Starting phenix.real_space_refine
on Tue Sep 24 05:20:49 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg9_29999/09_2024/8gg9_29999.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg9_29999/09_2024/8gg9_29999.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg9_29999/09_2024/8gg9_29999.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg9_29999/09_2024/8gg9_29999.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg9_29999/09_2024/8gg9_29999.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg9_29999/09_2024/8gg9_29999.cif"
  }
  resolution = 3.4
  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=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      42      5.16       5
     C    4461      2.51       5
     N    1226      2.21       5
     O    1291      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 7023
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2173
          Classifications: {'peptide': 300}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 84}
          Link IDs: {'PTRANS': 6, 'TRANS': 293}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 316
          Unresolved non-hydrogen angles: 388
          Unresolved non-hydrogen dihedrals: 252
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 201
    Chain: "B"
      Number of atoms: 2467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2467
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 125
          Unresolved non-hydrogen angles: 154
          Unresolved non-hydrogen dihedrals: 96
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 101
    Chain: "G"
      Number of atoms: 355
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 355
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "R"
      Number of atoms: 1981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 1981
          Classifications: {'peptide': 282}
          Incomplete info: {'truncation_to_alanine': 82}
          Link IDs: {'PTRANS': 7, 'TRANS': 274}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 299
          Unresolved non-hydrogen angles: 379
          Unresolved non-hydrogen dihedrals: 244
          Unresolved non-hydrogen chiralities: 32
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 155
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.74, per 1000 atoms: 0.67
  Number of scatterers: 7023
  At special positions: 0
  Unit cell: (83.2992, 136.229, 98.9178, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     P       3     15.00
     O    1291      8.00
     N    1226      7.00
     C    4461      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.55
  Conformation dependent library (CDL) restraints added in 937.4 milliseconds
  

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1850

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 8 sheets defined
      49.5% alpha, 14.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 4.171A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ALA A  18 " --> pdb=" O   ASN A  14 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   GLN A  31 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 65
      removed outlier: 3.510A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ARG A  61 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 110
    Processing helix  chain 'A' and resid 111 through 112
      No H-bonds generated for 'chain 'A' and resid 111 through 112'
    Processing helix  chain 'A' and resid 160 through 166
    Processing helix  chain 'A' and resid 174 through 180
    Processing helix  chain 'A' and resid 195 through 200
      removed outlier: 3.687A  pdb=" N   CYS A 200 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.584A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.389A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.649A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 390
      removed outlier: 3.828A  pdb=" N   VAL A 375 " --> pdb=" O   ASN A 371 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE A 376 " --> pdb=" O   ILE A 372 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE A 383 " --> pdb=" O   CYS A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'B' and resid 5 through 24
      removed outlier: 3.882A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ARG B  19 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.618A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 3.510A  pdb=" N   GLY B 131 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ASN B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 128 through 132'
    Processing helix  chain 'G' and resid 10 through 24
      removed outlier: 3.573A  pdb=" N   GLU G  22 " --> pdb=" O   GLN G  18 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.704A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.616A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.760A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   VAL R  52 " --> pdb=" O   VAL R  48 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LEU R  53 " --> pdb=" O   PHE R  49 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA R  59 " --> pdb=" O   ILE R  55 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 86
      removed outlier: 4.000A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 97
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.586A  pdb=" N   ILE R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU R 122 " --> pdb=" O   THR R 118 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   CYS R 125 " --> pdb=" O   ILE R 121 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   VAL R 126 " --> pdb=" O   GLU R 122 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.670A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 238
      removed outlier: 3.621A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 3.582A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.780A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 326
      removed outlier: 3.821A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 339
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213
      removed outlier: 6.256A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.321A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.650A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.818A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.819A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA B  73 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103
      removed outlier: 7.024A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.916A  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: 6.953A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.621A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.871A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277
      removed outlier: 3.775A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)

    361 hydrogen bonds defined for protein.
    1056 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.85

  Time building geometry restraints manager: 1.84 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1242
        1.32 -     1.45: 1903
        1.45 -     1.57: 3958
        1.57 -     1.69: 4
        1.69 -     1.81: 57
  Bond restraints: 7164
  Sorted by residual:
  bond pdb=" N   VAL A 224 "
       pdb=" CA  VAL A 224 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.24e-02 6.50e+03 8.67e+00
  bond pdb=" N   ASP A 223 "
       pdb=" CA  ASP A 223 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.21e-02 6.83e+03 8.37e+00
  bond pdb=" N   VAL A 202 "
       pdb=" CA  VAL A 202 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.19e-02 7.06e+03 8.33e+00
  bond pdb=" C2  GTP A 401 "
       pdb=" N3  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.380  1.324  0.056 2.00e-02 2.50e+03 7.91e+00
  bond pdb=" N   LEU A 203 "
       pdb=" CA  LEU A 203 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.34e-02 5.57e+03 6.87e+00
  ... (remaining 7159 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 9652
        2.37 -     4.75: 120
        4.75 -     7.12: 16
        7.12 -     9.49: 6
        9.49 -    11.87: 4
  Bond angle restraints: 9798
  Sorted by residual:
  angle pdb=" N   GLY B  53 "
        pdb=" CA  GLY B  53 "
        pdb=" C   GLY B  53 "
      ideal   model   delta    sigma   weight residual
     115.64  125.19   -9.55 1.46e+00 4.69e-01 4.27e+01
  angle pdb=" N   GLN A 227 "
        pdb=" CA  GLN A 227 "
        pdb=" C   GLN A 227 "
      ideal   model   delta    sigma   weight residual
     111.07  105.47    5.60 1.07e+00 8.73e-01 2.74e+01
  angle pdb=" CA  GLY A 226 "
        pdb=" C   GLY A 226 "
        pdb=" O   GLY A 226 "
      ideal   model   delta    sigma   weight residual
     121.57  117.35    4.22 8.70e-01 1.32e+00 2.35e+01
  angle pdb=" N   LYS A 233 "
        pdb=" CA  LYS A 233 "
        pdb=" C   LYS A 233 "
      ideal   model   delta    sigma   weight residual
     113.17  107.78    5.39 1.26e+00 6.30e-01 1.83e+01
  angle pdb=" CA  GLY A 226 "
        pdb=" C   GLY A 226 "
        pdb=" N   GLN A 227 "
      ideal   model   delta    sigma   weight residual
     114.98  119.67   -4.69 1.14e+00 7.69e-01 1.69e+01
  ... (remaining 9793 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.97: 4091
       33.97 -    67.95: 68
       67.95 -   101.92: 5
      101.92 -   135.89: 1
      135.89 -   169.86: 4
  Dihedral angle restraints: 4169
    sinusoidal: 1326
      harmonic: 2843
  Sorted by residual:
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -65.27  169.86     1      2.00e+01 2.50e-03 4.76e+01
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  -96.66  165.93     1      2.00e+01 2.50e-03 4.73e+01
  dihedral pdb=" O3A GTP A 401 "
           pdb=" O3B GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PG  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     303.79  157.34  146.45     1      2.00e+01 2.50e-03 4.40e+01
  ... (remaining 4166 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 869
       0.045 -    0.090: 221
       0.090 -    0.135: 65
       0.135 -    0.180: 7
       0.180 -    0.226: 4
  Chirality restraints: 1166
  Sorted by residual:
  chirality pdb=" C2' GTP A 401 "
            pdb=" C1' GTP A 401 "
            pdb=" C3' GTP A 401 "
            pdb=" O2' GTP A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.70    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  GLN A 227 "
            pdb=" N   GLN A 227 "
            pdb=" C   GLN A 227 "
            pdb=" CB  GLN A 227 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  ARG A 231 "
            pdb=" N   ARG A 231 "
            pdb=" C   ARG A 231 "
            pdb=" CB  ARG A 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.91e-01
  ... (remaining 1163 not shown)

  Planarity restraints: 1248
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 201 "   -0.013 2.00e-02 2.50e+03   2.62e-02 6.89e+00
        pdb=" C   ARG A 201 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ARG A 201 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   VAL A 202 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 222 "    0.012 2.00e-02 2.50e+03   2.40e-02 5.75e+00
        pdb=" C   PHE A 222 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   PHE A 222 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASP A 223 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  52 "    0.008 2.00e-02 2.50e+03   1.69e-02 2.85e+00
        pdb=" C   ARG B  52 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ARG B  52 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLY B  53 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1245 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 562
        2.74 -     3.28: 6747
        3.28 -     3.82: 10871
        3.82 -     4.36: 11858
        4.36 -     4.90: 22147
  Nonbonded interactions: 52185
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" NE2 HIS B 142 "
            pdb=" OG  SER B 161 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" NE2 GLN A 213 "
            pdb=" OD1 ASN A 218 "
     model   vdw
     2.315 3.120
  nonbonded pdb=" O   LYS B  57 "
            pdb=" OG  SER B  74 "
     model   vdw
     2.320 3.040
  ... (remaining 52180 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:             2.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     18.760
  Find NCS groups from input model:        0.100
  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:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
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      :  0.004   0.056   7164  Z= 0.317
  Angle     :  0.681  11.867   9798  Z= 0.377
  Chirality :  0.045   0.226   1166
  Planarity :  0.003   0.034   1248
  Dihedral  : 14.830 169.863   2319
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  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:  0.44 (0.27), residues: 955
  helix:  1.59 (0.26), residues: 411
  sheet: -0.33 (0.44), residues: 150
  loop : -0.83 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 234 
 HIS   0.007   0.001   HIS B  54 
 PHE   0.013   0.001   PHE B 235 
 TYR   0.011   0.001   TYR R 308 
 ARG   0.003   0.000   ARG R 131 

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
REVERT: A  233 LYS cc_start: 0.8861 (tptt) cc_final: 0.8657 (tttp)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1668
  time to fit residues: 20.5123
Evaluate side-chains
  72 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 229 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7164  Z= 0.243
  Angle     :  0.518   6.612   9798  Z= 0.282
  Chirality :  0.042   0.148   1166
  Planarity :  0.003   0.037   1248
  Dihedral  : 10.819 169.477   1061
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  8.43 %
    Favored  : 90.62 %
  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:  0.71 (0.28), residues: 955
  helix:  1.89 (0.26), residues: 436
  sheet: -0.34 (0.41), residues: 171
  loop : -0.90 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.013   0.001   PHE B 235 
 TYR   0.011   0.001   TYR R 308 
 ARG   0.003   0.000   ARG A 265 

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.769 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 79
  average time/residue: 0.1577
  time to fit residues: 17.9845
Evaluate side-chains
  75 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain R residue  117 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 48 optimal weight:    0.0870
   chunk 27 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 87 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 86 optimal weight:    0.0000
   chunk 29 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.7566

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7164  Z= 0.175
  Angle     :  0.464   6.677   9798  Z= 0.250
  Chirality :  0.041   0.135   1166
  Planarity :  0.003   0.036   1248
  Dihedral  : 10.367 165.869   1061
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 11.61 %
    Favored  : 87.44 %
  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:  0.99 (0.28), residues: 955
  helix:  2.15 (0.26), residues: 440
  sheet: -0.16 (0.43), residues: 162
  loop : -0.85 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 277 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.004   0.000   ARG R 328 

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.688 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7997 (mm-30)
REVERT: A  255 MET cc_start: 0.8782 (mpp) cc_final: 0.8313 (mtt)
  outliers start: 6
  outliers final: 4
  residues processed: 79
  average time/residue: 0.1737
  time to fit residues: 19.0096
Evaluate side-chains
  75 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLN
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain R residue  232 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    0.0270
   chunk 65 optimal weight:    3.9990
   chunk 45 optimal weight:    0.3980
   chunk 9 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.6240

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

Flipped N/Q/H residues before XYZ refinement:
R 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7164  Z= 0.149
  Angle     :  0.444   6.331   9798  Z= 0.238
  Chirality :  0.040   0.135   1166
  Planarity :  0.003   0.034   1248
  Dihedral  : 10.036 163.116   1061
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 12.24 %
    Favored  : 86.17 %
  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:  1.16 (0.28), residues: 955
  helix:  2.32 (0.26), residues: 441
  sheet: -0.15 (0.43), residues: 164
  loop : -0.79 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 234 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.010   0.001   PHE B 241 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 328 

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.741 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7955 (mm-30)
REVERT: A  255 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.7980 (mtp)
  outliers start: 10
  outliers final: 8
  residues processed: 80
  average time/residue: 0.1381
  time to fit residues: 16.3880
Evaluate side-chains
  80 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 69 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R 229 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7164  Z= 0.227
  Angle     :  0.483   6.576   9798  Z= 0.259
  Chirality :  0.042   0.129   1166
  Planarity :  0.003   0.036   1248
  Dihedral  :  9.943 162.248   1061
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 13.35 %
    Favored  : 84.10 %
  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:  1.08 (0.28), residues: 955
  helix:  2.28 (0.26), residues: 441
  sheet: -0.26 (0.42), residues: 169
  loop : -0.82 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.015   0.001   PHE B 241 
 TYR   0.010   0.001   TYR R 308 
 ARG   0.001   0.000   ARG B  96 

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.755 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7976 (mm-30)
REVERT: A  255 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.7986 (mtp)
REVERT: B  142 HIS cc_start: 0.8589 (OUTLIER) cc_final: 0.8295 (t70)
  outliers start: 16
  outliers final: 12
  residues processed: 83
  average time/residue: 0.1624
  time to fit residues: 18.9907
Evaluate side-chains
  84 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain R residue  117 VAL
Chi-restraints excluded: chain R residue  166 PHE
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0970
   chunk 92 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 30 optimal weight:   20.0000
   chunk 48 optimal weight:    0.9990
   chunk 89 optimal weight:    6.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
R 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7164  Z= 0.237
  Angle     :  0.486   6.461   9798  Z= 0.261
  Chirality :  0.042   0.132   1166
  Planarity :  0.003   0.037   1248
  Dihedral  :  9.880 161.923   1061
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.67 %
    Favored  : 83.94 %
  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:  1.05 (0.28), residues: 955
  helix:  2.26 (0.26), residues: 442
  sheet: -0.33 (0.41), residues: 169
  loop : -0.83 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.015   0.001   PHE B 241 
 TYR   0.012   0.001   TYR R 308 
 ARG   0.003   0.000   ARG R 328 

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.711 
Fit side-chains
REVERT: A  255 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.7948 (mtp)
REVERT: B  123 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8682 (mt)
  outliers start: 15
  outliers final: 10
  residues processed: 80
  average time/residue: 0.1599
  time to fit residues: 18.2568
Evaluate side-chains
  82 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 52 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   chunk 78 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 55 optimal weight:    0.3980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 229 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7164  Z= 0.156
  Angle     :  0.445   6.058   9798  Z= 0.239
  Chirality :  0.041   0.126   1166
  Planarity :  0.003   0.035   1248
  Dihedral  :  9.645 159.900   1061
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.31 %
    Favored  : 83.78 %
  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:  1.22 (0.28), residues: 955
  helix:  2.39 (0.25), residues: 442
  sheet: -0.23 (0.42), residues: 169
  loop : -0.75 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 277 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.012   0.001   PHE B 241 
 TYR   0.009   0.001   TYR R 308 
 ARG   0.002   0.000   ARG R 131 

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.787 
Fit side-chains
REVERT: A  255 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8245 (mtt)
REVERT: B  123 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8661 (mt)
  outliers start: 12
  outliers final: 6
  residues processed: 84
  average time/residue: 0.1644
  time to fit residues: 19.5435
Evaluate side-chains
  79 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 63 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 80 optimal weight:    0.8980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
R 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7164  Z= 0.220
  Angle     :  0.479   6.181   9798  Z= 0.257
  Chirality :  0.042   0.133   1166
  Planarity :  0.003   0.036   1248
  Dihedral  :  9.580 158.543   1061
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 14.31 %
    Favored  : 83.47 %
  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:  1.15 (0.28), residues: 955
  helix:  2.33 (0.25), residues: 442
  sheet: -0.29 (0.42), residues: 169
  loop : -0.77 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 277 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.014   0.001   PHE B 241 
 TYR   0.012   0.001   TYR R 308 
 ARG   0.003   0.000   ARG R 328 

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A  255 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8289 (mtt)
REVERT: B  123 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8677 (mt)
  outliers start: 14
  outliers final: 10
  residues processed: 79
  average time/residue: 0.1567
  time to fit residues: 17.7050
Evaluate side-chains
  81 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    0.2980
   chunk 88 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0040
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7164  Z= 0.133
  Angle     :  0.431   6.000   9798  Z= 0.231
  Chirality :  0.040   0.128   1166
  Planarity :  0.003   0.034   1248
  Dihedral  :  9.299 156.506   1061
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 14.94 %
    Favored  : 83.47 %
  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:  1.36 (0.28), residues: 955
  helix:  2.50 (0.25), residues: 438
  sheet: -0.06 (0.44), residues: 162
  loop : -0.69 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 277 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.010   0.001   PHE B 241 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 328 

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.650 
Fit side-chains
REVERT: A  255 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8263 (mtt)
  outliers start: 10
  outliers final: 6
  residues processed: 85
  average time/residue: 0.1527
  time to fit residues: 18.7552
Evaluate side-chains
  82 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0020
   chunk 76 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.7590

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

Flipped N/Q/H residues before XYZ refinement:
R 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7164  Z= 0.167
  Angle     :  0.452   6.013   9798  Z= 0.242
  Chirality :  0.041   0.126   1166
  Planarity :  0.003   0.035   1248
  Dihedral  :  9.185 154.890   1061
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.63 %
    Favored  : 83.94 %
  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:  1.34 (0.28), residues: 955
  helix:  2.46 (0.25), residues: 443
  sheet: -0.09 (0.43), residues: 162
  loop : -0.70 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 277 
 HIS   0.002   0.001   HIS R 178 
 PHE   0.012   0.001   PHE B 241 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 328 

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.860 
Fit side-chains
REVERT: A  255 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8253 (mtt)
  outliers start: 9
  outliers final: 7
  residues processed: 78
  average time/residue: 0.1602
  time to fit residues: 18.2291
Evaluate side-chains
  81 residues out of total 844 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    0.0060
   chunk 70 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 78 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    0.8798

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R 229 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.153754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.124342 restraints weight = 9847.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 2.12
r_work: 0.3296 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7164  Z= 0.185
  Angle     :  0.463   6.013   9798  Z= 0.248
  Chirality :  0.041   0.131   1166
  Planarity :  0.003   0.035   1248
  Dihedral  :  9.093 153.721   1061
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 14.47 %
    Favored  : 83.94 %
  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:  1.31 (0.28), residues: 955
  helix:  2.45 (0.25), residues: 443
  sheet: -0.20 (0.42), residues: 169
  loop : -0.68 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 277 
 HIS   0.002   0.001   HIS R 178 
 PHE   0.013   0.001   PHE B 241 
 TYR   0.010   0.001   TYR R 308 
 ARG   0.003   0.000   ARG R 328 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1663.45 seconds
wall clock time: 30 minutes 25.62 seconds (1825.62 seconds total)