Starting phenix.real_space_refine
on Sat Apr  6 02:02:08 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/04_2024/8uo3_42426_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/04_2024/8uo3_42426.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/04_2024/8uo3_42426.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/04_2024/8uo3_42426.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/04_2024/8uo3_42426_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo3_42426/04_2024/8uo3_42426_updated.pdb"
  }
  resolution = 3.5
  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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      33      5.16       5
     C    4187      2.51       5
     N    1204      2.21       5
     O    1222      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib"
  Total number of atoms: 6650
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2559
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 359, 2559
          Classifications: {'peptide': 359}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 115}
          Link IDs: {'PTRANS': 13, 'TRANS': 345}
          Chain breaks: 3
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 425
          Unresolved non-hydrogen angles: 531
          Unresolved non-hydrogen dihedrals: 337
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 20, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 286
    Chain: "B"
      Number of atoms: 2418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2418
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 183
          Unresolved non-hydrogen angles: 225
          Unresolved non-hydrogen dihedrals: 141
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 8, 'ARG:plan': 10, 'ASN:plan1': 5, 'ASP:plan': 9}
          Unresolved non-hydrogen planarities: 148
    Chain: "G"
      Number of atoms: 352
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 352
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 90
          Unresolved non-hydrogen dihedrals: 64
          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': 2}
          Unresolved non-hydrogen planarities: 39
    Chain: "R"
      Number of atoms: 1273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1273
          Classifications: {'peptide': 224}
          Incomplete info: {'truncation_to_alanine': 155}
          Link IDs: {'PTRANS': 6, 'TRANS': 217}
          Chain breaks: 7
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 540
          Unresolved non-hydrogen angles: 714
          Unresolved non-hydrogen dihedrals: 440
          Unresolved non-hydrogen chiralities: 81
          Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 11, 'GLU:plan': 5, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 255
    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}
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.70, per 1000 atoms: 0.71
  Number of scatterers: 6650
  At special positions: 0
  Unit cell: (82.4315, 134.493, 102.389, 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      33     16.00
     P       3     15.00
     Mg      1     11.99
     O    1222      8.00
     N    1204      7.00
     C    4187      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: 2.51
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1858

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      31 helices and 8 sheets defined
      44.2% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 4.097A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   TYR A  37 " --> pdb=" O   ASP A  33 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 64
      removed outlier: 3.708A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A  62 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 108
      removed outlier: 3.704A  pdb=" N   ILE A  95 " --> pdb=" O   LYS A  91 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LYS A  96 " --> pdb=" O   VAL A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 112
      No H-bonds generated for 'chain 'A' and resid 110 through 112'
    Processing helix  chain 'A' and resid 125 through 134
      removed outlier: 3.897A  pdb=" N   ASP A 129 " --> pdb=" O   GLN A 125 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   TYR A 130 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 155
      removed outlier: 3.587A  pdb=" N   GLU A 148 " --> pdb=" O   PRO A 144 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   HIS A 149 " --> pdb=" O   GLU A 145 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LYS A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ALA A 152 " --> pdb=" O   GLU A 148 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU A 153 " --> pdb=" O   HIS A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 164
    Processing helix  chain 'A' and resid 175 through 186
      removed outlier: 3.550A  pdb=" N   LYS A 181 " --> pdb=" O   TYR A 177 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ILE A 182 " --> pdb=" O   PHE A 178 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   ASP A 183 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   VAL A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 198
    Processing helix  chain 'A' and resid 233 through 237
      removed outlier: 4.033A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 277
      removed outlier: 3.772A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 302
    Processing helix  chain 'A' and resid 308 through 311
      No H-bonds generated for 'chain 'A' and resid 308 through 311'
    Processing helix  chain 'A' and resid 313 through 317
      removed outlier: 3.715A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 317'
    Processing helix  chain 'A' and resid 332 through 351
      removed outlier: 3.758A  pdb=" N   ARG A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ALA A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   TYR A 339 " --> pdb=" O   THR A 335 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   PHE A 340 " --> pdb=" O   ARG A 336 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 381
      removed outlier: 3.815A  pdb=" N   ARG A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL A 375 " --> pdb=" O   ASN A 371 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   ASN A 377 " --> pdb=" O   ARG A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 391
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.775A  pdb=" N   ASN B  16 " --> pdb=" O   GLU B  12 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   GLN B  17 " --> pdb=" O   GLN B  13 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ALA B  24 " --> pdb=" O   ASP B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 33
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'B' and resid 129 through 131
      No H-bonds generated for 'chain 'B' and resid 129 through 131'
    Processing helix  chain 'G' and resid 8 through 23
      removed outlier: 4.003A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLU G  22 " --> pdb=" O   GLN G  18 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 30 through 43
      removed outlier: 4.438A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLU G  42 " --> pdb=" O   MET G  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 36 through 57
      removed outlier: 3.990A  pdb=" N   ILE R  47 " --> pdb=" O   ILE R  43 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   VAL R  48 " --> pdb=" O   VAL R  44 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   PHE R  49 " --> pdb=" O   LEU R  45 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLY R  50 " --> pdb=" O   ALA R  46 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 94
      removed outlier: 4.028A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER R  74 " --> pdb=" O   TYR R  70 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   LEU R  75 " --> pdb=" O   PHE R  71 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA R  76 " --> pdb=" O   ILE R  72 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   VAL R  81 " --> pdb=" O   CYS R  77 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLY R  83 " --> pdb=" O   ASP R  79 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   LEU R  84 " --> pdb=" O   LEU R  80 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 105 through 136
      removed outlier: 3.513A  pdb=" N   TRP R 109 " --> pdb=" O   TRP R 105 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   THR R 110 " --> pdb=" O   CYS R 106 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 151 through 171
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 179 through 185
    Processing helix  chain 'R' and resid 199 through 207
    Processing helix  chain 'R' and resid 209 through 231
      removed outlier: 3.533A  pdb=" N   PHE R 217 " --> pdb=" O   VAL R 213 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU R 230 " --> pdb=" O   ALA R 226 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLN R 231 " --> pdb=" O   LYS R 227 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 295
      removed outlier: 4.336A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.615A  pdb=" N   VAL R 295 " --> pdb=" O   ILE R 291 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 306 through 326
      removed outlier: 4.921A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing sheet with id=  A, first strand: chain 'A' and resid 286 through 292
      removed outlier: 3.894A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU A  44 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   ASN A 218 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 8.804A  pdb=" N   LEU A  43 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   HIS A 220 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.186A  pdb=" N   LEU A  45 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.082A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   SER B  72 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 111 through 113
      removed outlier: 3.523A  pdb=" N   VAL B 112 " --> pdb=" O   TYR B 124 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 178 through 181
      removed outlier: 3.768A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER B 160 " --> pdb=" O   CYS B 148 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 208 through 212
      removed outlier: 3.528A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.769A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.882A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.751A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU B 308 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 318 through 320
      removed outlier: 3.606A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)

    287 hydrogen bonds defined for protein.
    846 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: 1.86

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1376
        1.33 -     1.45: 1590
        1.45 -     1.57: 3754
        1.57 -     1.69: 5
        1.69 -     1.81: 45
  Bond restraints: 6770
  Sorted by residual:
  bond pdb=" C   VAL A 375 "
       pdb=" O   VAL A 375 "
    ideal  model  delta    sigma   weight residual
    1.237  1.290 -0.053 1.17e-02 7.31e+03 2.04e+01
  bond pdb=" C   ARG A 374 "
       pdb=" O   ARG A 374 "
    ideal  model  delta    sigma   weight residual
    1.235  1.290 -0.055 1.40e-02 5.10e+03 1.57e+01
  bond pdb=" N   VAL R 222 "
       pdb=" CA  VAL R 222 "
    ideal  model  delta    sigma   weight residual
    1.461  1.500 -0.039 1.19e-02 7.06e+03 1.07e+01
  bond pdb=" N   VAL R 216 "
       pdb=" CA  VAL R 216 "
    ideal  model  delta    sigma   weight residual
    1.461  1.499 -0.039 1.19e-02 7.06e+03 1.06e+01
  bond pdb=" N   ARG A 374 "
       pdb=" CA  ARG A 374 "
    ideal  model  delta    sigma   weight residual
    1.458  1.498 -0.040 1.28e-02 6.10e+03 9.90e+00
  ... (remaining 6765 not shown)

  Histogram of bond angle deviations from ideal:
       99.32 -   106.31: 153
      106.31 -   113.30: 3726
      113.30 -   120.28: 2423
      120.28 -   127.27: 2898
      127.27 -   134.26: 72
  Bond angle restraints: 9272
  Sorted by residual:
  angle pdb=" N   TYR R 199 "
        pdb=" CA  TYR R 199 "
        pdb=" C   TYR R 199 "
      ideal   model   delta    sigma   weight residual
     111.28  103.70    7.58 1.09e+00 8.42e-01 4.84e+01
  angle pdb=" N   GLN A 384 "
        pdb=" CA  GLN A 384 "
        pdb=" C   GLN A 384 "
      ideal   model   delta    sigma   weight residual
     111.71  105.11    6.60 1.15e+00 7.56e-01 3.30e+01
  angle pdb=" N   ASN R 196 "
        pdb=" CA  ASN R 196 "
        pdb=" C   ASN R 196 "
      ideal   model   delta    sigma   weight residual
     109.65  101.00    8.65 1.56e+00 4.11e-01 3.07e+01
  angle pdb=" C   THR R 164 "
        pdb=" N   SER R 165 "
        pdb=" CA  SER R 165 "
      ideal   model   delta    sigma   weight residual
     122.54  113.57    8.97 1.65e+00 3.67e-01 2.96e+01
  angle pdb=" C   TYR R 209 "
        pdb=" N   VAL R 210 "
        pdb=" CA  VAL R 210 "
      ideal   model   delta    sigma   weight residual
     120.24  116.93    3.31 6.30e-01 2.52e+00 2.76e+01
  ... (remaining 9267 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.24: 3890
       35.24 -    70.48: 54
       70.48 -   105.71: 4
      105.71 -   140.95: 3
      140.95 -   176.19: 2
  Dihedral angle restraints: 3953
    sinusoidal: 1106
      harmonic: 2847
  Sorted by residual:
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -71.60  176.19     1      2.00e+01 2.50e-03 4.79e+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  109.41  151.46     1      2.00e+01 2.50e-03 4.51e+01
  dihedral pdb=" O3A GTP A 401 "
           pdb=" O3B GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PG  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     303.79  174.17  129.62     1      2.00e+01 2.50e-03 3.93e+01
  ... (remaining 3950 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 851
       0.056 -    0.111: 178
       0.111 -    0.167: 56
       0.167 -    0.223: 20
       0.223 -    0.278: 6
  Chirality restraints: 1111
  Sorted by residual:
  chirality pdb=" CA  ILE G   9 "
            pdb=" N   ILE G   9 "
            pdb=" C   ILE G   9 "
            pdb=" CB  ILE G   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  ILE A 382 "
            pdb=" N   ILE A 382 "
            pdb=" C   ILE A 382 "
            pdb=" CB  ILE A 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" C3' GTP A 401 "
            pdb=" C2' GTP A 401 "
            pdb=" C4' GTP A 401 "
            pdb=" O3' GTP A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.73    0.26 2.00e-01 2.50e+01 1.66e+00
  ... (remaining 1108 not shown)

  Planarity restraints: 1198
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 373 "    0.023 2.00e-02 2.50e+03   4.46e-02 1.99e+01
        pdb=" C   ARG A 373 "   -0.077 2.00e-02 2.50e+03
        pdb=" O   ARG A 373 "    0.028 2.00e-02 2.50e+03
        pdb=" N   ARG A 374 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 195 "   -0.020 2.00e-02 2.50e+03   4.05e-02 1.64e+01
        pdb=" C   THR R 195 "    0.070 2.00e-02 2.50e+03
        pdb=" O   THR R 195 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   ASN R 196 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 153 "   -0.018 2.00e-02 2.50e+03   3.68e-02 1.36e+01
        pdb=" C   ILE R 153 "    0.064 2.00e-02 2.50e+03
        pdb=" O   ILE R 153 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   ILE R 154 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1195 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1395
        2.78 -     3.31: 6313
        3.31 -     3.84: 9966
        3.84 -     4.37: 10648
        4.37 -     4.90: 19115
  Nonbonded interactions: 47437
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.246 2.440
  nonbonded pdb=" O   ASN A 377 "
            pdb=" CG  ARG A 380 "
     model   vdw
     2.259 3.440
  nonbonded pdb=" OG1 THR B 184 "
            pdb=" OD2 ASP B 205 "
     model   vdw
     2.271 2.440
  nonbonded pdb=" O   HIS R 172 "
            pdb=" C   TRP R 173 "
     model   vdw
     2.273 3.270
  nonbonded pdb=" OD1 ASP A 223 "
            pdb=" N   VAL A 224 "
     model   vdw
     2.275 2.520
  ... (remaining 47432 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:             1.900
  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:          8.370
  Check model and map are aligned:         0.110
  Set scattering table:                    0.060
  Process input model:                     23.980
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   6770  Z= 0.425
  Angle     :  0.871  10.363   9272  Z= 0.604
  Chirality :  0.059   0.278   1111
  Planarity :  0.005   0.119   1198
  Dihedral  : 14.929 176.189   2095
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.39 %
    Favored  : 99.41 %
  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:  0.16 (0.27), residues: 949
  helix:  2.09 (0.27), residues: 363
  sheet: -1.17 (0.38), residues: 174
  loop : -1.13 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 154 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.024   0.001   PHE A 376 
 TYR   0.014   0.001   TYR R 326 
 ARG   0.002   0.000   ARG A 374 

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.763 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1681
  time to fit residues: 18.8774
Evaluate side-chains
  66 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 72 optimal weight:    0.2980
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.2980
   chunk 38 optimal weight:   10.0000
   chunk 74 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6770  Z= 0.190
  Angle     :  0.493   6.640   9272  Z= 0.266
  Chirality :  0.042   0.154   1111
  Planarity :  0.003   0.029   1198
  Dihedral  :  9.943 161.724   1054
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  9.27 %
    Favored  : 90.14 %
  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:  0.13 (0.27), residues: 949
  helix:  1.74 (0.26), residues: 396
  sheet: -1.05 (0.39), residues: 168
  loop : -1.13 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 313 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.012   0.001   TYR R 316 
 ARG   0.002   0.000   ARG A 380 

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.782 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 69
  average time/residue: 0.1517
  time to fit residues: 15.0798
Evaluate side-chains
  63 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue  173 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 58 optimal weight:    0.3980
   chunk 23 optimal weight:    4.9990
   chunk 86 optimal weight:    0.0970
   chunk 93 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6770  Z= 0.156
  Angle     :  0.442   5.537   9272  Z= 0.237
  Chirality :  0.040   0.143   1111
  Planarity :  0.003   0.029   1198
  Dihedral  :  8.498 151.081   1054
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 11.24 %
    Favored  : 87.57 %
  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:  0.31 (0.27), residues: 949
  helix:  2.02 (0.26), residues: 398
  sheet: -1.14 (0.38), residues: 174
  loop : -1.10 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 313 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.010   0.001   PHE B 241 
 TYR   0.014   0.001   TYR R 219 
 ARG   0.001   0.000   ARG A 380 

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.680 
Fit side-chains
REVERT: B   95 LEU cc_start: 0.9110 (mt) cc_final: 0.8890 (mt)
REVERT: R  194 PHE cc_start: 0.7743 (m-80) cc_final: 0.7226 (m-80)
  outliers start: 6
  outliers final: 4
  residues processed: 68
  average time/residue: 0.1420
  time to fit residues: 14.3694
Evaluate side-chains
  67 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain R residue  326 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 85 optimal weight:    0.0030
   chunk 64 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 9 optimal weight:    0.0570
   chunk 41 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0000
   chunk 91 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0050
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.1526

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

Flipped N/Q/H residues before XYZ refinement:
A  64 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.023   6770  Z= 0.101
  Angle     :  0.410   5.791   9272  Z= 0.217
  Chirality :  0.039   0.142   1111
  Planarity :  0.002   0.028   1198
  Dihedral  :  7.414 138.849   1054
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 12.82 %
    Favored  : 86.00 %
  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:  0.55 (0.27), residues: 949
  helix:  2.22 (0.26), residues: 408
  sheet: -0.98 (0.39), residues: 164
  loop : -1.10 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 313 
 HIS   0.002   0.000   HIS A 357 
 PHE   0.014   0.001   PHE R 139 
 TYR   0.011   0.001   TYR R 219 
 ARG   0.002   0.000   ARG A 380 

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.753 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 70
  average time/residue: 0.1444
  time to fit residues: 14.9648
Evaluate side-chains
  67 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain R residue  326 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 78 optimal weight:    0.0000
   chunk 63 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 82 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
A  64 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6770  Z= 0.144
  Angle     :  0.422   5.669   9272  Z= 0.225
  Chirality :  0.040   0.157   1111
  Planarity :  0.002   0.027   1198
  Dihedral  :  7.118 134.788   1054
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.00 %
    Favored  : 83.83 %
  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:  0.72 (0.28), residues: 949
  helix:  2.38 (0.26), residues: 408
  sheet: -0.75 (0.40), residues: 159
  loop : -1.10 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 313 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.010   0.001   PHE B 241 
 TYR   0.008   0.001   TYR R 219 
 ARG   0.002   0.000   ARG A 380 

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.752 
Fit side-chains
REVERT: B  292 PHE cc_start: 0.8597 (m-10) cc_final: 0.8286 (m-10)
  outliers start: 11
  outliers final: 6
  residues processed: 75
  average time/residue: 0.1337
  time to fit residues: 14.8061
Evaluate side-chains
  72 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue  326 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0370
   chunk 18 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0870
   chunk 76 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0870
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.3414

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

Flipped N/Q/H residues before XYZ refinement:
A  64 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6770  Z= 0.108
  Angle     :  0.413   7.161   9272  Z= 0.217
  Chirality :  0.039   0.142   1111
  Planarity :  0.002   0.026   1198
  Dihedral  :  6.705 128.403   1054
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.99 %
    Favored  : 83.43 %
  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 (0.28), residues: 949
  helix:  2.45 (0.26), residues: 408
  sheet: -0.70 (0.41), residues: 161
  loop : -1.09 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 313 
 HIS   0.002   0.000   HIS B 142 
 PHE   0.015   0.001   PHE R 194 
 TYR   0.009   0.001   TYR R 219 
 ARG   0.001   0.000   ARG A 380 

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.822 
Fit side-chains
REVERT: B  292 PHE cc_start: 0.8645 (m-10) cc_final: 0.8346 (m-10)
REVERT: R  194 PHE cc_start: 0.7563 (m-80) cc_final: 0.7194 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 73
  average time/residue: 0.1418
  time to fit residues: 15.2991
Evaluate side-chains
  70 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  326 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   chunk 67 optimal weight:    8.9990
   chunk 77 optimal weight:   20.0000
   chunk 51 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   chunk 57 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6770  Z= 0.321
  Angle     :  0.520   7.294   9272  Z= 0.279
  Chirality :  0.043   0.154   1111
  Planarity :  0.003   0.028   1198
  Dihedral  :  7.164 130.833   1054
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.78 %
    Favored  : 82.05 %
  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:  0.54 (0.28), residues: 949
  helix:  2.25 (0.27), residues: 402
  sheet: -0.80 (0.39), residues: 169
  loop : -1.19 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  63 
 HIS   0.007   0.001   HIS B 183 
 PHE   0.019   0.002   PHE B 241 
 TYR   0.012   0.001   TYR A 360 
 ARG   0.004   0.000   ARG B 314 

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.726 
Fit side-chains
REVERT: B  292 PHE cc_start: 0.8924 (m-10) cc_final: 0.8492 (m-10)
REVERT: R  194 PHE cc_start: 0.7495 (m-80) cc_final: 0.6998 (m-80)
  outliers start: 11
  outliers final: 10
  residues processed: 74
  average time/residue: 0.1400
  time to fit residues: 15.3911
Evaluate side-chains
  73 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue  326 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 54 optimal weight:    0.1980
   chunk 27 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0570
   chunk 8 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 80 optimal weight:    7.9990
   overall best weight:    0.4900

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A  64 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6770  Z= 0.132
  Angle     :  0.436   6.302   9272  Z= 0.231
  Chirality :  0.040   0.142   1111
  Planarity :  0.002   0.028   1198
  Dihedral  :  6.498 121.803   1054
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.37 %
    Favored  : 81.46 %
  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 (0.28), residues: 949
  helix:  2.44 (0.27), residues: 407
  sheet: -0.79 (0.39), residues: 170
  loop : -1.19 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 154 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.009   0.001   PHE R 139 
 TYR   0.009   0.001   TYR R 219 
 ARG   0.001   0.000   ARG A 380 

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.872 
Fit side-chains
REVERT: B  292 PHE cc_start: 0.8862 (m-10) cc_final: 0.8446 (m-10)
REVERT: R  194 PHE cc_start: 0.7584 (m-80) cc_final: 0.7052 (m-80)
  outliers start: 11
  outliers final: 7
  residues processed: 70
  average time/residue: 0.1419
  time to fit residues: 15.0508
Evaluate side-chains
  70 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 85 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 67 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 80 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A  64 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6770  Z= 0.314
  Angle     :  0.509   6.538   9272  Z= 0.272
  Chirality :  0.042   0.152   1111
  Planarity :  0.003   0.029   1198
  Dihedral  :  6.827 123.882   1054
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.96 %
    Favored  : 81.07 %
  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:  0.50 (0.28), residues: 949
  helix:  2.19 (0.27), residues: 407
  sheet: -0.86 (0.39), residues: 169
  loop : -1.21 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  63 
 HIS   0.006   0.001   HIS B 183 
 PHE   0.016   0.002   PHE B 241 
 TYR   0.010   0.001   TYR B 111 
 ARG   0.003   0.000   ARG B 219 

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.789 
Fit side-chains
REVERT: B  142 HIS cc_start: 0.8951 (OUTLIER) cc_final: 0.8682 (t-170)
REVERT: B  292 PHE cc_start: 0.8952 (m-10) cc_final: 0.8557 (m-10)
REVERT: R  194 PHE cc_start: 0.7548 (m-80) cc_final: 0.6966 (m-80)
  outliers start: 10
  outliers final: 7
  residues processed: 70
  average time/residue: 0.1367
  time to fit residues: 14.4152
Evaluate side-chains
  71 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 94 optimal weight:    0.0970
   chunk 87 optimal weight:    1.9990
   chunk 75 optimal weight:   20.0000
   chunk 7 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 23 optimal weight:    0.1980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A  64 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6770  Z= 0.143
  Angle     :  0.441   6.267   9272  Z= 0.234
  Chirality :  0.040   0.145   1111
  Planarity :  0.003   0.028   1198
  Dihedral  :  6.358 117.546   1054
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 17.95 %
    Favored  : 80.47 %
  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:  0.64 (0.28), residues: 949
  helix:  2.38 (0.27), residues: 402
  sheet: -0.75 (0.39), residues: 169
  loop : -1.19 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 154 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.008   0.001   TYR R 219 
 ARG   0.001   0.000   ARG A 380 

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.815 
Fit side-chains
REVERT: B  292 PHE cc_start: 0.8923 (m-10) cc_final: 0.8478 (m-10)
REVERT: R  194 PHE cc_start: 0.7491 (m-80) cc_final: 0.6899 (m-80)
  outliers start: 8
  outliers final: 7
  residues processed: 70
  average time/residue: 0.1383
  time to fit residues: 14.4189
Evaluate side-chains
  72 residues out of total 847 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0270
   chunk 20 optimal weight:    0.1980
   chunk 75 optimal weight:   20.0000
   chunk 31 optimal weight:    0.9990
   chunk 77 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.6240

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

Flipped N/Q/H residues before XYZ refinement:
A  64 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.136949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.106286 restraints weight = 11908.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.109312 restraints weight = 6505.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.111283 restraints weight = 4539.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6770  Z= 0.142
  Angle     :  0.433   5.976   9272  Z= 0.228
  Chirality :  0.040   0.140   1111
  Planarity :  0.002   0.028   1198
  Dihedral  :  6.022 111.263   1054
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 17.95 %
    Favored  : 80.28 %
  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:  0.74 (0.28), residues: 949
  helix:  2.51 (0.27), residues: 402
  sheet: -0.71 (0.41), residues: 159
  loop : -1.20 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 154 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.009   0.001   TYR R 219 
 ARG   0.001   0.000   ARG A 380 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1503.64 seconds
wall clock time: 28 minutes 2.68 seconds (1682.68 seconds total)