Starting phenix.real_space_refine
on Thu Nov 14 14:17:09 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggc_40002/11_2024/8ggc_40002.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggc_40002/11_2024/8ggc_40002.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/8ggc_40002/11_2024/8ggc_40002.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggc_40002/11_2024/8ggc_40002.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggc_40002/11_2024/8ggc_40002.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggc_40002/11_2024/8ggc_40002.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=   0.021
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      38      5.16       5
     C    4112      2.51       5
     N    1152      2.21       5
     O    1210      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 6515
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 2123
          Classifications: {'peptide': 294}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 287}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 321
          Unresolved non-hydrogen angles: 394
          Unresolved non-hydrogen dihedrals: 254
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 17, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 205
    Chain: "B"
      Number of atoms: 2452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2452
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 140
          Unresolved non-hydrogen angles: 172
          Unresolved non-hydrogen dihedrals: 108
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 109
    Chain: "G"
      Number of atoms: 348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 348
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 3
          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: 1545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 1545
          Classifications: {'peptide': 247}
          Incomplete info: {'truncation_to_alanine': 135}
          Link IDs: {'PTRANS': 5, 'TRANS': 241}
          Chain breaks: 6
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 467
          Unresolved non-hydrogen angles: 616
          Unresolved non-hydrogen dihedrals: 380
          Unresolved non-hydrogen chiralities: 67
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 222
    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: 5.59, per 1000 atoms: 0.86
  Number of scatterers: 6515
  At special positions: 0
  Unit cell: (84.1669, 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      38     16.00
     P       3     15.00
     O    1210      8.00
     N    1152      7.00
     C    4112      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: 1.92
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1770

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 8 sheets defined
      46.2% alpha, 14.2% 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: 3.570A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.506A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   MET A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ARG A  61 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 110
      removed outlier: 3.530A  pdb=" N   LEU A  99 " --> pdb=" O   ILE A  95 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLU A 104 " --> pdb=" O   LYS A 100 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA A 109 " --> pdb=" O   THR A 105 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   MET A 110 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 165
      removed outlier: 3.634A  pdb=" N   ARG A 165 " --> pdb=" O   ALA A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'A' and resid 196 through 200
      removed outlier: 4.190A  pdb=" N   CYS A 200 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 196 through 200'
    Processing helix  chain 'A' and resid 232 through 237
      removed outlier: 3.830A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.605A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.047A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 3.604A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.723A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 372
    Processing helix  chain 'A' and resid 373 through 383
      removed outlier: 4.313A  pdb=" N   ASN A 377 " --> pdb=" O   ARG A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 392
      removed outlier: 3.835A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   GLU A 392 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 25
      removed outlier: 3.515A  pdb=" N   ASN B  16 " --> pdb=" O   GLU B  12 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ARG B  19 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.895A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 3.938A  pdb=" N   ASN B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 24
      removed outlier: 3.622A  pdb=" N   GLN G  18 " --> pdb=" O   LYS G  14 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS G  20 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.510A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 32 through 55
      removed outlier: 3.507A  pdb=" N   PHE R  49 " --> pdb=" O   LEU R  45 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY R  50 " --> pdb=" O   ALA R  46 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 95
      removed outlier: 3.976A  pdb=" N   SER R  74 " --> pdb=" O   TYR R  70 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   LEU R  75 " --> pdb=" O   PHE R  71 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
      removed outlier: 3.877A  pdb=" N   ALA R  91 " --> pdb=" O   VAL R  87 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ALA R  92 " --> pdb=" O   PRO R  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.747A  pdb=" N   ASP R 113 " --> pdb=" O   TRP R 109 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   VAL R 114 " --> pdb=" O   THR R 110 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU R 115 " --> pdb=" O   SER R 111 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   CYS R 125 " --> pdb=" O   ILE R 121 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 152 through 172
      removed outlier: 3.763A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
      removed outlier: 3.999A  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 198 through 208
    Processing helix  chain 'R' and resid 208 through 235
      removed outlier: 3.502A  pdb=" N   VAL R 216 " --> pdb=" O   LEU R 212 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   PHE R 217 " --> pdb=" O   VAL R 213 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ARG R 221 " --> pdb=" O   PHE R 217 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL R 222 " --> pdb=" O   VAL R 218 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE R 233 " --> pdb=" O   GLN R 229 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 4.353A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.099A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 316
    Processing helix  chain 'R' and resid 316 through 322
      removed outlier: 4.450A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 213
      removed outlier: 3.546A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 9.380A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.621A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.741A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.453A  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: 3.901A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.896A  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: 7.028A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.008A  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: 4.243A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER B 160 " --> pdb=" O   CYS B 148 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.858A  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: 6.771A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.480A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.683A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)

    306 hydrogen bonds defined for protein.
    888 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: 2.19 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: 1094
        1.32 -     1.44: 1819
        1.44 -     1.57: 3662
        1.57 -     1.69: 6
        1.69 -     1.81: 52
  Bond restraints: 6633
  Sorted by residual:
  bond pdb=" CA  GLU A 392 "
       pdb=" C   GLU A 392 "
    ideal  model  delta    sigma   weight residual
    1.521  1.446  0.075 1.21e-02 6.83e+03 3.85e+01
  bond pdb=" CA  TYR A 391 "
       pdb=" C   TYR A 391 "
    ideal  model  delta    sigma   weight residual
    1.523  1.454  0.069 1.30e-02 5.92e+03 2.81e+01
  bond pdb=" N   LEU A 393 "
       pdb=" CA  LEU A 393 "
    ideal  model  delta    sigma   weight residual
    1.456  1.397  0.060 1.28e-02 6.10e+03 2.19e+01
  bond pdb=" N   GLU A 392 "
       pdb=" CA  GLU A 392 "
    ideal  model  delta    sigma   weight residual
    1.456  1.413  0.042 1.23e-02 6.61e+03 1.19e+01
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.586 -0.063 2.00e-02 2.50e+03 9.88e+00
  ... (remaining 6628 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 8901
        2.32 -     4.64: 127
        4.64 -     6.96: 22
        6.96 -     9.27: 11
        9.27 -    11.59: 7
  Bond angle restraints: 9068
  Sorted by residual:
  angle pdb=" N   GLN A 390 "
        pdb=" CA  GLN A 390 "
        pdb=" C   GLN A 390 "
      ideal   model   delta    sigma   weight residual
     111.28  121.54  -10.26 1.09e+00 8.42e-01 8.85e+01
  angle pdb=" N   LEU A 393 "
        pdb=" CA  LEU A 393 "
        pdb=" C   LEU A 393 "
      ideal   model   delta    sigma   weight residual
     110.10   98.51   11.59 1.49e+00 4.50e-01 6.05e+01
  angle pdb=" N   GLU A 392 "
        pdb=" CA  GLU A 392 "
        pdb=" C   GLU A 392 "
      ideal   model   delta    sigma   weight residual
     108.79   99.59    9.20 1.53e+00 4.27e-01 3.62e+01
  angle pdb=" N   PRO R 138 "
        pdb=" CA  PRO R 138 "
        pdb=" C   PRO R 138 "
      ideal   model   delta    sigma   weight residual
     113.53  121.74   -8.21 1.39e+00 5.18e-01 3.49e+01
  angle pdb=" C   ARG A 231 "
        pdb=" N   ARG A 232 "
        pdb=" CA  ARG A 232 "
      ideal   model   delta    sigma   weight residual
     122.68  114.35    8.33 1.47e+00 4.63e-01 3.21e+01
  ... (remaining 9063 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.35: 3751
       29.35 -    58.71: 95
       58.71 -    88.06: 5
       88.06 -   117.42: 4
      117.42 -   146.77: 2
  Dihedral angle restraints: 3857
    sinusoidal: 1143
      harmonic: 2714
  Sorted by residual:
  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  157.02  146.77     1      2.00e+01 2.50e-03 4.41e+01
  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  -15.68  120.28     1      2.00e+01 2.50e-03 3.61e+01
  dihedral pdb=" C4' GTP A 401 "
           pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     260.87  146.58  114.29     1      2.00e+01 2.50e-03 3.39e+01
  ... (remaining 3854 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 876
       0.055 -    0.109: 165
       0.109 -    0.164: 27
       0.164 -    0.219: 9
       0.219 -    0.273: 3
  Chirality restraints: 1080
  Sorted by residual:
  chirality pdb=" CA  GLU A 230 "
            pdb=" N   GLU A 230 "
            pdb=" C   GLU A 230 "
            pdb=" CB  GLU A 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" CA  VAL A 224 "
            pdb=" N   VAL A 224 "
            pdb=" C   VAL A 224 "
            pdb=" CB  VAL A 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  PRO R 138 "
            pdb=" N   PRO R 138 "
            pdb=" C   PRO R 138 "
            pdb=" CB  PRO R 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 1077 not shown)

  Planarity restraints: 1167
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 223 "   -0.019 2.00e-02 2.50e+03   3.84e-02 1.47e+01
        pdb=" C   ASP A 223 "    0.066 2.00e-02 2.50e+03
        pdb=" O   ASP A 223 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   VAL A 224 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 225 "   -0.014 2.00e-02 2.50e+03   2.87e-02 8.24e+00
        pdb=" C   GLY A 225 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLY A 225 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLY A 226 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 324 "   -0.011 2.00e-02 2.50e+03   2.28e-02 5.21e+00
        pdb=" C   ALA A 324 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA A 324 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   THR A 325 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1164 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1456
        2.78 -     3.31: 5922
        3.31 -     3.84: 9808
        3.84 -     4.37: 10609
        4.37 -     4.90: 19403
  Nonbonded interactions: 47198
  Sorted by model distance:
  nonbonded pdb=" CD1 ILE A 207 "
            pdb=" O   ASP A 223 "
     model   vdw
     2.250 3.460
  nonbonded pdb=" O   CYS A 162 "
            pdb=" OH  TYR A 169 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OG  SER B  97 "
            pdb=" OD2 ASP B 118 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.315 3.040
  ... (remaining 47193 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:             1.730
  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:             0.020
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.380
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
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   0.075   6633  Z= 0.277
  Angle     :  0.731  11.592   9068  Z= 0.424
  Chirality :  0.046   0.273   1080
  Planarity :  0.004   0.040   1167
  Dihedral  : 14.244 146.773   2087
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.12 %
    Favored  : 98.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.28), residues: 904
  helix:  1.58 (0.26), residues: 377
  sheet: -0.76 (0.41), residues: 176
  loop : -1.36 (0.30), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  99 
 HIS   0.004   0.001   HIS A 387 
 PHE   0.011   0.001   PHE A 208 
 TYR   0.016   0.001   TYR R 316 
 ARG   0.005   0.000   ARG G  27 

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.720 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 95
  average time/residue: 0.1740
  time to fit residues: 22.8108
Evaluate side-chains
  82 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 68 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 46 optimal weight:    0.0010
   chunk 36 optimal weight:    2.9990
   chunk 71 optimal weight:    8.9990
   chunk 27 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    1.3192

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6633  Z= 0.252
  Angle     :  0.525   8.014   9068  Z= 0.283
  Chirality :  0.043   0.162   1080
  Planarity :  0.003   0.035   1167
  Dihedral  :  8.829 131.796   1011
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  9.74 %
    Favored  : 89.14 %
  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:  0.49 (0.29), residues: 904
  helix:  2.06 (0.26), residues: 398
  sheet: -0.63 (0.44), residues: 165
  loop : -1.30 (0.31), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.011   0.001   HIS B 142 
 PHE   0.017   0.002   PHE A 290 
 TYR   0.013   0.001   TYR A 360 
 ARG   0.008   0.001   ARG G  27 

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 1.006 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 94
  average time/residue: 0.1520
  time to fit residues: 20.6637
Evaluate side-chains
  83 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 1.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  167 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0770
   chunk 68 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 89 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    1.6146

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

Flipped N/Q/H residues before XYZ refinement:
A 176 GLN
A 213 GLN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
B 220 GLN
R 229 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6633  Z= 0.283
  Angle     :  0.525   8.717   9068  Z= 0.280
  Chirality :  0.043   0.151   1080
  Planarity :  0.003   0.038   1167
  Dihedral  :  8.287 113.445   1009
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.92 %
    Favored  : 82.02 %
  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:  0.59 (0.29), residues: 904
  helix:  2.15 (0.26), residues: 397
  sheet: -0.51 (0.44), residues: 159
  loop : -1.27 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  99 
 HIS   0.009   0.002   HIS B 142 
 PHE   0.018   0.002   PHE B 241 
 TYR   0.015   0.001   TYR A 360 
 ARG   0.007   0.000   ARG A  38 

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.684 
Fit side-chains
REVERT: R  212 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6528 (mp)
  outliers start: 11
  outliers final: 5
  residues processed: 87
  average time/residue: 0.1476
  time to fit residues: 18.3355
Evaluate side-chains
  78 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 176 GLN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
R 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   6633  Z= 0.404
  Angle     :  0.598  11.498   9068  Z= 0.318
  Chirality :  0.045   0.163   1080
  Planarity :  0.004   0.045   1167
  Dihedral  :  8.169 110.273   1009
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 19.85 %
    Favored  : 77.34 %
  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:  0.35 (0.29), residues: 904
  helix:  2.01 (0.27), residues: 395
  sheet: -0.78 (0.43), residues: 161
  loop : -1.38 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 286 
 HIS   0.008   0.002   HIS B 142 
 PHE   0.023   0.002   PHE B 241 
 TYR   0.017   0.002   TYR A 360 
 ARG   0.008   0.001   ARG G  27 

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A  347 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6898 (ptp-110)
REVERT: R  212 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6674 (mp)
  outliers start: 15
  outliers final: 13
  residues processed: 87
  average time/residue: 0.1565
  time to fit residues: 18.9973
Evaluate side-chains
  83 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 176 GLN
B 142 HIS
B 340 ASN
R 229 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6633  Z= 0.210
  Angle     :  0.505  11.395   9068  Z= 0.264
  Chirality :  0.042   0.131   1080
  Planarity :  0.003   0.039   1167
  Dihedral  :  7.689 107.672   1009
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 21.16 %
    Favored  : 75.66 %
  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:  0.51 (0.29), residues: 904
  helix:  2.19 (0.27), residues: 396
  sheet: -0.73 (0.43), residues: 164
  loop : -1.35 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  99 
 HIS   0.008   0.001   HIS B 142 
 PHE   0.017   0.002   PHE A 376 
 TYR   0.013   0.001   TYR A 360 
 ARG   0.005   0.000   ARG A  38 

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.770 
Fit side-chains
REVERT: G   18 GLN cc_start: 0.9015 (tt0) cc_final: 0.8800 (tt0)
  outliers start: 17
  outliers final: 13
  residues processed: 87
  average time/residue: 0.1578
  time to fit residues: 19.5382
Evaluate side-chains
  85 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  387 HIS
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 79 optimal weight:    0.0020
   chunk 17 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.9792

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

Flipped N/Q/H residues before XYZ refinement:
A 176 GLN
B 142 HIS
R 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6633  Z= 0.190
  Angle     :  0.496  11.227   9068  Z= 0.258
  Chirality :  0.041   0.142   1080
  Planarity :  0.003   0.038   1167
  Dihedral  :  7.423 107.891   1009
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 20.79 %
    Favored  : 75.66 %
  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:  0.62 (0.29), residues: 904
  helix:  2.27 (0.27), residues: 397
  sheet: -0.71 (0.43), residues: 164
  loop : -1.28 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  99 
 HIS   0.007   0.001   HIS B 142 
 PHE   0.016   0.001   PHE A 376 
 TYR   0.012   0.001   TYR A 360 
 ARG   0.006   0.000   ARG A  38 

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A  209 GLU cc_start: 0.8525 (mt-10) cc_final: 0.7930 (mt-10)
REVERT: G   18 GLN cc_start: 0.9010 (tt0) cc_final: 0.8786 (tt0)
  outliers start: 19
  outliers final: 13
  residues processed: 89
  average time/residue: 0.1781
  time to fit residues: 22.0251
Evaluate side-chains
  84 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  387 HIS
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 74 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 35 optimal weight:    0.1980
   chunk 52 optimal weight:    0.0040
   overall best weight:    0.4592

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

Flipped N/Q/H residues before XYZ refinement:
A 176 GLN
B 142 HIS
R 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6633  Z= 0.123
  Angle     :  0.473  10.526   9068  Z= 0.244
  Chirality :  0.041   0.136   1080
  Planarity :  0.003   0.039   1167
  Dihedral  :  7.118 105.211   1009
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 21.72 %
    Favored  : 75.47 %
  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:  0.70 (0.29), residues: 904
  helix:  2.37 (0.27), residues: 398
  sheet: -0.76 (0.42), residues: 170
  loop : -1.23 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.021   0.001   HIS B 142 
 PHE   0.015   0.001   PHE R 208 
 TYR   0.011   0.001   TYR A 360 
 ARG   0.009   0.000   ARG G  27 

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.843 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7329 (ptp-170)
REVERT: B  258 ASP cc_start: 0.7108 (t70) cc_final: 0.6460 (t0)
  outliers start: 15
  outliers final: 9
  residues processed: 86
  average time/residue: 0.1938
  time to fit residues: 22.4710
Evaluate side-chains
  80 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  387 HIS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0970
   chunk 59 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 68 optimal weight:    6.9990
   chunk 79 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0060
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
A 176 GLN
B 142 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6633  Z= 0.123
  Angle     :  0.470  10.390   9068  Z= 0.241
  Chirality :  0.041   0.132   1080
  Planarity :  0.003   0.038   1167
  Dihedral  :  6.867 101.838   1009
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 20.97 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.29), residues: 904
  helix:  2.47 (0.27), residues: 399
  sheet: -0.75 (0.41), residues: 172
  loop : -1.20 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.014   0.001   HIS B 142 
 PHE   0.014   0.001   PHE R 208 
 TYR   0.011   0.001   TYR A 360 
 ARG   0.007   0.000   ARG A  38 

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7379 (ptp-170)
REVERT: B  258 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6502 (t0)
REVERT: R  229 GLN cc_start: 0.6649 (tp-100) cc_final: 0.6437 (tp-100)
  outliers start: 17
  outliers final: 12
  residues processed: 87
  average time/residue: 0.1763
  time to fit residues: 21.1768
Evaluate side-chains
  87 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  387 HIS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  258 ASP
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0040
   chunk 73 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 86 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.9594

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

Flipped N/Q/H residues before XYZ refinement:
A 176 GLN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6633  Z= 0.184
  Angle     :  0.491  10.751   9068  Z= 0.251
  Chirality :  0.041   0.132   1080
  Planarity :  0.003   0.037   1167
  Dihedral  :  6.820 102.026   1009
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 21.16 %
    Favored  : 75.66 %
  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:  0.82 (0.29), residues: 904
  helix:  2.50 (0.27), residues: 398
  sheet: -0.77 (0.42), residues: 172
  loop : -1.19 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.010   0.001   HIS B 142 
 PHE   0.016   0.001   PHE B 241 
 TYR   0.011   0.001   TYR A 360 
 ARG   0.007   0.000   ARG G  27 

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.866 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7404 (ptp-170)
REVERT: B  258 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6385 (t0)
  outliers start: 17
  outliers final: 15
  residues processed: 90
  average time/residue: 0.2251
  time to fit residues: 27.3510
Evaluate side-chains
  92 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  387 HIS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  258 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 90 optimal weight:    5.9990
   chunk 83 optimal weight:    0.9990
   chunk 72 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 55 optimal weight:    0.0970
   chunk 44 optimal weight:    0.8980
   chunk 57 optimal weight:    0.4980
   chunk 76 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6633  Z= 0.138
  Angle     :  0.470  10.251   9068  Z= 0.239
  Chirality :  0.040   0.130   1080
  Planarity :  0.003   0.036   1167
  Dihedral  :  6.514  99.877   1009
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 21.16 %
    Favored  : 75.66 %
  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:  0.84 (0.29), residues: 904
  helix:  2.55 (0.27), residues: 399
  sheet: -0.82 (0.42), residues: 170
  loop : -1.19 (0.31), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.008   0.001   HIS B 142 
 PHE   0.014   0.001   PHE A 376 
 TYR   0.011   0.001   TYR A 360 
 ARG   0.007   0.000   ARG G  27 

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7361 (ptp-170)
REVERT: B  258 ASP cc_start: 0.7019 (t70) cc_final: 0.6380 (t0)
  outliers start: 17
  outliers final: 14
  residues processed: 88
  average time/residue: 0.1700
  time to fit residues: 20.5180
Evaluate side-chains
  87 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  387 HIS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0770
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
A 176 GLN
R 229 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.156028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.119087 restraints weight = 9944.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.70
r_work: 0.3467 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6633  Z= 0.146
  Angle     :  0.483  10.270   9068  Z= 0.246
  Chirality :  0.040   0.129   1080
  Planarity :  0.003   0.043   1167
  Dihedral  :  6.368  99.465   1009
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 21.54 %
    Favored  : 75.09 %
  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:  0.90 (0.29), residues: 904
  helix:  2.59 (0.27), residues: 400
  sheet: -0.71 (0.42), residues: 166
  loop : -1.21 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.014   0.001   PHE A 376 
 TYR   0.011   0.001   TYR A 360 
 ARG   0.011   0.000   ARG G  27 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1757.45 seconds
wall clock time: 32 minutes 55.41 seconds (1975.41 seconds total)