Starting phenix.real_space_refine
on Tue Feb 13 15:49:51 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7c_8998/02_2024/6e7c_8998_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7c_8998/02_2024/6e7c_8998.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7c_8998/02_2024/6e7c_8998.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7c_8998/02_2024/6e7c_8998.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7c_8998/02_2024/6e7c_8998_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7c_8998/02_2024/6e7c_8998_updated.pdb"
  }
  resolution = 3.65
  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
-------------------------------------------------------------------------------
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=   0.228 sd=   1.115
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      49      5.16       5
     C    4259      2.51       5
     N    1156      2.21       5
     O    1308      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B ARG   46": "NH1" <-> "NH2"
    Residue "B ARG   86": "NH1" <-> "NH2"
    Residue "B ARG  318": "NH1" <-> "NH2"
    Residue "B ARG  391": "NH1" <-> "NH2"
    Residue "A PHE   49": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG   64": "NH1" <-> "NH2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG   84": "NH1" <-> "NH2"
    Residue "A PHE  255": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  320": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 6780
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 3356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3356
          Classifications: {'peptide': 426}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405}
    Chain: "A"
      Number of atoms: 3358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 428, 3358
          Classifications: {'peptide': 428}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'G2P': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.16, per 1000 atoms: 0.61
  Number of scatterers: 6780
  At special positions: 0
  Unit cell: (74, 73, 107, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      49     16.00
     P       6     15.00
     Mg      2     11.99
     O    1308      8.00
     N    1156      7.00
     C    4259      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  - 3.50
        Amino acid           : False - 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: 2.88
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1582

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      33 helices and 5 sheets defined
      43.0% alpha, 9.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.64
  Creating SS restraints...
    Processing helix  chain 'B' and resid 11 through 27
      removed outlier: 3.644A  pdb=" N   GLN B  15 " --> pdb=" O   GLN B  11 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LYS B  19 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLU B  22 " --> pdb=" O   ALA B  18 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ASP B  26 " --> pdb=" O   GLU B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 49
      No H-bonds generated for 'chain 'B' and resid 47 through 49'
    Processing helix  chain 'B' and resid 70 through 78
      removed outlier: 3.860A  pdb=" N   SER B  75 " --> pdb=" O   GLY B  71 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   SER B  78 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 99
      No H-bonds generated for 'chain 'B' and resid 97 through 99'
    Processing helix  chain 'B' and resid 113 through 125
      removed outlier: 3.832A  pdb=" N   ASP B 118 " --> pdb=" O   ASP B 114 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   VAL B 119 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL B 120 " --> pdb=" O   VAL B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 158
      removed outlier: 3.613A  pdb=" N   GLY B 148 " --> pdb=" O   GLY B 144 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   THR B 149 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   LEU B 150 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU B 151 " --> pdb=" O   MET B 147 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ILE B 155 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ARG B 156 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   GLU B 157 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 195
      removed outlier: 3.556A  pdb=" N   LEU B 187 " --> pdb=" O   TYR B 183 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   HIS B 190 " --> pdb=" O   THR B 186 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   GLN B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   GLU B 194 " --> pdb=" O   HIS B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 212
      removed outlier: 3.665A  pdb=" N   ASP B 209 " --> pdb=" O   GLU B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 225
      No H-bonds generated for 'chain 'B' and resid 222 through 225'
    Processing helix  chain 'B' and resid 229 through 241
      removed outlier: 3.928A  pdb=" N   MET B 233 " --> pdb=" O   VAL B 229 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   VAL B 236 " --> pdb=" O   THR B 232 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   CYS B 239 " --> pdb=" O   GLY B 235 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   LEU B 240 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 255
    Processing helix  chain 'B' and resid 277 through 279
      No H-bonds generated for 'chain 'B' and resid 277 through 279'
    Processing helix  chain 'B' and resid 286 through 294
      removed outlier: 3.618A  pdb=" N   GLN B 292 " --> pdb=" O   GLU B 288 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   MET B 293 " --> pdb=" O   LEU B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 336
      removed outlier: 3.544A  pdb=" N   GLN B 329 " --> pdb=" O   GLU B 325 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   MET B 330 " --> pdb=" O   VAL B 326 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLN B 334 " --> pdb=" O   MET B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 389
      removed outlier: 3.529A  pdb=" N   LYS B 379 " --> pdb=" O   GLU B 376 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE B 381 " --> pdb=" O   PHE B 378 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   GLU B 383 " --> pdb=" O   ARG B 380 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   PHE B 385 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   THR B 386 " --> pdb=" O   GLU B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 399
    Processing helix  chain 'B' and resid 405 through 425
      removed outlier: 3.738A  pdb=" N   THR B 409 " --> pdb=" O   GLU B 405 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   GLU B 421 " --> pdb=" O   ASP B 417 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TYR B 422 " --> pdb=" O   LEU B 418 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   TYR B 425 " --> pdb=" O   GLU B 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 10 through 27
      removed outlier: 3.509A  pdb=" N   VAL A  14 " --> pdb=" O   GLY A  10 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ALA A  19 " --> pdb=" O   GLN A  15 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLU A  22 " --> pdb=" O   ASN A  18 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LEU A  23 " --> pdb=" O   ALA A  19 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TYR A  24 " --> pdb=" O   CYS A  20 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   LEU A  26 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 51
      removed outlier: 3.663A  pdb=" N   THR A  51 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 48 through 51'
    Processing helix  chain 'A' and resid 72 through 80
    Processing helix  chain 'A' and resid 103 through 107
    Processing helix  chain 'A' and resid 111 through 128
      removed outlier: 3.927A  pdb=" N   ILE A 115 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   ASP A 116 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL A 118 " --> pdb=" O   ILE A 115 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   LEU A 119 " --> pdb=" O   ASP A 116 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   ILE A 122 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ALA A 126 " --> pdb=" O   ARG A 123 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ASP A 127 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 160
      removed outlier: 4.206A  pdb=" N   GLU A 155 " --> pdb=" O   SER A 151 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ARG A 156 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 197
      removed outlier: 4.509A  pdb=" N   ILE A 188 " --> pdb=" O   PRO A 184 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   THR A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   GLU A 196 " --> pdb=" O   HIS A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 213
      removed outlier: 3.747A  pdb=" N   TYR A 210 " --> pdb=" O   ASN A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 243
      removed outlier: 3.682A  pdb=" N   LEU A 230 " --> pdb=" O   ASN A 226 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLN A 233 " --> pdb=" O   ARG A 229 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ILE A 234 " --> pdb=" O   LEU A 230 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   VAL A 235 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 4.851A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.295A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 259
      removed outlier: 3.981A  pdb=" N   GLN A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   THR A 257 " --> pdb=" O   THR A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 281
      No H-bonds generated for 'chain 'A' and resid 278 through 281'
    Processing helix  chain 'A' and resid 288 through 293
    Processing helix  chain 'A' and resid 325 through 337
      removed outlier: 3.791A  pdb=" N   LYS A 336 " --> pdb=" O   ILE A 332 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 401
      removed outlier: 3.711A  pdb=" N   TRP A 388 " --> pdb=" O   ALA A 385 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA A 389 " --> pdb=" O   GLU A 386 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   ASP A 392 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE A 395 " --> pdb=" O   ASP A 392 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LEU A 397 " --> pdb=" O   LYS A 394 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   MET A 398 " --> pdb=" O   PHE A 395 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   TYR A 399 " --> pdb=" O   ASP A 396 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   ALA A 400 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 411
    Processing helix  chain 'A' and resid 415 through 436
      removed outlier: 3.796A  pdb=" N   ARG A 422 " --> pdb=" O   SER A 419 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   GLU A 423 " --> pdb=" O   GLU A 420 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASP A 424 " --> pdb=" O   ALA A 421 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   VAL A 435 " --> pdb=" O   TYR A 432 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLY A 436 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'B' and resid 63 through 66
      removed outlier: 8.986A  pdb=" N   ILE B  64 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   HIS B   6 " --> pdb=" O   ILE B  64 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   VAL B  66 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   GLN B   8 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   VAL B   5 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
      removed outlier: 4.732A  pdb=" N   PHE B 133 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   ILE B   7 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   LEU B 135 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   ALA B   9 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   HIS B 137 " --> pdb=" O   ALA B   9 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 51 through 54
      removed outlier: 3.501A  pdb=" N   VAL B  60 " --> pdb=" O   ASN B  52 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS B  58 " --> pdb=" O   ALA B  54 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 267 through 269
    Processing sheet with id=  D, first strand: chain 'A' and resid 65 through 68
      removed outlier: 9.209A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   GLY A 131 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 8.406A  pdb=" N   ILE A   5 " --> pdb=" O   GLY A 131 " (cutoff:3.500A)
      removed outlier: 9.004A  pdb=" N   GLN A 133 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 13.063A  pdb=" N   ILE A   7 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 10.054A  pdb=" N   PHE A 135 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 12.424A  pdb=" N   VAL A   9 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 9.431A  pdb=" N   VAL A 137 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   SER A 165 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 7.516A  pdb=" N   VAL A 137 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   LEU A 167 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   HIS A 139 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   PHE A 169 " --> pdb=" O   HIS A 139 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  D
    Processing sheet with id=  E, first strand: chain 'A' and resid 269 through 273
      removed outlier: 3.608A  pdb=" N   ALA A 374 " --> pdb=" O   ARG A 320 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LEU A 378 " --> pdb=" O   CYS A 316 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   CYS A 316 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)

    185 hydrogen bonds defined for protein.
    426 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: 1.74

  Time building geometry restraints manager: 3.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2228
        1.34 -     1.46: 1131
        1.46 -     1.57: 3485
        1.57 -     1.69: 10
        1.69 -     1.81: 80
  Bond restraints: 6934
  Sorted by residual:
  bond pdb=" O3B G2P B 502 "
       pdb=" PG  G2P B 502 "
    ideal  model  delta    sigma   weight residual
    1.716  1.603  0.113 2.00e-02 2.50e+03 3.22e+01
  bond pdb=" O1A G2P B 502 "
       pdb=" PA  G2P B 502 "
    ideal  model  delta    sigma   weight residual
    1.507  1.608 -0.101 2.00e-02 2.50e+03 2.55e+01
  bond pdb=" O1B G2P B 502 "
       pdb=" PB  G2P B 502 "
    ideal  model  delta    sigma   weight residual
    1.510  1.608 -0.098 2.00e-02 2.50e+03 2.38e+01
  bond pdb=" C5  GTP A 502 "
       pdb=" C6  GTP A 502 "
    ideal  model  delta    sigma   weight residual
    1.390  1.479 -0.089 2.00e-02 2.50e+03 1.96e+01
  bond pdb=" C4  G2P B 502 "
       pdb=" C5  G2P B 502 "
    ideal  model  delta    sigma   weight residual
    1.384  1.463 -0.079 2.00e-02 2.50e+03 1.56e+01
  ... (remaining 6929 not shown)

  Histogram of bond angle deviations from ideal:
       98.02 -   105.87: 173
      105.87 -   113.73: 3801
      113.73 -   121.59: 3778
      121.59 -   129.45: 1608
      129.45 -   137.30: 57
  Bond angle restraints: 9417
  Sorted by residual:
  angle pdb=" C3A G2P B 502 "
        pdb=" PA  G2P B 502 "
        pdb=" O5' G2P B 502 "
      ideal   model   delta    sigma   weight residual
      99.14  111.54  -12.40 3.00e+00 1.11e-01 1.71e+01
  angle pdb=" PA  G2P B 502 "
        pdb=" C3A G2P B 502 "
        pdb=" PB  G2P B 502 "
      ideal   model   delta    sigma   weight residual
     120.83  108.52   12.31 3.00e+00 1.11e-01 1.68e+01
  angle pdb=" O1B GTP A 502 "
        pdb=" PB  GTP A 502 "
        pdb=" O2B GTP A 502 "
      ideal   model   delta    sigma   weight residual
     109.50  120.92  -11.42 3.00e+00 1.11e-01 1.45e+01
  angle pdb=" O1A GTP A 502 "
        pdb=" PA  GTP A 502 "
        pdb=" O2A GTP A 502 "
      ideal   model   delta    sigma   weight residual
     109.50  120.33  -10.83 3.00e+00 1.11e-01 1.30e+01
  angle pdb=" C   LEU A 217 "
        pdb=" N   ASP A 218 "
        pdb=" CA  ASP A 218 "
      ideal   model   delta    sigma   weight residual
     122.82  127.24   -4.42 1.42e+00 4.96e-01 9.68e+00
  ... (remaining 9412 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.38: 4092
       33.38 -    66.77: 41
       66.77 -   100.15: 8
      100.15 -   133.54: 1
      133.54 -   166.92: 3
  Dihedral angle restraints: 4145
    sinusoidal: 1678
      harmonic: 2467
  Sorted by residual:
  dihedral pdb=" C4' GTP A 502 "
           pdb=" C5' GTP A 502 "
           pdb=" O5' GTP A 502 "
           pdb=" PA  GTP A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     260.87   93.95  166.92     1      2.00e+01 2.50e-03 4.74e+01
  dihedral pdb=" C8  GTP A 502 "
           pdb=" C1' GTP A 502 "
           pdb=" N9  GTP A 502 "
           pdb=" O4' GTP A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -62.13  166.73     1      2.00e+01 2.50e-03 4.74e+01
  dihedral pdb=" O2G GTP A 502 "
           pdb=" O3B GTP A 502 "
           pdb=" PG  GTP A 502 "
           pdb=" PB  GTP A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.30  -35.43 -147.27     1      2.00e+01 2.50e-03 4.42e+01
  ... (remaining 4142 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 600
       0.032 -    0.064: 284
       0.064 -    0.096: 82
       0.096 -    0.128: 53
       0.128 -    0.160: 8
  Chirality restraints: 1027
  Sorted by residual:
  chirality pdb=" CA  ILE B 368 "
            pdb=" N   ILE B 368 "
            pdb=" C   ILE B 368 "
            pdb=" CB  ILE B 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CA  VAL A 324 "
            pdb=" N   VAL A 324 "
            pdb=" C   VAL A 324 "
            pdb=" CB  VAL A 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.52e-01
  chirality pdb=" CA  ASP A 218 "
            pdb=" N   ASP A 218 "
            pdb=" C   ASP A 218 "
            pdb=" CB  ASP A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.34e-01
  ... (remaining 1024 not shown)

  Planarity restraints: 1224
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B  69 "   -0.030 5.00e-02 4.00e+02   4.55e-02 3.31e+00
        pdb=" N   PRO B  70 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B  70 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B  70 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 221 "    0.029 5.00e-02 4.00e+02   4.33e-02 3.00e+00
        pdb=" N   PRO A 222 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A 222 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 222 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 391 "    0.008 2.00e-02 2.50e+03   1.63e-02 2.65e+00
        pdb=" C   ARG B 391 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   ARG B 391 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LYS B 392 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1221 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 57
        2.50 -     3.10: 5468
        3.10 -     3.70: 10630
        3.70 -     4.30: 16020
        4.30 -     4.90: 25520
  Nonbonded interactions: 57695
  Sorted by model distance:
  nonbonded pdb="MG    MG B 501 "
            pdb=" O2B G2P B 502 "
     model   vdw
     1.901 2.170
  nonbonded pdb="MG    MG A 501 "
            pdb=" O2G GTP A 502 "
     model   vdw
     1.946 2.170
  nonbonded pdb="MG    MG A 501 "
            pdb=" O1B GTP A 502 "
     model   vdw
     2.028 2.170
  nonbonded pdb=" O1A G2P B 502 "
            pdb=" O1B G2P B 502 "
     model   vdw
     2.078 3.040
  nonbonded pdb="MG    MG B 501 "
            pdb=" O1G G2P B 502 "
     model   vdw
     2.127 2.170
  ... (remaining 57690 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             7.150
  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:          26.280
  Check model and map are aligned:         0.100
  Set scattering table:                    0.070
  Process input model:                     22.920
  Find NCS groups from input model:        0.200
  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:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.113   6934  Z= 0.421
  Angle     :  0.847  12.404   9417  Z= 0.408
  Chirality :  0.045   0.160   1027
  Planarity :  0.005   0.045   1224
  Dihedral  : 12.698 166.923   2563
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -4.32 (0.25), residues: 848
  helix: -3.40 (0.17), residues: 343
  sheet: -3.87 (0.36), residues: 130
  loop : -1.67 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP A 388 
 HIS   0.011   0.002   HIS B   6 
 PHE   0.016   0.002   PHE A 169 
 TYR   0.017   0.002   TYR B  50 
 ARG   0.008   0.001   ARG A  64 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  155 ILE cc_start: 0.6379 (pt) cc_final: 0.6129 (pt)
REVERT: A  188 ILE cc_start: 0.6807 (pp) cc_final: 0.6453 (pt)
REVERT: A  285 GLN cc_start: 0.7785 (pm20) cc_final: 0.6558 (mm110)
REVERT: A  346 TRP cc_start: 0.6759 (p-90) cc_final: 0.5916 (m-10)
REVERT: A  351 PHE cc_start: 0.6785 (m-80) cc_final: 0.6180 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.2259
  time to fit residues: 55.5847
Evaluate side-chains
  121 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 42 optimal weight:    6.9990
   chunk 34 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 40 optimal weight:   10.0000
   chunk 49 optimal weight:    0.7980
   chunk 76 optimal weight:    4.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B  99 ASN
B 131 GLN
** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 396 HIS
** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 101 ASN
** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 356 ASN
A 358 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.2886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6934  Z= 0.196
  Angle     :  0.626   8.263   9417  Z= 0.317
  Chirality :  0.045   0.162   1027
  Planarity :  0.005   0.045   1224
  Dihedral  : 12.449 168.641    974
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  9.99 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -3.34 (0.25), residues: 848
  helix: -2.06 (0.23), residues: 360
  sheet: -3.18 (0.40), residues: 131
  loop : -1.75 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 344 
 HIS   0.009   0.001   HIS B   6 
 PHE   0.030   0.002   PHE A 255 
 TYR   0.017   0.002   TYR B 159 
 ARG   0.006   0.001   ARG B 320 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  247 ASN cc_start: 0.7547 (m-40) cc_final: 0.7079 (m110)
REVERT: A   35 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7925 (mm110)
REVERT: A   90 GLU cc_start: 0.6748 (tt0) cc_final: 0.6506 (tp30)
REVERT: A  188 ILE cc_start: 0.5904 (pp) cc_final: 0.5539 (pt)
REVERT: A  192 HIS cc_start: 0.7455 (t-90) cc_final: 0.7170 (t-170)
REVERT: A  351 PHE cc_start: 0.7223 (m-80) cc_final: 0.6765 (m-80)
REVERT: A  380 ASN cc_start: 0.6295 (t0) cc_final: 0.6058 (t0)
  outliers start: 16
  outliers final: 8
  residues processed: 145
  average time/residue: 0.2092
  time to fit residues: 39.7225
Evaluate side-chains
  120 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  376 CYS
Chi-restraints excluded: chain A residue  424 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 21 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
B  11 GLN
B 100 ASN
B 131 GLN
B 195 ASN
B 307 HIS
** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 426 GLN
A 216 ASN
** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 GLN
A 358 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.3781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6934  Z= 0.239
  Angle     :  0.619   8.075   9417  Z= 0.313
  Chirality :  0.045   0.149   1027
  Planarity :  0.005   0.049   1224
  Dihedral  : 11.990 168.931    974
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.86 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -3.04 (0.26), residues: 848
  helix: -1.74 (0.24), residues: 367
  sheet: -2.93 (0.41), residues: 129
  loop : -1.72 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP B 344 
 HIS   0.005   0.001   HIS B   6 
 PHE   0.035   0.002   PHE A 255 
 TYR   0.021   0.002   TYR A 161 
 ARG   0.007   0.001   ARG A  64 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 ILE cc_start: 0.6463 (pp) cc_final: 0.6111 (pt)
REVERT: A  192 HIS cc_start: 0.7527 (t-90) cc_final: 0.7246 (t-170)
REVERT: A  244 PHE cc_start: 0.7908 (m-80) cc_final: 0.7707 (m-80)
  outliers start: 16
  outliers final: 10
  residues processed: 144
  average time/residue: 0.1907
  time to fit residues: 36.7516
Evaluate side-chains
  117 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  376 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 57 optimal weight:    9.9990
   chunk 39 optimal weight:   20.0000
   chunk 8 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 76 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 40 optimal weight:   10.0000
   chunk 72 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    4.5788

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

Flipped N/Q/H residues before XYZ refinement:
** B  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 134 GLN
B 204 ASN
B 226 ASN
** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 423 GLN
** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.5057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.065   6934  Z= 0.475
  Angle     :  0.776   8.719   9417  Z= 0.395
  Chirality :  0.051   0.160   1027
  Planarity :  0.005   0.052   1224
  Dihedral  : 12.396 167.276    974
  Min Nonbonded Distance : 1.718

Molprobity Statistics.
  All-atom Clashscore : 24.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.37 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -3.00 (0.26), residues: 848
  helix: -1.80 (0.25), residues: 354
  sheet: -2.96 (0.41), residues: 126
  loop : -1.61 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP B 344 
 HIS   0.008   0.002   HIS A 192 
 PHE   0.027   0.003   PHE A  67 
 TYR   0.028   0.003   TYR B 159 
 ARG   0.007   0.001   ARG B 320 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7794 (m-10)
REVERT: A  188 ILE cc_start: 0.7407 (pp) cc_final: 0.7147 (pt)
  outliers start: 19
  outliers final: 16
  residues processed: 137
  average time/residue: 0.1901
  time to fit residues: 34.8306
Evaluate side-chains
  119 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  138 PHE
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  424 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 69 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
B  11 GLN
B  15 GLN
B 227 HIS
** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 426 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.5310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6934  Z= 0.272
  Angle     :  0.649   9.404   9417  Z= 0.323
  Chirality :  0.046   0.155   1027
  Planarity :  0.004   0.051   1224
  Dihedral  : 11.894 166.981    974
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 19.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 18.06 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -2.70 (0.27), residues: 848
  helix: -1.56 (0.26), residues: 354
  sheet: -2.73 (0.43), residues: 130
  loop : -1.44 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 344 
 HIS   0.009   0.002   HIS B 190 
 PHE   0.017   0.002   PHE B 167 
 TYR   0.013   0.001   TYR A 103 
 ARG   0.004   0.000   ARG A 214 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 121
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   15 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7356 (mp10)
REVERT: B  183 TYR cc_start: 0.6839 (m-80) cc_final: 0.6214 (m-80)
REVERT: A  138 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7598 (m-10)
  outliers start: 27
  outliers final: 17
  residues processed: 140
  average time/residue: 0.1813
  time to fit residues: 34.3080
Evaluate side-chains
  133 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   15 GLN
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  138 PHE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  424 ASP
Chi-restraints excluded: chain A residue  425 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 73 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
B  15 GLN
B 204 ASN
B 298 ASN
** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 348 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.5448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6934  Z= 0.217
  Angle     :  0.625  10.151   9417  Z= 0.307
  Chirality :  0.044   0.151   1027
  Planarity :  0.004   0.050   1224
  Dihedral  : 11.605 167.605    974
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 18.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 18.88 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -2.56 (0.27), residues: 848
  helix: -1.38 (0.26), residues: 361
  sheet: -2.42 (0.45), residues: 118
  loop : -1.61 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 344 
 HIS   0.009   0.001   HIS B 190 
 PHE   0.021   0.002   PHE A 351 
 TYR   0.011   0.001   TYR A 103 
 ARG   0.007   0.001   ARG A 214 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   15 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7287 (mp10)
REVERT: B  183 TYR cc_start: 0.6704 (m-80) cc_final: 0.6225 (m-80)
REVERT: A  138 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7475 (m-10)
  outliers start: 29
  outliers final: 18
  residues processed: 144
  average time/residue: 0.1827
  time to fit residues: 35.6047
Evaluate side-chains
  134 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   15 GLN
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  138 PHE
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  424 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   chunk 59 optimal weight:    0.4980
   chunk 45 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 37 optimal weight:    0.1980
   chunk 32 optimal weight:    9.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B  15 GLN
B 204 ASN
** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.5559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6934  Z= 0.186
  Angle     :  0.619  10.334   9417  Z= 0.300
  Chirality :  0.043   0.151   1027
  Planarity :  0.004   0.049   1224
  Dihedral  : 11.402 167.623    974
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 17.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 20.38 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -2.35 (0.28), residues: 848
  helix: -1.16 (0.27), residues: 361
  sheet: -2.36 (0.44), residues: 121
  loop : -1.51 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 344 
 HIS   0.009   0.001   HIS B 190 
 PHE   0.014   0.002   PHE B 133 
 TYR   0.012   0.001   TYR A 357 
 ARG   0.006   0.000   ARG A 214 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   15 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7425 (mp10)
REVERT: B  183 TYR cc_start: 0.6728 (m-80) cc_final: 0.6331 (m-80)
REVERT: A  169 PHE cc_start: 0.8372 (m-80) cc_final: 0.7765 (m-10)
  outliers start: 23
  outliers final: 19
  residues processed: 144
  average time/residue: 0.1840
  time to fit residues: 35.9552
Evaluate side-chains
  141 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 1.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   15 GLN
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  424 ASP
Chi-restraints excluded: chain A residue  425 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 55 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   chunk 63 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9980
   chunk 77 optimal weight:    8.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B  15 GLN
** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.5698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6934  Z= 0.186
  Angle     :  0.624  10.262   9417  Z= 0.300
  Chirality :  0.043   0.149   1027
  Planarity :  0.004   0.048   1224
  Dihedral  : 11.251 167.281    974
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 17.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 21.34 %
    Favored  : 74.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -2.19 (0.28), residues: 848
  helix: -1.09 (0.27), residues: 356
  sheet: -2.22 (0.44), residues: 121
  loop : -1.38 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP B 344 
 HIS   0.008   0.001   HIS B 190 
 PHE   0.012   0.001   PHE B 167 
 TYR   0.009   0.001   TYR A  24 
 ARG   0.006   0.000   ARG A 214 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 124
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   15 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7322 (mp10)
REVERT: B  183 TYR cc_start: 0.6734 (m-80) cc_final: 0.6364 (m-80)
REVERT: A   50 ASN cc_start: 0.7212 (t0) cc_final: 0.6997 (t0)
REVERT: A  169 PHE cc_start: 0.8386 (m-80) cc_final: 0.7777 (m-10)
REVERT: A  414 GLU cc_start: 0.5762 (OUTLIER) cc_final: 0.5197 (pt0)
  outliers start: 27
  outliers final: 20
  residues processed: 145
  average time/residue: 0.1761
  time to fit residues: 34.6770
Evaluate side-chains
  138 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   15 GLN
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  350 LYS
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  414 GLU
Chi-restraints excluded: chain A residue  424 ASP
Chi-restraints excluded: chain A residue  425 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 32 optimal weight:   10.0000
   chunk 59 optimal weight:    0.0980
   chunk 23 optimal weight:   10.0000
   chunk 68 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 49 optimal weight:    0.4980
   chunk 79 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.5782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6934  Z= 0.179
  Angle     :  0.611  10.444   9417  Z= 0.298
  Chirality :  0.043   0.150   1027
  Planarity :  0.004   0.046   1224
  Dihedral  : 11.054 161.293    974
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 20.11 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -2.14 (0.28), residues: 848
  helix: -1.01 (0.28), residues: 352
  sheet: -2.20 (0.44), residues: 124
  loop : -1.37 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.003   TRP B 344 
 HIS   0.008   0.001   HIS B 190 
 PHE   0.013   0.001   PHE A 351 
 TYR   0.013   0.001   TYR A 103 
 ARG   0.007   0.000   ARG B 320 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  183 TYR cc_start: 0.6710 (m-80) cc_final: 0.6346 (m-80)
REVERT: A   50 ASN cc_start: 0.7189 (t0) cc_final: 0.6982 (t0)
REVERT: A  352 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7194 (mmtt)
REVERT: A  370 LYS cc_start: 0.8335 (tptt) cc_final: 0.7921 (tttp)
REVERT: A  414 GLU cc_start: 0.5711 (OUTLIER) cc_final: 0.5197 (pt0)
  outliers start: 26
  outliers final: 21
  residues processed: 147
  average time/residue: 0.1784
  time to fit residues: 35.6039
Evaluate side-chains
  141 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  414 GLU
Chi-restraints excluded: chain A residue  424 ASP
Chi-restraints excluded: chain A residue  425 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 55 optimal weight:   10.0000
   chunk 83 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 66 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   chunk 70 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B 195 ASN
** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 216 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.5857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6934  Z= 0.175
  Angle     :  0.634  10.831   9417  Z= 0.301
  Chirality :  0.043   0.151   1027
  Planarity :  0.004   0.046   1224
  Dihedral  : 10.947 159.572    974
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 15.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.66 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -2.04 (0.28), residues: 848
  helix: -0.93 (0.28), residues: 350
  sheet: -2.05 (0.44), residues: 123
  loop : -1.35 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP B 344 
 HIS   0.007   0.001   HIS B   6 
 PHE   0.010   0.001   PHE B 167 
 TYR   0.012   0.001   TYR A 103 
 ARG   0.007   0.000   ARG B 320 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  183 TYR cc_start: 0.6679 (m-80) cc_final: 0.6356 (m-80)
REVERT: A   50 ASN cc_start: 0.7166 (t0) cc_final: 0.6958 (t0)
REVERT: A  352 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7050 (mmtt)
REVERT: A  370 LYS cc_start: 0.8324 (tptt) cc_final: 0.7945 (tttp)
REVERT: A  414 GLU cc_start: 0.5270 (OUTLIER) cc_final: 0.5014 (pt0)
  outliers start: 21
  outliers final: 19
  residues processed: 139
  average time/residue: 0.1878
  time to fit residues: 35.5244
Evaluate side-chains
  142 residues out of total 731 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  350 LYS
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  414 GLU
Chi-restraints excluded: chain A residue  425 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9980
   chunk 27 optimal weight:    8.9990
   chunk 68 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 12 optimal weight:    0.3980
   chunk 58 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.127540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.108200 restraints weight = 10165.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.112068 restraints weight = 5519.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.114755 restraints weight = 3622.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.5979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6934  Z= 0.269
  Angle     :  0.670  10.230   9417  Z= 0.323
  Chirality :  0.045   0.151   1027
  Planarity :  0.004   0.045   1224
  Dihedral  : 11.179 160.610    974
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 19.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 21.34 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -2.13 (0.28), residues: 848
  helix: -1.04 (0.27), residues: 358
  sheet: -2.06 (0.45), residues: 124
  loop : -1.39 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP B 344 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.021   0.002   PHE A 169 
 TYR   0.016   0.002   TYR A 103 
 ARG   0.007   0.001   ARG B 320 

===============================================================================
Job complete
usr+sys time: 1996.68 seconds
wall clock time: 37 minutes 19.62 seconds (2239.62 seconds total)