Starting phenix.real_space_refine
on Thu Jan 16 18:54:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8utr_42547/01_2025/8utr_42547.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8utr_42547/01_2025/8utr_42547.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8utr_42547/01_2025/8utr_42547.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8utr_42547/01_2025/8utr_42547.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8utr_42547/01_2025/8utr_42547.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8utr_42547/01_2025/8utr_42547.cif"
  }
  resolution = 3.3
  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=   0.002
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       7      5.49       5
     Mg      1      5.21       5
     S      66      5.16       5
     C    6118      2.51       5
     N    1679      2.21       5
     O    1921      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 9792
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "K"
      Number of atoms: 2798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 2798
          Classifications: {'peptide': 357}
          Link IDs: {'PTRANS': 12, 'TRANS': 344}
    Chain: "A"
      Number of atoms: 3437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 440, 3437
          Classifications: {'peptide': 440}
          Link IDs: {'PTRANS': 20, 'TRANS': 419}
    Chain: "B"
      Number of atoms: 3407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 433, 3407
          Classifications: {'peptide': 433}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412}
    Chain: "K"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 62
          Unusual residues: {'TA1': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" N   THR B 429 " occ=0.50
      ... (5 atoms not shown)
      pdb=" CG2 THR B 429 " occ=0.50
    residue:
      pdb=" N   ALA B 430 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  ALA B 430 " occ=0.50
    residue:
      pdb=" N   ASP B 431 " occ=0.50
      ... (6 atoms not shown)
      pdb=" OD2 ASP B 431 " occ=0.50
    residue:
      pdb=" N   GLU B 432 " occ=0.50
      ... (7 atoms not shown)
      pdb=" OE2 GLU B 432 " occ=0.50
    residue:
      pdb=" N   GLN B 433 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NE2 GLN B 433 " occ=0.50
  Time building chain proxies: 7.47, per 1000 atoms: 0.76
  Number of scatterers: 9792
  At special positions: 0
  Unit cell: (108.876, 74.272, 111.408, 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      66     16.00
     P       7     15.00
     Mg      1     11.99
     O    1921      8.00
     N    1679      7.00
     C    6118      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: 2.55
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2288

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 10 sheets defined
      48.0% alpha, 20.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'K' and resid 16 through 22
    Processing helix  chain 'K' and resid 69 through 77
    Processing helix  chain 'K' and resid 77 through 87
    Processing helix  chain 'K' and resid 103 through 108
    Processing helix  chain 'K' and resid 117 through 134
      removed outlier: 3.545A  pdb=" N   GLN K 121 " --> pdb=" O   GLY K 117 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 188 through 202
      removed outlier: 3.547A  pdb=" N   ALA K 202 " --> pdb=" O   SER K 198 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 262 through 296
      Proline residue:  K 292  - end of helix
    Processing helix  chain 'K' and resid 305 through 308
      removed outlier: 3.861A  pdb=" N   ASP K 308 " --> pdb=" O   PRO K 305 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 305 through 308'
    Processing helix  chain 'K' and resid 309 through 315
    Processing helix  chain 'K' and resid 334 through 336
      No H-bonds generated for 'chain 'K' and resid 334 through 336'
    Processing helix  chain 'K' and resid 337 through 349
    Processing helix  chain 'A' and resid 10 through 29
    Processing helix  chain 'A' and resid 36 through 43
      removed outlier: 4.216A  pdb=" N   LYS A  40 " --> pdb=" O   MET A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 80
      removed outlier: 4.633A  pdb=" N   ILE A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   GLU A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   VAL A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 114 through 128
    Processing helix  chain 'A' and resid 143 through 161
    Processing helix  chain 'A' and resid 182 through 190
      removed outlier: 3.625A  pdb=" N   ASN A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 197
      removed outlier: 3.573A  pdb=" N   HIS A 197 " --> pdb=" O   THR A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 223 through 240
      removed outlier: 3.766A  pdb=" N   LEU A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 243
      No H-bonds generated for 'chain 'A' and resid 241 through 243'
    Processing helix  chain 'A' and resid 251 through 260
      removed outlier: 4.076A  pdb=" N   VAL A 260 " --> pdb=" O   GLN A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 266
      removed outlier: 4.154A  pdb=" N   HIS A 266 " --> pdb=" O   PRO A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 3.984A  pdb=" N   TYR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 297
      removed outlier: 3.881A  pdb=" N   PHE A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLU A 297 " --> pdb=" O   ASN A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 301
      removed outlier: 3.622A  pdb=" N   GLN A 301 " --> pdb=" O   PRO A 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 298 through 301'
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 338
      removed outlier: 3.597A  pdb=" N   THR A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LYS A 338 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 400
      removed outlier: 3.782A  pdb=" N   ALA A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   LEU A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 4.077A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 436
      removed outlier: 4.167A  pdb=" N   PHE A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 29
    Processing helix  chain 'B' and resid 40 through 45
      removed outlier: 3.725A  pdb=" N   GLN B  43 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 49
    Processing helix  chain 'B' and resid 70 through 78
    Processing helix  chain 'B' and resid 86 through 88
      No H-bonds generated for 'chain 'B' and resid 86 through 88'
    Processing helix  chain 'B' and resid 100 through 106
    Processing helix  chain 'B' and resid 108 through 126
      removed outlier: 3.711A  pdb=" N   LEU B 112 " --> pdb=" O   GLU B 108 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   ASP B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   SER B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   SER B 126 " --> pdb=" O   LYS B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 159
      removed outlier: 3.541A  pdb=" N   GLY B 146 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 195
      removed outlier: 3.651A  pdb=" N   ASN B 184 " --> pdb=" O   VAL B 180 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLN B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 214
    Processing helix  chain 'B' and resid 221 through 237
      removed outlier: 3.662A  pdb=" N   LEU B 225 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   THR B 237 " --> pdb=" O   MET B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 241
    Processing helix  chain 'B' and resid 249 through 258
    Processing helix  chain 'B' and resid 285 through 294
    Processing helix  chain 'B' and resid 295 through 299
    Processing helix  chain 'B' and resid 304 through 308
    Processing helix  chain 'B' and resid 322 through 337
      removed outlier: 3.530A  pdb=" N   VAL B 326 " --> pdb=" O   SER B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 341
      removed outlier: 3.506A  pdb=" N   PHE B 341 " --> pdb=" O   SER B 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 338 through 341'
    Processing helix  chain 'B' and resid 373 through 390
      removed outlier: 4.266A  pdb=" N   LEU B 377 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   PHE B 378 " --> pdb=" O   ILE B 374 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 400
      removed outlier: 4.303A  pdb=" N   TYR B 398 " --> pdb=" O   PHE B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 425
      removed outlier: 4.378A  pdb=" N   PHE B 408 " --> pdb=" O   ASP B 404 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   THR B 409 " --> pdb=" O   GLU B 405 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   TYR B 425 " --> pdb=" O   GLU B 421 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 54 through 57
      removed outlier: 8.520A  pdb=" N   TYR K  54 " --> pdb=" O   VAL K   6 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   VAL K   8 " --> pdb=" O   TYR K  54 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   TYR K  56 " --> pdb=" O   VAL K   8 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL K  10 " --> pdb=" O   TYR K  56 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   LYS K   7 " --> pdb=" O   MET K 327 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   ALA K 329 " --> pdb=" O   LYS K   7 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ALA K   9 " --> pdb=" O   ALA K 329 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   LEU K 331 " --> pdb=" O   ALA K   9 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ARG K  11 " --> pdb=" O   LEU K 331 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ARG K 324 " --> pdb=" O   ASN K  90 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   CYS K  92 " --> pdb=" O   ARG K 324 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA K 326 " --> pdb=" O   CYS K  92 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   VAL K  91 " --> pdb=" O   SER K 245 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   VAL K 247 " --> pdb=" O   VAL K  91 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ILE K  93 " --> pdb=" O   VAL K 247 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   THR K 238 " --> pdb=" O   ARG K 229 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ARG K 229 " --> pdb=" O   THR K 238 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LYS K 240 " --> pdb=" O   GLN K 227 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 54 through 57
      removed outlier: 8.520A  pdb=" N   TYR K  54 " --> pdb=" O   VAL K   6 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   VAL K   8 " --> pdb=" O   TYR K  54 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   TYR K  56 " --> pdb=" O   VAL K   8 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL K  10 " --> pdb=" O   TYR K  56 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   LYS K   7 " --> pdb=" O   MET K 327 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   ALA K 329 " --> pdb=" O   LYS K   7 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ALA K   9 " --> pdb=" O   ALA K 329 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   LEU K 331 " --> pdb=" O   ALA K   9 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ARG K  11 " --> pdb=" O   LEU K 331 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ARG K 324 " --> pdb=" O   ASN K  90 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   CYS K  92 " --> pdb=" O   ARG K 324 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA K 326 " --> pdb=" O   CYS K  92 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   VAL K  91 " --> pdb=" O   SER K 245 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   VAL K 247 " --> pdb=" O   VAL K  91 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ILE K  93 " --> pdb=" O   VAL K 247 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   THR K 238 " --> pdb=" O   ARG K 229 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ARG K 229 " --> pdb=" O   THR K 238 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LYS K 240 " --> pdb=" O   GLN K 227 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'K' and resid 28 through 31
    Processing sheet with id=AA4, first strand: chain 'K' and resid 168 through 171
    Processing sheet with id=AA5, first strand: chain 'K' and resid 205 through 206
    Processing sheet with id=AA6, first strand: chain 'A' and resid 65 through 68
      removed outlier: 7.242A  pdb=" N   GLU A   3 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 8.477A  pdb=" N   LEU A 136 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   ILE A   5 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   PHE A 138 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ILE A   7 " --> pdb=" O   PHE A 138 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   GLN A 133 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   LEU A 167 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   PHE A 135 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   CYS A 200 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 272
      removed outlier: 3.606A  pdb=" N   ALA A 314 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92
      removed outlier: 8.274A  pdb=" N   VAL B  91 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   LEU B  65 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 8.570A  pdb=" N   ILE B  64 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   HIS B   6 " --> pdb=" O   ILE B  64 " (cutoff:3.500A)
      removed outlier: 8.099A  pdb=" N   VAL B  66 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   GLN B   8 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   GLU B   3 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   PHE B 133 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   VAL B   5 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   LEU B 135 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ILE B   7 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   HIS B 137 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   ALA B   9 " --> pdb=" O   HIS B 137 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   GLN B 131 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   ASN B 165 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
      removed outlier: 5.840A  pdb=" N   PHE B 133 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   PHE B 167 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   LEU B 135 " --> pdb=" O   PHE B 167 " (cutoff:3.500A)
      removed outlier: 8.004A  pdb=" N   VAL B 169 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   HIS B 137 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   THR B 199 " --> pdb=" O   PHE B 266 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   CYS B 201 " --> pdb=" O   PRO B 268 " (cutoff:3.500A)
      removed outlier: 10.355A  pdb=" N   PHE B 270 " --> pdb=" O   CYS B 201 " (cutoff:3.500A)
      removed outlier: 13.802A  pdb=" N   ASP B 203 " --> pdb=" O   PHE B 270 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   PHE B 265 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   SER B 371 " --> pdb=" O   PHE B 265 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 51 through 53

    473 hydrogen bonds defined for protein.
    1359 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: 3.22

  Time building geometry restraints manager: 2.92 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1825
        1.33 -     1.45: 2572
        1.45 -     1.58: 5480
        1.58 -     1.70: 16
        1.70 -     1.82: 107
  Bond restraints: 10000
  Sorted by residual:
  bond pdb=" N   LYS K 300 "
       pdb=" CA  LYS K 300 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.29e-02 6.01e+03 6.45e+00
  bond pdb=" N   LYS K 298 "
       pdb=" CA  LYS K 298 "
    ideal  model  delta    sigma   weight residual
    1.462  1.489 -0.028 1.27e-02 6.20e+03 4.77e+00
  bond pdb=" N   LYS K 299 "
       pdb=" CA  LYS K 299 "
    ideal  model  delta    sigma   weight residual
    1.461  1.489 -0.028 1.30e-02 5.92e+03 4.56e+00
  bond pdb=" CB  ILE K  77 "
       pdb=" CG2 ILE K  77 "
    ideal  model  delta    sigma   weight residual
    1.521  1.586 -0.065 3.30e-02 9.18e+02 3.84e+00
  bond pdb=" CB  ASN K 159 "
       pdb=" CG  ASN K 159 "
    ideal  model  delta    sigma   weight residual
    1.516  1.564 -0.048 2.50e-02 1.60e+03 3.62e+00
  ... (remaining 9995 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 12960
        1.61 -     3.23: 447
        3.23 -     4.84: 123
        4.84 -     6.45: 35
        6.45 -     8.06: 6
  Bond angle restraints: 13571
  Sorted by residual:
  angle pdb=" CB  GLU A 411 "
        pdb=" CG  GLU A 411 "
        pdb=" CD  GLU A 411 "
      ideal   model   delta    sigma   weight residual
     112.60  118.52   -5.92 1.70e+00 3.46e-01 1.21e+01
  angle pdb=" CA  ASN K 159 "
        pdb=" CB  ASN K 159 "
        pdb=" CG  ASN K 159 "
      ideal   model   delta    sigma   weight residual
     112.60  115.99   -3.39 1.00e+00 1.00e+00 1.15e+01
  angle pdb=" CA  TYR K  74 "
        pdb=" CB  TYR K  74 "
        pdb=" CG  TYR K  74 "
      ideal   model   delta    sigma   weight residual
     113.90  119.56   -5.66 1.80e+00 3.09e-01 9.88e+00
  angle pdb=" CG  LYS B 122 "
        pdb=" CD  LYS B 122 "
        pdb=" CE  LYS B 122 "
      ideal   model   delta    sigma   weight residual
     111.30  118.07   -6.77 2.30e+00 1.89e-01 8.68e+00
  angle pdb=" CB  GLU K 317 "
        pdb=" CG  GLU K 317 "
        pdb=" CD  GLU K 317 "
      ideal   model   delta    sigma   weight residual
     112.60  117.46   -4.86 1.70e+00 3.46e-01 8.17e+00
  ... (remaining 13566 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.60: 5751
       29.60 -    59.20: 286
       59.20 -    88.79: 28
       88.79 -   118.39: 5
      118.39 -   147.99: 10
  Dihedral angle restraints: 6080
    sinusoidal: 2516
      harmonic: 3564
  Sorted by residual:
  dihedral pdb=" C8  GTP A 501 "
           pdb=" C1' GTP A 501 "
           pdb=" N9  GTP A 501 "
           pdb=" O4' GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -42.18  146.78     1      2.00e+01 2.50e-03 4.41e+01
  dihedral pdb=" O2A ADP K 801 "
           pdb=" O3A ADP K 801 "
           pdb=" PA  ADP K 801 "
           pdb=" PB  ADP K 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   65.36 -125.36     1      2.00e+01 2.50e-03 3.79e+01
  dihedral pdb=" C2' ADP K 801 "
           pdb=" C1' ADP K 801 "
           pdb=" N9  ADP K 801 "
           pdb=" C4  ADP K 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
      91.55 -151.67 -116.78     1      2.00e+01 2.50e-03 3.48e+01
  ... (remaining 6077 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 870
       0.032 -    0.064: 410
       0.064 -    0.096: 113
       0.096 -    0.127: 70
       0.127 -    0.159: 26
  Chirality restraints: 1489
  Sorted by residual:
  chirality pdb=" CA  ILE K 304 "
            pdb=" N   ILE K 304 "
            pdb=" C   ILE K 304 "
            pdb=" CB  ILE K 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.35e-01
  chirality pdb=" CA  ASP B  31 "
            pdb=" N   ASP B  31 "
            pdb=" C   ASP B  31 "
            pdb=" CB  ASP B  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.23e-01
  chirality pdb=" CA  MET A   1 "
            pdb=" N   MET A   1 "
            pdb=" C   MET A   1 "
            pdb=" CB  MET A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.13e-01
  ... (remaining 1486 not shown)

  Planarity restraints: 1761
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY K 291 "    0.063 5.00e-02 4.00e+02   9.53e-02 1.45e+01
        pdb=" N   PRO K 292 "   -0.165 5.00e-02 4.00e+02
        pdb=" CA  PRO K 292 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO K 292 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 429 "   -0.010 2.00e-02 2.50e+03   2.07e-02 4.30e+00
        pdb=" C   GLU A 429 "    0.036 2.00e-02 2.50e+03
        pdb=" O   GLU A 429 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LYS A 430 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A  88 "   -0.034 5.00e-02 4.00e+02   5.17e-02 4.28e+00
        pdb=" N   PRO A  89 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A  89 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A  89 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1758 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.40: 22
        2.40 -     3.03: 5729
        3.03 -     3.65: 14222
        3.65 -     4.28: 21191
        4.28 -     4.90: 36634
  Nonbonded interactions: 77798
  Sorted by model distance:
  nonbonded pdb=" CE  LYS K 299 "
            pdb=" O   GLN B 433 "
     model   vdw
     1.777 3.440
  nonbonded pdb=" OD2 ASP A  98 "
            pdb="MG    MG A 502 "
     model   vdw
     1.975 2.170
  nonbonded pdb=" OE2 GLU A  71 "
            pdb="MG    MG A 502 "
     model   vdw
     1.981 2.170
  nonbonded pdb=" O3B GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     2.040 2.170
  nonbonded pdb=" OG  SER B 172 "
            pdb=" OD1 ASP B 203 "
     model   vdw
     2.065 3.040
  ... (remaining 77793 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=0.50 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:             4.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.320
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
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   0.065  10000  Z= 0.296
  Angle     :  0.784   8.065  13571  Z= 0.403
  Chirality :  0.046   0.159   1489
  Planarity :  0.006   0.095   1761
  Dihedral  : 18.166 147.991   3792
  Min Nonbonded Distance : 1.777

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.25 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 13.34 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    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:  0.03 (0.24), residues: 1224
  helix:  1.24 (0.23), residues: 487
  sheet: -0.11 (0.34), residues: 227
  loop : -1.10 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 344 
 HIS   0.005   0.001   HIS A 283 
 PHE   0.027   0.002   PHE A  49 
 TYR   0.034   0.002   TYR K 150 
 ARG   0.006   0.001   ARG A   2 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 246
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  125 ASP cc_start: 0.7593 (t0) cc_final: 0.7226 (t0)
REVERT: K  148 GLU cc_start: 0.8020 (pt0) cc_final: 0.7624 (pp20)
REVERT: K  152 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7684 (mm-30)
REVERT: K  298 LYS cc_start: 0.4993 (OUTLIER) cc_final: 0.4520 (ptpt)
REVERT: K  300 LYS cc_start: -0.0801 (OUTLIER) cc_final: -0.1083 (mmtp)
REVERT: A    1 MET cc_start: 0.7043 (mmm) cc_final: 0.6711 (mmm)
REVERT: A   24 TYR cc_start: 0.8554 (m-10) cc_final: 0.8231 (m-10)
REVERT: A  154 MET cc_start: 0.8647 (mmm) cc_final: 0.8164 (mtp)
REVERT: B  356 ILE cc_start: 0.8918 (mm) cc_final: 0.8709 (mm)
  outliers start: 7
  outliers final: 2
  residues processed: 252
  average time/residue: 0.2346
  time to fit residues: 81.0058
Evaluate side-chains
  231 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 227
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  298 LYS
Chi-restraints excluded: chain K residue  300 LYS
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue  108 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 92 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 110 optimal weight:    0.7980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
K  70 GLN
** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
B 204 ASN
** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.122870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.096153 restraints weight = 14205.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.35
r_work: 0.3091 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2934
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2934
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10000  Z= 0.216
  Angle     :  0.593   9.145  13571  Z= 0.291
  Chirality :  0.045   0.250   1489
  Planarity :  0.005   0.088   1761
  Dihedral  : 12.562 144.876   1497
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.43 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.87 %
    Favored  : 85.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    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:  0.63 (0.24), residues: 1224
  helix:  1.83 (0.24), residues: 495
  sheet:  0.21 (0.34), residues: 240
  loop : -0.95 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  21 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.013   0.001   PHE K  15 
 TYR   0.022   0.001   TYR K 177 
 ARG   0.003   0.000   ARG B 241 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 250
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  138 MET cc_start: 0.4239 (mmt) cc_final: 0.3568 (mmm)
REVERT: K  152 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7902 (mm-30)
REVERT: K  159 ASN cc_start: 0.8273 (t0) cc_final: 0.7967 (t0)
REVERT: K  210 MET cc_start: 0.7253 (mtp) cc_final: 0.7020 (mtp)
REVERT: K  347 TYR cc_start: 0.8738 (t80) cc_final: 0.8222 (t80)
REVERT: A    1 MET cc_start: 0.7624 (mmm) cc_final: 0.6848 (mmm)
REVERT: A    3 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7384 (pt0)
REVERT: A   24 TYR cc_start: 0.8582 (m-10) cc_final: 0.8231 (m-80)
REVERT: A   69 ASP cc_start: 0.8221 (t0) cc_final: 0.7981 (t0)
REVERT: A  265 ILE cc_start: 0.8598 (pt) cc_final: 0.8367 (mt)
REVERT: A  322 ASP cc_start: 0.8935 (t0) cc_final: 0.8715 (t0)
REVERT: B    1 MET cc_start: 0.6117 (OUTLIER) cc_final: 0.4864 (mmm)
REVERT: B   67 ASP cc_start: 0.8276 (t0) cc_final: 0.7904 (t70)
REVERT: B   74 ASP cc_start: 0.8478 (m-30) cc_final: 0.8235 (m-30)
REVERT: B  388 MET cc_start: 0.8513 (mtt) cc_final: 0.8176 (mtp)
REVERT: B  417 ASP cc_start: 0.8343 (m-30) cc_final: 0.8081 (m-30)
  outliers start: 22
  outliers final: 9
  residues processed: 261
  average time/residue: 0.2222
  time to fit residues: 82.2596
Evaluate side-chains
  236 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 226
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   26 CYS
Chi-restraints excluded: chain K residue   60 THR
Chi-restraints excluded: chain K residue  118 ILE
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 78 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 115 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 82 optimal weight:    0.0570
   overall best weight:    1.4106

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

Flipped N/Q/H residues before XYZ refinement:
** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 318 ASN
A  61 HIS
A 258 ASN
B 190 HIS
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.121633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.094846 restraints weight = 14478.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 2.34
r_work: 0.3066 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10000  Z= 0.245
  Angle     :  0.586   8.158  13571  Z= 0.287
  Chirality :  0.047   0.491   1489
  Planarity :  0.005   0.082   1761
  Dihedral  : 10.049 144.881   1485
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.43 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 14.66 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    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 (0.24), residues: 1224
  helix:  1.93 (0.24), residues: 492
  sheet:  0.39 (0.35), residues: 240
  loop : -0.99 (0.26), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  21 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.013   0.001   PHE B 367 
 TYR   0.017   0.001   TYR K 177 
 ARG   0.004   0.000   ARG B 241 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 236
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  152 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7859 (mm-30)
REVERT: K  159 ASN cc_start: 0.8274 (t0) cc_final: 0.7954 (t0)
REVERT: K  210 MET cc_start: 0.7211 (mtp) cc_final: 0.6998 (mtp)
REVERT: K  346 ARG cc_start: 0.8403 (mtt90) cc_final: 0.7939 (mmt90)
REVERT: A   24 TYR cc_start: 0.8635 (m-10) cc_final: 0.8296 (m-10)
REVERT: A   69 ASP cc_start: 0.8285 (t0) cc_final: 0.7955 (t0)
REVERT: A  172 TYR cc_start: 0.8468 (t80) cc_final: 0.8171 (t80)
REVERT: B   67 ASP cc_start: 0.8301 (t0) cc_final: 0.7901 (t70)
REVERT: B   74 ASP cc_start: 0.8464 (m-30) cc_final: 0.8097 (m-30)
REVERT: B  232 THR cc_start: 0.8662 (m) cc_final: 0.8360 (t)
REVERT: B  239 CYS cc_start: 0.9189 (m) cc_final: 0.8853 (m)
REVERT: B  417 ASP cc_start: 0.8353 (m-30) cc_final: 0.8078 (m-30)
REVERT: B  423 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8587 (tm-30)
REVERT: B  424 GLN cc_start: 0.8945 (tt0) cc_final: 0.8525 (tt0)
  outliers start: 22
  outliers final: 17
  residues processed: 249
  average time/residue: 0.2442
  time to fit residues: 84.2706
Evaluate side-chains
  237 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 220
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   26 CYS
Chi-restraints excluded: chain K residue   38 VAL
Chi-restraints excluded: chain K residue   60 THR
Chi-restraints excluded: chain K residue   82 LEU
Chi-restraints excluded: chain K residue  118 ILE
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  157 LEU
Chi-restraints excluded: chain K residue  220 VAL
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  419 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 112 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 8 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 52 optimal weight:    0.1980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
B 424 GLN
** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.121429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.094515 restraints weight = 14454.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 2.40
r_work: 0.3057 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2905
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2905
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10000  Z= 0.238
  Angle     :  0.569   6.880  13571  Z= 0.278
  Chirality :  0.046   0.356   1489
  Planarity :  0.005   0.078   1761
  Dihedral  :  9.361 144.987   1485
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.35 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.61 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    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 (0.24), residues: 1224
  helix:  1.94 (0.24), residues: 494
  sheet:  0.52 (0.35), residues: 240
  loop : -1.05 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  21 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.013   0.001   PHE B 367 
 TYR   0.015   0.001   TYR K 177 
 ARG   0.005   0.000   ARG A 214 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 237
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   31 SER cc_start: 0.7645 (t) cc_final: 0.7279 (p)
REVERT: K   42 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8024 (mp10)
REVERT: K  152 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7828 (mm-30)
REVERT: K  159 ASN cc_start: 0.8330 (t0) cc_final: 0.7965 (t0)
REVERT: K  195 LEU cc_start: 0.9162 (mt) cc_final: 0.8935 (mp)
REVERT: K  322 ASN cc_start: 0.8280 (t0) cc_final: 0.7945 (t0)
REVERT: K  327 MET cc_start: 0.8729 (ttp) cc_final: 0.8406 (ttt)
REVERT: K  346 ARG cc_start: 0.8347 (mtt90) cc_final: 0.7916 (mmt90)
REVERT: A    3 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7529 (pt0)
REVERT: A   24 TYR cc_start: 0.8633 (m-10) cc_final: 0.8270 (m-10)
REVERT: A   69 ASP cc_start: 0.8283 (t0) cc_final: 0.7962 (t0)
REVERT: A   98 ASP cc_start: 0.6882 (t0) cc_final: 0.6649 (t70)
REVERT: B   67 ASP cc_start: 0.8326 (t0) cc_final: 0.7924 (t70)
REVERT: B  108 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8220 (mm-30)
REVERT: B  239 CYS cc_start: 0.9212 (m) cc_final: 0.8912 (m)
REVERT: B  416 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8589 (m-40)
REVERT: B  423 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8536 (tm-30)
  outliers start: 26
  outliers final: 15
  residues processed: 257
  average time/residue: 0.2318
  time to fit residues: 83.0724
Evaluate side-chains
  243 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 226
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   26 CYS
Chi-restraints excluded: chain K residue   28 ILE
Chi-restraints excluded: chain K residue   42 GLN
Chi-restraints excluded: chain K residue   60 THR
Chi-restraints excluded: chain K residue   82 LEU
Chi-restraints excluded: chain K residue  118 ILE
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  157 LEU
Chi-restraints excluded: chain K residue  258 THR
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  416 ASN
Chi-restraints excluded: chain B residue  419 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 3 optimal weight:    8.9990
   chunk 35 optimal weight:    4.9990
   chunk 81 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 101 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 104 optimal weight:    1.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS
K 116 GLN
** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 ASN
B 190 HIS
** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.119032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.092095 restraints weight = 14583.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.38
r_work: 0.3019 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2863
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2863
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  10000  Z= 0.309
  Angle     :  0.597   7.148  13571  Z= 0.295
  Chirality :  0.046   0.260   1489
  Planarity :  0.005   0.076   1761
  Dihedral  :  9.263 144.822   1485
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.68 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.80 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    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:  0.67 (0.24), residues: 1224
  helix:  1.86 (0.24), residues: 493
  sheet:  0.54 (0.36), residues: 241
  loop : -1.09 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  21 
 HIS   0.007   0.001   HIS B 190 
 PHE   0.016   0.002   PHE B 367 
 TYR   0.015   0.002   TYR B  50 
 ARG   0.006   0.000   ARG A 214 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 232
  time to evaluate  : 1.111 
Fit side-chains
   revert: symmetry clash
REVERT: K   42 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8096 (mp10)
REVERT: K  152 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7816 (mm-30)
REVERT: K  159 ASN cc_start: 0.8322 (t0) cc_final: 0.7923 (t0)
REVERT: K  322 ASN cc_start: 0.8375 (t0) cc_final: 0.8091 (t0)
REVERT: K  327 MET cc_start: 0.8757 (ttp) cc_final: 0.8456 (ttt)
REVERT: K  347 TYR cc_start: 0.8746 (t80) cc_final: 0.8201 (t80)
REVERT: A   24 TYR cc_start: 0.8639 (m-10) cc_final: 0.8324 (m-10)
REVERT: A   62 VAL cc_start: 0.8829 (t) cc_final: 0.8498 (m)
REVERT: A   69 ASP cc_start: 0.8371 (t0) cc_final: 0.7966 (t70)
REVERT: B   67 ASP cc_start: 0.8326 (t0) cc_final: 0.7899 (t70)
REVERT: B  108 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8234 (mm-30)
REVERT: B  232 THR cc_start: 0.8684 (m) cc_final: 0.8410 (t)
REVERT: B  239 CYS cc_start: 0.9235 (m) cc_final: 0.8880 (m)
REVERT: B  388 MET cc_start: 0.8670 (mtt) cc_final: 0.8457 (mtp)
REVERT: B  417 ASP cc_start: 0.8395 (m-30) cc_final: 0.8152 (m-30)
REVERT: B  423 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8562 (tm-30)
REVERT: B  424 GLN cc_start: 0.8950 (tt0) cc_final: 0.8536 (tt0)
  outliers start: 27
  outliers final: 22
  residues processed: 248
  average time/residue: 0.2149
  time to fit residues: 74.9664
Evaluate side-chains
  246 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 223
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    8 VAL
Chi-restraints excluded: chain K residue   26 CYS
Chi-restraints excluded: chain K residue   28 ILE
Chi-restraints excluded: chain K residue   42 GLN
Chi-restraints excluded: chain K residue   60 THR
Chi-restraints excluded: chain K residue   82 LEU
Chi-restraints excluded: chain K residue   91 VAL
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  157 LEU
Chi-restraints excluded: chain K residue  258 THR
Chi-restraints excluded: chain K residue  336 ILE
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  419 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 13 optimal weight:   20.0000
   chunk 55 optimal weight:    0.8980
   chunk 19 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 82 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0670
   chunk 91 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.7120

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

Flipped N/Q/H residues before XYZ refinement:
** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.122500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.095726 restraints weight = 14409.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.39
r_work: 0.3078 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2927
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2927
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10000  Z= 0.162
  Angle     :  0.549   7.607  13571  Z= 0.266
  Chirality :  0.044   0.220   1489
  Planarity :  0.004   0.075   1761
  Dihedral  :  8.959 145.135   1485
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 16.27 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    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:  0.85 (0.24), residues: 1224
  helix:  2.02 (0.24), residues: 495
  sheet:  0.69 (0.36), residues: 238
  loop : -1.06 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  21 
 HIS   0.007   0.001   HIS B 190 
 PHE   0.011   0.001   PHE B 367 
 TYR   0.023   0.001   TYR K 189 
 ARG   0.006   0.000   ARG A 214 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 230
  time to evaluate  : 1.245 
Fit side-chains
   revert: symmetry clash
REVERT: K   31 SER cc_start: 0.7686 (t) cc_final: 0.7341 (p)
REVERT: K   42 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7992 (mp10)
REVERT: K  152 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7836 (mm-30)
REVERT: K  159 ASN cc_start: 0.8326 (t0) cc_final: 0.7902 (t0)
REVERT: K  181 LEU cc_start: 0.8636 (tp) cc_final: 0.8433 (tp)
REVERT: K  322 ASN cc_start: 0.8327 (t0) cc_final: 0.7954 (t0)
REVERT: K  327 MET cc_start: 0.8664 (ttp) cc_final: 0.8427 (ttt)
REVERT: K  347 TYR cc_start: 0.8710 (t80) cc_final: 0.8040 (t80)
REVERT: A    3 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7558 (pt0)
REVERT: A   62 VAL cc_start: 0.8797 (t) cc_final: 0.8450 (m)
REVERT: A   69 ASP cc_start: 0.8336 (t0) cc_final: 0.7896 (t70)
REVERT: A   98 ASP cc_start: 0.6783 (t0) cc_final: 0.6565 (t0)
REVERT: A  108 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7836 (p90)
REVERT: A  398 MET cc_start: 0.8377 (ttp) cc_final: 0.7991 (ttm)
REVERT: B   67 ASP cc_start: 0.8262 (t0) cc_final: 0.7869 (t70)
REVERT: B  239 CYS cc_start: 0.9191 (m) cc_final: 0.8909 (m)
REVERT: B  417 ASP cc_start: 0.8350 (m-30) cc_final: 0.8026 (m-30)
REVERT: B  423 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8534 (tm-30)
REVERT: B  424 GLN cc_start: 0.8919 (tt0) cc_final: 0.8496 (tt0)
REVERT: B  426 GLN cc_start: 0.8718 (tt0) cc_final: 0.8444 (tt0)
  outliers start: 26
  outliers final: 17
  residues processed: 245
  average time/residue: 0.2184
  time to fit residues: 75.5902
Evaluate side-chains
  240 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 221
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    6 VAL
Chi-restraints excluded: chain K residue   26 CYS
Chi-restraints excluded: chain K residue   28 ILE
Chi-restraints excluded: chain K residue   42 GLN
Chi-restraints excluded: chain K residue   60 THR
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  157 LEU
Chi-restraints excluded: chain K residue  258 THR
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue  194 GLU
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 117 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 105 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 120 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0370
   overall best weight:    2.8066

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS
** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.117527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.090732 restraints weight = 14764.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 2.32
r_work: 0.2998 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2845
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2845
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.075  10000  Z= 0.437
  Angle     :  0.648   7.523  13571  Z= 0.319
  Chirality :  0.048   0.232   1489
  Planarity :  0.005   0.073   1761
  Dihedral  :  9.235 144.819   1485
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 16.18 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    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 (0.24), residues: 1224
  helix:  1.75 (0.24), residues: 493
  sheet:  0.53 (0.36), residues: 235
  loop : -1.19 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  21 
 HIS   0.007   0.002   HIS A  88 
 PHE   0.015   0.002   PHE B 367 
 TYR   0.019   0.002   TYR K 189 
 ARG   0.005   0.001   ARG A 214 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 233
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
REVERT: K   42 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8158 (mp10)
REVERT: K  152 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7812 (mm-30)
REVERT: K  159 ASN cc_start: 0.8356 (t0) cc_final: 0.7982 (t0)
REVERT: K  322 ASN cc_start: 0.8441 (t0) cc_final: 0.8188 (t0)
REVERT: K  327 MET cc_start: 0.8756 (ttp) cc_final: 0.8482 (ttt)
REVERT: K  347 TYR cc_start: 0.8724 (t80) cc_final: 0.8184 (t80)
REVERT: A   24 TYR cc_start: 0.8628 (m-10) cc_final: 0.8366 (m-10)
REVERT: A   62 VAL cc_start: 0.8832 (t) cc_final: 0.8512 (m)
REVERT: A   69 ASP cc_start: 0.8430 (t0) cc_final: 0.8044 (t70)
REVERT: A   98 ASP cc_start: 0.6861 (t0) cc_final: 0.6643 (t0)
REVERT: A  172 TYR cc_start: 0.8560 (t80) cc_final: 0.8078 (t80)
REVERT: A  417 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7048 (tt0)
REVERT: B   67 ASP cc_start: 0.8380 (t0) cc_final: 0.7937 (t70)
REVERT: B  232 THR cc_start: 0.8703 (m) cc_final: 0.8452 (t)
REVERT: B  239 CYS cc_start: 0.9268 (m) cc_final: 0.8924 (m)
REVERT: B  388 MET cc_start: 0.8732 (mtt) cc_final: 0.8511 (mtm)
REVERT: B  423 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8680 (tm-30)
REVERT: B  424 GLN cc_start: 0.8962 (tt0) cc_final: 0.8530 (tt0)
  outliers start: 29
  outliers final: 25
  residues processed: 249
  average time/residue: 0.2202
  time to fit residues: 76.7428
Evaluate side-chains
  255 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 228
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    6 VAL
Chi-restraints excluded: chain K residue    8 VAL
Chi-restraints excluded: chain K residue   26 CYS
Chi-restraints excluded: chain K residue   28 ILE
Chi-restraints excluded: chain K residue   42 GLN
Chi-restraints excluded: chain K residue   60 THR
Chi-restraints excluded: chain K residue  118 ILE
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  157 LEU
Chi-restraints excluded: chain K residue  258 THR
Chi-restraints excluded: chain K residue  340 GLU
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  419 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0040
   chunk 65 optimal weight:    0.3980
   chunk 114 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 108 optimal weight:    0.7980
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS
** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.122793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.096234 restraints weight = 14630.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 2.36
r_work: 0.3102 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2935
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2935
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10000  Z= 0.157
  Angle     :  0.564   7.403  13571  Z= 0.273
  Chirality :  0.044   0.213   1489
  Planarity :  0.004   0.074   1761
  Dihedral  :  8.839 142.218   1485
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.41 %
    Favored  : 80.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    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 (0.24), residues: 1224
  helix:  1.92 (0.24), residues: 495
  sheet:  0.61 (0.36), residues: 230
  loop : -1.11 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  21 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.011   0.001   PHE A 255 
 TYR   0.015   0.001   TYR K 189 
 ARG   0.007   0.000   ARG A 214 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 230
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
REVERT: K   31 SER cc_start: 0.7838 (t) cc_final: 0.7518 (p)
REVERT: K   42 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8075 (mp10)
REVERT: K  152 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7858 (mm-30)
REVERT: K  159 ASN cc_start: 0.8332 (t0) cc_final: 0.7905 (t0)
REVERT: K  322 ASN cc_start: 0.8385 (t0) cc_final: 0.8033 (t0)
REVERT: K  327 MET cc_start: 0.8665 (ttp) cc_final: 0.8439 (ttt)
REVERT: K  347 TYR cc_start: 0.8617 (t80) cc_final: 0.8026 (t80)
REVERT: A    3 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7535 (pt0)
REVERT: A   62 VAL cc_start: 0.8802 (t) cc_final: 0.8469 (m)
REVERT: A   69 ASP cc_start: 0.8381 (t0) cc_final: 0.8009 (t70)
REVERT: A  108 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7780 (p90)
REVERT: B   67 ASP cc_start: 0.8262 (t0) cc_final: 0.7873 (t70)
REVERT: B  213 ARG cc_start: 0.8368 (mtm180) cc_final: 0.8070 (mtm180)
REVERT: B  239 CYS cc_start: 0.9181 (m) cc_final: 0.8919 (m)
REVERT: B  282 ARG cc_start: 0.8853 (ttt90) cc_final: 0.8316 (mmm160)
REVERT: B  423 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8545 (tm-30)
REVERT: B  424 GLN cc_start: 0.8922 (tt0) cc_final: 0.8493 (tt0)
REVERT: B  426 GLN cc_start: 0.8694 (tt0) cc_final: 0.8436 (tt0)
  outliers start: 20
  outliers final: 14
  residues processed: 245
  average time/residue: 0.2191
  time to fit residues: 75.3092
Evaluate side-chains
  240 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 224
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    6 VAL
Chi-restraints excluded: chain K residue   26 CYS
Chi-restraints excluded: chain K residue   28 ILE
Chi-restraints excluded: chain K residue   42 GLN
Chi-restraints excluded: chain K residue   60 THR
Chi-restraints excluded: chain K residue   82 LEU
Chi-restraints excluded: chain K residue   91 VAL
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  157 LEU
Chi-restraints excluded: chain K residue  258 THR
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 111 optimal weight:    0.7980
   chunk 59 optimal weight:    6.9990
   chunk 65 optimal weight:    0.8980
   chunk 107 optimal weight:    3.9990
   chunk 98 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0980
   chunk 117 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 79 optimal weight:    0.4980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS
** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.121383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.094499 restraints weight = 14600.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 2.43
r_work: 0.3072 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2903
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2903
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10000  Z= 0.206
  Angle     :  0.591  13.020  13571  Z= 0.285
  Chirality :  0.045   0.217   1489
  Planarity :  0.005   0.073   1761
  Dihedral  :  8.875 143.557   1485
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 18.07 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    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:  0.76 (0.24), residues: 1224
  helix:  1.93 (0.24), residues: 493
  sheet:  0.64 (0.36), residues: 232
  loop : -1.06 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  21 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.016   0.001   PHE A 255 
 TYR   0.047   0.001   TYR K 189 
 ARG   0.008   0.000   ARG A 390 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 231
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
REVERT: K   31 SER cc_start: 0.7895 (t) cc_final: 0.7582 (p)
REVERT: K   42 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8144 (mp10)
REVERT: K  152 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7846 (mm-30)
REVERT: K  159 ASN cc_start: 0.8346 (t0) cc_final: 0.7926 (t0)
REVERT: K  322 ASN cc_start: 0.8420 (t0) cc_final: 0.8085 (t0)
REVERT: K  327 MET cc_start: 0.8696 (ttp) cc_final: 0.8470 (ttt)
REVERT: K  347 TYR cc_start: 0.8695 (t80) cc_final: 0.8056 (t80)
REVERT: A    3 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7407 (pt0)
REVERT: A   24 TYR cc_start: 0.8602 (m-10) cc_final: 0.8339 (m-10)
REVERT: A   62 VAL cc_start: 0.8819 (t) cc_final: 0.8476 (m)
REVERT: A   69 ASP cc_start: 0.8445 (t0) cc_final: 0.8003 (t70)
REVERT: A   98 ASP cc_start: 0.6869 (t0) cc_final: 0.6643 (t0)
REVERT: A  108 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.7803 (p90)
REVERT: B  239 CYS cc_start: 0.9188 (m) cc_final: 0.8919 (m)
REVERT: B  282 ARG cc_start: 0.8881 (ttt90) cc_final: 0.8391 (mtp85)
REVERT: B  417 ASP cc_start: 0.8381 (m-30) cc_final: 0.8076 (m-30)
REVERT: B  423 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8542 (tm-30)
REVERT: B  424 GLN cc_start: 0.8954 (tt0) cc_final: 0.8500 (tt0)
REVERT: B  426 GLN cc_start: 0.8701 (tt0) cc_final: 0.8444 (tt0)
  outliers start: 19
  outliers final: 14
  residues processed: 244
  average time/residue: 0.2174
  time to fit residues: 74.7317
Evaluate side-chains
  244 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 228
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    6 VAL
Chi-restraints excluded: chain K residue   26 CYS
Chi-restraints excluded: chain K residue   28 ILE
Chi-restraints excluded: chain K residue   42 GLN
Chi-restraints excluded: chain K residue   60 THR
Chi-restraints excluded: chain K residue   91 VAL
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  157 LEU
Chi-restraints excluded: chain K residue  258 THR
Chi-restraints excluded: chain K residue  340 GLU
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:   20.0000
   chunk 20 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 98 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS
** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.119214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.092302 restraints weight = 14623.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 2.34
r_work: 0.3043 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2888
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2888
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  10000  Z= 0.316
  Angle     :  0.627   9.385  13571  Z= 0.306
  Chirality :  0.046   0.208   1489
  Planarity :  0.005   0.073   1761
  Dihedral  :  8.993 144.702   1485
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.79 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    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 (0.24), residues: 1224
  helix:  1.75 (0.24), residues: 495
  sheet:  0.57 (0.36), residues: 230
  loop : -1.18 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  21 
 HIS   0.007   0.001   HIS B 190 
 PHE   0.016   0.002   PHE B 367 
 TYR   0.037   0.002   TYR K 189 
 ARG   0.008   0.000   ARG A 390 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 237
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
REVERT: K   31 SER cc_start: 0.7992 (t) cc_final: 0.7708 (p)
REVERT: K   42 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8165 (mp10)
REVERT: K  152 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7818 (mm-30)
REVERT: K  159 ASN cc_start: 0.8365 (t0) cc_final: 0.8001 (t0)
REVERT: K  322 ASN cc_start: 0.8485 (t0) cc_final: 0.8171 (t0)
REVERT: K  327 MET cc_start: 0.8711 (ttp) cc_final: 0.8481 (ttt)
REVERT: A    3 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7403 (pt0)
REVERT: A   24 TYR cc_start: 0.8622 (m-10) cc_final: 0.8303 (m-10)
REVERT: A   62 VAL cc_start: 0.8829 (t) cc_final: 0.8505 (m)
REVERT: A   69 ASP cc_start: 0.8509 (t0) cc_final: 0.8069 (t70)
REVERT: A   98 ASP cc_start: 0.6917 (t0) cc_final: 0.6664 (t0)
REVERT: B  232 THR cc_start: 0.8660 (m) cc_final: 0.8350 (t)
REVERT: B  239 CYS cc_start: 0.9212 (m) cc_final: 0.8910 (m)
REVERT: B  282 ARG cc_start: 0.8914 (ttt90) cc_final: 0.8423 (mtp85)
REVERT: B  423 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8577 (tm-30)
REVERT: B  424 GLN cc_start: 0.8966 (tt0) cc_final: 0.8565 (tt0)
REVERT: B  426 GLN cc_start: 0.8727 (tt0) cc_final: 0.8457 (tt0)
  outliers start: 19
  outliers final: 16
  residues processed: 250
  average time/residue: 0.2063
  time to fit residues: 73.0783
Evaluate side-chains
  250 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 233
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    6 VAL
Chi-restraints excluded: chain K residue    8 VAL
Chi-restraints excluded: chain K residue   26 CYS
Chi-restraints excluded: chain K residue   28 ILE
Chi-restraints excluded: chain K residue   42 GLN
Chi-restraints excluded: chain K residue   60 THR
Chi-restraints excluded: chain K residue   91 VAL
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  157 LEU
Chi-restraints excluded: chain K residue  258 THR
Chi-restraints excluded: chain K residue  340 GLU
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 120 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 66 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0980
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS
** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.123103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.096358 restraints weight = 14481.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.35
r_work: 0.3100 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2946
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10000  Z= 0.165
  Angle     :  0.583   9.712  13571  Z= 0.281
  Chirality :  0.044   0.222   1489
  Planarity :  0.005   0.073   1761
  Dihedral  :  8.757 144.697   1485
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 18.07 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    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 (0.24), residues: 1224
  helix:  1.93 (0.24), residues: 494
  sheet:  0.64 (0.36), residues: 227
  loop : -1.12 (0.26), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  21 
 HIS   0.007   0.001   HIS B 190 
 PHE   0.018   0.001   PHE A 255 
 TYR   0.030   0.001   TYR K 189 
 ARG   0.009   0.000   ARG A 390 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4792.12 seconds
wall clock time: 86 minutes 27.19 seconds (5187.19 seconds total)