113.65  121.59   -7.94 1.35e+00 5.49e-01 3.46e+01
  angle pdb=" C   VAL R 281 "
        pdb=" N   VAL R 282 "
        pdb=" CA  VAL R 282 "
      ideal   model   delta    sigma   weight residual
     120.33  125.01   -4.68 8.00e-01 1.56e+00 3.42e+01
  angle pdb=" C   TRP R  72 "
        pdb=" N   PRO R  73 "
        pdb=" CA  PRO R  73 "
      ideal   model   delta    sigma   weight residual
     119.92  125.12   -5.20 1.07e+00 8.73e-01 2.36e+01
  angle pdb=" N   LEU R 268 "
        pdb=" CA  LEU R 268 "
        pdb=" C   LEU R 268 "
      ideal   model   delta    sigma   weight residual
     112.41  106.10    6.31 1.30e+00 5.92e-01 2.36e+01
  ... (remaining 12354 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 4911
       17.84 -    35.68: 425
       35.68 -    53.52: 65
       53.52 -    71.36: 5
       71.36 -    89.20: 8
  Dihedral angle restraints: 5414
    sinusoidal: 2061
      harmonic: 3353
  Sorted by residual:
  dihedral pdb=" CB  CYS R 226 "
           pdb=" SG  CYS R 226 "
           pdb=" SG  CYS R 296 "
           pdb=" CB  CYS R 296 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  144.85  -51.85     1      1.00e+01 1.00e-02 3.67e+01
  dihedral pdb=" CA  PHE R 230 "
           pdb=" C   PHE R 230 "
           pdb=" N   LEU R 231 "
           pdb=" CA  LEU R 231 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.90   28.10     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" CA  TYR R 291 "
           pdb=" C   TYR R 291 "
           pdb=" N   GLU R 292 "
           pdb=" CA  GLU R 292 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.48  -25.52     0      5.00e+00 4.00e-02 2.61e+01
  ... (remaining 5411 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1150
       0.068 -    0.136: 206
       0.136 -    0.203: 27
       0.203 -    0.271: 4
       0.271 -    0.339: 2
  Chirality restraints: 1389
  Sorted by residual:
  chirality pdb=" CA  PRO R 358 "
            pdb=" N   PRO R 358 "
            pdb=" C   PRO R 358 "
            pdb=" CB  PRO R 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.38    0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" CA  MET R 303 "
            pdb=" N   MET R 303 "
            pdb=" C   MET R 303 "
            pdb=" CB  MET R 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CA  PHE R 280 "
            pdb=" N   PHE R 280 "
            pdb=" C   PHE R 280 "
            pdb=" CB  PHE R 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.82e+00
  ... (remaining 1386 not shown)

  Planarity restraints: 1580
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS R 383 "   -0.020 2.00e-02 2.50e+03   3.98e-02 1.58e+01
        pdb=" C   LYS R 383 "    0.069 2.00e-02 2.50e+03
        pdb=" O   LYS R 383 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   LEU R 384 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL G  54 "   -0.064 5.00e-02 4.00e+02   9.69e-02 1.50e+01
        pdb=" N   PRO G  55 "    0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO G  55 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO G  55 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU R 294 "   -0.012 2.00e-02 2.50e+03   2.54e-02 6.45e+00
        pdb=" C   GLU R 294 "    0.044 2.00e-02 2.50e+03
        pdb=" O   GLU R 294 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   GLY R 295 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1577 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 227
        2.68 -     3.23: 8467
        3.23 -     3.79: 11765
        3.79 -     4.34: 16467
        4.34 -     4.90: 27069
  Nonbonded interactions: 63995
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" O   ALA B  56 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OG1 THR A 369 "
            pdb=" OD1 ASN A 371 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OH  TYR B 145 "
            pdb=" OD2 ASP B 186 "
     model   vdw
     2.199 3.040
  ... (remaining 63990 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 group one per residue
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:             0.890
  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:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     22.320
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
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      :  0.006   0.046   9120  Z= 0.382
  Angle     :  0.901  11.826  12359  Z= 0.591
  Chirality :  0.055   0.339   1389
  Planarity :  0.005   0.097   1580
  Dihedral  : 13.684  89.195   3224
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.05 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.22 (0.22), residues: 1129
  helix: -2.86 (0.23), residues: 382
  sheet: -3.15 (0.34), residues: 188
  loop : -2.55 (0.24), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.006   0.001   HIS G  44 
 PHE   0.026   0.002   PHE N 108 
 TYR   0.011   0.001   TYR A 360 
 ARG   0.007   0.000   ARG A 228 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 160
  time to evaluate  : 1.039 
Fit side-chains
REVERT: A   14 ASN cc_start: 0.7611 (m110) cc_final: 0.7407 (m110)
REVERT: R  204 MET cc_start: 0.5246 (ttt) cc_final: 0.4968 (tmm)
REVERT: R  224 LEU cc_start: 0.8116 (tp) cc_final: 0.7749 (mm)
REVERT: R  267 ARG cc_start: 0.8189 (mmt180) cc_final: 0.7670 (ptm160)
REVERT: R  351 LYS cc_start: 0.7412 (tptt) cc_final: 0.6745 (tttm)
REVERT: R  371 MET cc_start: 0.6187 (ppp) cc_final: 0.5239 (ppp)
REVERT: R  414 ARG cc_start: 0.7097 (tpp-160) cc_final: 0.6026 (ttm110)
  outliers start: 1
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2565
  time to fit residues: 55.0423
Evaluate side-chains
  127 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 84 optimal weight:   50.0000
   chunk 47 optimal weight:    0.4980
   chunk 28 optimal weight:    0.3980
   chunk 57 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 87 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 101 optimal weight:    5.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9120  Z= 0.170
  Angle     :  0.616  10.478  12359  Z= 0.327
  Chirality :  0.042   0.160   1389
  Planarity :  0.005   0.074   1580
  Dihedral  :  5.241  25.087   1247
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  8.32 %
    Favored  : 90.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.64 (0.22), residues: 1129
  helix: -2.16 (0.23), residues: 406
  sheet: -2.67 (0.34), residues: 196
  loop : -2.42 (0.24), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.011   0.001   HIS R 171 
 PHE   0.018   0.001   PHE R 280 
 TYR   0.014   0.001   TYR A 360 
 ARG   0.003   0.000   ARG B 197 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 1.015 
Fit side-chains
REVERT: A   31 GLN cc_start: 0.7806 (mm110) cc_final: 0.7508 (tp40)
REVERT: B   59 TYR cc_start: 0.8755 (m-80) cc_final: 0.8452 (m-80)
REVERT: G   32 LYS cc_start: 0.8612 (mmtm) cc_final: 0.7943 (ttmm)
REVERT: R  345 ILE cc_start: 0.6847 (mm) cc_final: 0.6594 (mt)
REVERT: R  351 LYS cc_start: 0.7243 (tptt) cc_final: 0.6723 (tttt)
REVERT: R  371 MET cc_start: 0.6139 (ppp) cc_final: 0.5221 (ppp)
REVERT: R  414 ARG cc_start: 0.6791 (tpp-160) cc_final: 0.6011 (ttm110)
  outliers start: 8
  outliers final: 4
  residues processed: 145
  average time/residue: 0.2617
  time to fit residues: 50.1658
Evaluate side-chains
  124 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 120
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain R residue  300 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  366 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 84 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 101 optimal weight:    8.9990
   chunk 110 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 81 optimal weight:   50.0000
   chunk 100 optimal weight:    5.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9120  Z= 0.150
  Angle     :  0.566  10.041  12359  Z= 0.296
  Chirality :  0.040   0.170   1389
  Planarity :  0.004   0.059   1580
  Dihedral  :  4.738  23.683   1247
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 11.23 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.03 (0.23), residues: 1129
  helix: -1.57 (0.25), residues: 407
  sheet: -2.22 (0.35), residues: 197
  loop : -2.19 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 297 
 HIS   0.003   0.001   HIS R 171 
 PHE   0.013   0.001   PHE N 108 
 TYR   0.017   0.001   TYR R 291 
 ARG   0.002   0.000   ARG A 228 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.996 
Fit side-chains
REVERT: G   32 LYS cc_start: 0.8575 (mmtm) cc_final: 0.7919 (ttmm)
REVERT: R  230 PHE cc_start: 0.7178 (m-10) cc_final: 0.6144 (t80)
REVERT: R  345 ILE cc_start: 0.6695 (mm) cc_final: 0.6432 (mt)
REVERT: R  351 LYS cc_start: 0.7341 (tptt) cc_final: 0.6451 (tttt)
REVERT: R  371 MET cc_start: 0.6260 (ppp) cc_final: 0.5261 (ppp)
REVERT: R  414 ARG cc_start: 0.6833 (tpp-160) cc_final: 0.6067 (ttm110)
  outliers start: 10
  outliers final: 8
  residues processed: 135
  average time/residue: 0.2418
  time to fit residues: 43.8690
Evaluate side-chains
  122 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  147 ILE
Chi-restraints excluded: chain R residue  300 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  357 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 102 optimal weight:    0.8980
   chunk 108 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 29 optimal weight:    0.1980
   chunk 90 optimal weight:    0.9980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
N  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9120  Z= 0.160
  Angle     :  0.549  10.620  12359  Z= 0.286
  Chirality :  0.041   0.168   1389
  Planarity :  0.004   0.055   1580
  Dihedral  :  4.578  23.223   1247
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 11.88 %
    Favored  : 85.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.79 (0.24), residues: 1129
  helix: -1.29 (0.25), residues: 412
  sheet: -2.04 (0.36), residues: 199
  loop : -2.15 (0.25), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 297 
 HIS   0.002   0.001   HIS B  62 
 PHE   0.024   0.001   PHE R 280 
 TYR   0.017   0.001   TYR R 291 
 ARG   0.003   0.000   ARG B  19 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.989 
Fit side-chains
REVERT: G   32 LYS cc_start: 0.8578 (mmtm) cc_final: 0.7917 (ttmm)
REVERT: R  230 PHE cc_start: 0.7133 (m-10) cc_final: 0.6237 (t80)
REVERT: R  345 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6215 (tp)
REVERT: R  371 MET cc_start: 0.6433 (ppp) cc_final: 0.5355 (ppp)
REVERT: R  414 ARG cc_start: 0.6640 (tpp-160) cc_final: 0.5920 (ttm110)
  outliers start: 21
  outliers final: 12
  residues processed: 131
  average time/residue: 0.2277
  time to fit residues: 40.8771
Evaluate side-chains
  120 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue   76 LYS
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  147 ILE
Chi-restraints excluded: chain R residue  300 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  345 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   chunk 44 optimal weight:    0.3980
   chunk 92 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   chunk 0 optimal weight:    9.9990
   chunk 55 optimal weight:    0.8980
   chunk 97 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9120  Z= 0.146
  Angle     :  0.531  10.379  12359  Z= 0.278
  Chirality :  0.040   0.163   1389
  Planarity :  0.004   0.052   1580
  Dihedral  :  4.414  22.406   1247
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.71 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.53 (0.24), residues: 1129
  helix: -1.02 (0.26), residues: 412
  sheet: -1.92 (0.36), residues: 199
  loop : -2.05 (0.25), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 234 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.021   0.001   PHE P  22 
 TYR   0.018   0.001   TYR R 291 
 ARG   0.002   0.000   ARG B  19 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 1.041 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7470 (tt0)
REVERT: G   32 LYS cc_start: 0.8564 (mmtm) cc_final: 0.8007 (ttmm)
REVERT: R  230 PHE cc_start: 0.7007 (m-10) cc_final: 0.6203 (t80)
REVERT: R  345 ILE cc_start: 0.6615 (OUTLIER) cc_final: 0.6189 (tp)
  outliers start: 20
  outliers final: 13
  residues processed: 121
  average time/residue: 0.2414
  time to fit residues: 39.1693
Evaluate side-chains
  113 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue   76 LYS
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  147 ILE
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  300 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  345 ILE
Chi-restraints excluded: chain R residue  357 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 57.0582 > 50:
  distance: 30 - 52:  15.472
  distance: 36 - 63:  10.698
  distance: 41 - 70:  12.081
  distance: 47 - 52:  14.328
  distance: 48 - 78:  27.643
  distance: 52 - 53:  10.637
  distance: 53 - 54:   9.113
  distance: 53 - 56:  10.095
  distance: 54 - 55:  24.720
  distance: 54 - 63:   8.981
  distance: 56 - 57:   3.033
  distance: 57 - 58:   5.095
  distance: 58 - 59:   6.115
  distance: 59 - 60:   5.863
  distance: 60 - 61:   6.414
  distance: 60 - 62:   5.670
  distance: 63 - 64:  18.757
  distance: 64 - 65:   3.781
  distance: 64 - 67:  15.452
  distance: 65 - 66:  22.730
  distance: 65 - 70:  14.116
  distance: 67 - 68:   8.210
  distance: 67 - 69:  18.619
  distance: 70 - 71:   6.002
  distance: 71 - 72:  40.863
  distance: 71 - 74:   8.037
  distance: 72 - 73:  52.236
  distance: 72 - 78:   7.541
  distance: 74 - 75:  25.176
  distance: 74 - 76:  20.431
  distance: 75 - 77:   6.614
  distance: 78 - 79:   5.542
  distance: 79 - 80:  19.307
  distance: 79 - 82:  47.461
  distance: 80 - 81:  31.230
  distance: 80 - 84:  23.782
  distance: 82 - 83:  35.059
  distance: 84 - 85:   9.300
  distance: 85 - 86:  12.180
  distance: 85 - 88:  10.873
  distance: 86 - 87:  14.308
  distance: 86 - 92:  13.673
  distance: 87 - 112:  26.267
  distance: 88 - 89:  12.748
  distance: 88 - 90:  29.335
  distance: 89 - 91:  31.102
  distance: 92 - 93:  15.584
  distance: 93 - 94:  35.101
  distance: 93 - 96:  23.702
  distance: 94 - 95:   6.369
  distance: 94 - 99:  14.955
  distance: 96 - 97:  11.681
  distance: 96 - 98:  17.112
  distance: 99 - 100:  14.322
  distance: 100 - 101:   5.099
  distance: 100 - 103:  16.384
  distance: 101 - 102:  26.798
  distance: 101 - 106:  15.856
  distance: 102 - 129:  27.748
  distance: 103 - 104:  23.965
  distance: 103 - 105:  19.741
  distance: 106 - 107:   4.406
  distance: 107 - 108:   7.336
  distance: 107 - 110:  12.013
  distance: 108 - 109:   9.153
  distance: 108 - 112:   6.773
  distance: 110 - 111:  24.105
  distance: 112 - 113:   5.149
  distance: 113 - 114:  19.390
  distance: 113 - 116:  13.790
  distance: 114 - 115:  20.137
  distance: 114 - 121:  11.240
  distance: 115 - 141:  25.344
  distance: 116 - 117:   5.739
  distance: 118 - 119:  12.003
  distance: 119 - 120:  43.339
  distance: 121 - 122:   3.416
  distance: 122 - 123:   8.409
  distance: 122 - 125:  13.429
  distance: 123 - 124:  16.757
  distance: 123 - 129:   3.093
  distance: 125 - 126:   3.825
  distance: 126 - 127:  14.090
  distance: 126 - 128:   7.345