Starting phenix.real_space_refine
on Sun Jun  8 18:33:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8utr_42547/06_2025/8utr_42547.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8utr_42547/06_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_42547/06_2025/8utr_42547.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8utr_42547/06_2025/8utr_42547.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8utr_42547/06_2025/8utr_42547.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8utr_42547/06_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.57, per 1000 atoms: 0.67
  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: 2.38
  Conformation dependent library (CDL) restraints added in 1.0 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: 1.04
  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: 2.77

  Time building geometry restraints manager: 2.80 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:             5.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.270
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.990
-------------------------------------------------------------------------------
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= 0.196
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15561 (  448)
  hydrogen bonds       : angle       6.50415 ( 1359)
  covalent geometry    : bond        0.00444 (10000)
  covalent geometry    : angle       0.78395 (13571)

*********************** 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  : 1.023 
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: 0.2323
  time to fit residues: 80.4887
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  : 0.961 
-------------------------------------------------------------------------------
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 = 32)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.096195 restraints weight = 14205.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.34
r_work: 0.3094 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    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 = 0.2935 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: 0.8168
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= 0.143
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04163 (  448)
  hydrogen bonds       : angle       4.31943 ( 1359)
  covalent geometry    : bond        0.00329 (10000)
  covalent geometry    : angle       0.59326 (13571)

*********************** 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  : 1.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  138 MET cc_start: 0.4269 (mmt) cc_final: 0.3601 (mmm)
REVERT: K  152 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7903 (mm-30)
REVERT: K  159 ASN cc_start: 0.8273 (t0) cc_final: 0.7967 (t0)
REVERT: K  210 MET cc_start: 0.7248 (mtp) cc_final: 0.7014 (mtp)
REVERT: A    1 MET cc_start: 0.7617 (mmm) cc_final: 0.6842 (mmm)
REVERT: A    3 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7376 (pt0)
REVERT: A   24 TYR cc_start: 0.8583 (m-10) cc_final: 0.8230 (m-80)
REVERT: A   69 ASP cc_start: 0.8216 (t0) cc_final: 0.7977 (t0)
REVERT: A  265 ILE cc_start: 0.8596 (pt) cc_final: 0.8365 (mt)
REVERT: A  322 ASP cc_start: 0.8931 (t0) cc_final: 0.8711 (t0)
REVERT: B    1 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.4868 (mmm)
REVERT: B   67 ASP cc_start: 0.8277 (t0) cc_final: 0.7906 (t70)
REVERT: B   74 ASP cc_start: 0.8473 (m-30) cc_final: 0.8230 (m-30)
REVERT: B  388 MET cc_start: 0.8511 (mtt) cc_final: 0.8172 (mtp)
REVERT: B  417 ASP cc_start: 0.8339 (m-30) cc_final: 0.8076 (m-30)
  outliers start: 22
  outliers final: 9
  residues processed: 261
  average time/residue: 0.2334
  time to fit residues: 85.9817
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  : 1.125 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 8 optimal weight:    6.9990
   chunk 115 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 17 optimal weight:    0.0270
   chunk 29 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0980
   overall best weight:    0.6840

-------------------------------------------------------------------------------
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 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 = 0.3664 r_free = 0.3664 target = 0.124370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.097398 restraints weight = 14432.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 2.44
r_work: 0.3105 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2946
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10000  Z= 0.112
  Angle     :  0.558   8.499  13571  Z= 0.270
  Chirality :  0.045   0.496   1489
  Planarity :  0.004   0.081   1761
  Dihedral  :  9.997 144.703   1485
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.27 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.04 %
    Favored  : 83.16 %
  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:  0.84 (0.24), residues: 1224
  helix:  1.95 (0.24), residues: 498
  sheet:  0.44 (0.35), residues: 240
  loop : -0.85 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 344 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.011   0.001   PHE A 255 
 TYR   0.018   0.001   TYR K 177 
 ARG   0.003   0.000   ARG B 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03720 (  448)
  hydrogen bonds       : angle       4.02117 ( 1359)
  covalent geometry    : bond        0.00251 (10000)
  covalent geometry    : angle       0.55810 (13571)

*********************** 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
  254 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 235
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
REVERT: K   31 SER cc_start: 0.7721 (t) cc_final: 0.7357 (p)
REVERT: K  152 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7879 (mm-30)
REVERT: K  159 ASN cc_start: 0.8250 (t0) cc_final: 0.7916 (t0)
REVERT: K  210 MET cc_start: 0.7180 (mtp) cc_final: 0.6950 (mtp)
REVERT: K  346 ARG cc_start: 0.8351 (mtt90) cc_final: 0.8000 (mmt90)
REVERT: A    3 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7501 (pt0)
REVERT: A   69 ASP cc_start: 0.8245 (t0) cc_final: 0.7925 (t0)
REVERT: A  250 VAL cc_start: 0.9097 (t) cc_final: 0.8778 (m)
REVERT: B   67 ASP cc_start: 0.8295 (t0) cc_final: 0.7912 (t70)
REVERT: B   74 ASP cc_start: 0.8475 (m-30) cc_final: 0.8125 (m-30)
REVERT: B  108 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8147 (mm-30)
REVERT: B  417 ASP cc_start: 0.8333 (m-30) cc_final: 0.8015 (m-30)
REVERT: B  423 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8528 (tm-30)
REVERT: B  424 GLN cc_start: 0.8945 (tt0) cc_final: 0.8527 (tt0)
  outliers start: 19
  outliers final: 10
  residues processed: 247
  average time/residue: 0.2224
  time to fit residues: 76.9825
Evaluate side-chains
  237 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 227
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  220 VAL
Chi-restraints excluded: chain A residue    2 ARG
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 B residue   41 ASP
Chi-restraints excluded: chain B residue  415 MET
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:    5.9990
   chunk 112 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 52 optimal weight:    0.0020
   overall best weight:    1.9794

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

Flipped N/Q/H residues before XYZ refinement:
K 116 GLN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.119828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.093068 restraints weight = 14544.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.33
r_work: 0.3036 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2881
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  10000  Z= 0.205
  Angle     :  0.607   7.037  13571  Z= 0.299
  Chirality :  0.047   0.380   1489
  Planarity :  0.005   0.078   1761
  Dihedral  :  9.449 145.542   1483
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.17 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 14.85 %
    Favored  : 82.31 %
  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:  0.70 (0.24), residues: 1224
  helix:  1.90 (0.24), residues: 494
  sheet:  0.48 (0.35), residues: 240
  loop : -1.06 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 344 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.015   0.002   PHE B 367 
 TYR   0.016   0.002   TYR B  50 
 ARG   0.003   0.000   ARG B  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04569 (  448)
  hydrogen bonds       : angle       4.07760 ( 1359)
  covalent geometry    : bond        0.00490 (10000)
  covalent geometry    : angle       0.60688 (13571)

*********************** 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
  269 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 239
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
REVERT: K   42 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8057 (mp10)
REVERT: K  152 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7849 (mm-30)
REVERT: K  159 ASN cc_start: 0.8335 (t0) cc_final: 0.7933 (t0)
REVERT: K  195 LEU cc_start: 0.9195 (mt) cc_final: 0.8968 (mp)
REVERT: K  322 ASN cc_start: 0.8282 (t0) cc_final: 0.7942 (t0)
REVERT: K  327 MET cc_start: 0.8750 (ttp) cc_final: 0.8417 (ttt)
REVERT: K  346 ARG cc_start: 0.8350 (mtt90) cc_final: 0.7941 (mmt90)
REVERT: A   62 VAL cc_start: 0.8828 (t) cc_final: 0.8480 (m)
REVERT: A   69 ASP cc_start: 0.8336 (t0) cc_final: 0.8040 (t0)
REVERT: A   98 ASP cc_start: 0.6905 (t0) cc_final: 0.6660 (t70)
REVERT: B   67 ASP cc_start: 0.8325 (t0) cc_final: 0.7972 (t70)
REVERT: B  232 THR cc_start: 0.8715 (m) cc_final: 0.8462 (t)
REVERT: B  239 CYS cc_start: 0.9198 (m) cc_final: 0.8898 (m)
REVERT: B  323 MET cc_start: 0.8191 (mtp) cc_final: 0.7923 (mmm)
REVERT: B  388 MET cc_start: 0.8689 (mtt) cc_final: 0.8470 (mtp)
REVERT: B  417 ASP cc_start: 0.8394 (m-30) cc_final: 0.8151 (m-30)
REVERT: B  423 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8579 (tm-30)
REVERT: B  424 GLN cc_start: 0.8952 (tt0) cc_final: 0.8529 (tt0)
  outliers start: 30
  outliers final: 21
  residues processed: 255
  average time/residue: 0.2504
  time to fit residues: 89.5183
Evaluate side-chains
  250 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 228
  time to evaluate  : 1.357 
-------------------------------------------------------------------------------
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   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 K residue  336 ILE
Chi-restraints excluded: chain A residue   75 ILE
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  323 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  415 MET
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:    3.9990
   chunk 3 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 81 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 92 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 104 optimal weight:    0.8980
   overall best weight:    1.2782

-------------------------------------------------------------------------------
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 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 = 0.3622 r_free = 0.3622 target = 0.121243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.094409 restraints weight = 14533.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 2.34
r_work: 0.3059 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
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 = 0.42   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 = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10000  Z= 0.145
  Angle     :  0.563   6.763  13571  Z= 0.276
  Chirality :  0.045   0.280   1489
  Planarity :  0.005   0.077   1761
  Dihedral  :  9.094 145.229   1483
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.43 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.80 %
    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:  0.77 (0.24), residues: 1224
  helix:  1.96 (0.24), residues: 498
  sheet:  0.54 (0.35), residues: 241
  loop : -1.07 (0.26), residues: 485

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   0.014   0.001   TYR K 177 
 ARG   0.006   0.000   ARG A 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03939 (  448)
  hydrogen bonds       : angle       3.93827 ( 1359)
  covalent geometry    : bond        0.00341 (10000)
  covalent geometry    : angle       0.56330 (13571)

*********************** 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
  250 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 226
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   31 SER cc_start: 0.7728 (t) cc_final: 0.7366 (p)
REVERT: K   42 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8031 (mp10)
REVERT: K  152 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7796 (mm-30)
REVERT: K  159 ASN cc_start: 0.8321 (t0) cc_final: 0.7925 (t0)
REVERT: K  195 LEU cc_start: 0.9182 (mt) cc_final: 0.8976 (mp)
REVERT: K  327 MET cc_start: 0.8724 (ttp) cc_final: 0.8423 (ttt)
REVERT: K  347 TYR cc_start: 0.8686 (t80) cc_final: 0.8133 (t80)
REVERT: A   62 VAL cc_start: 0.8812 (t) cc_final: 0.8477 (m)
REVERT: A   69 ASP cc_start: 0.8355 (t0) cc_final: 0.7995 (t70)
REVERT: B   67 ASP cc_start: 0.8301 (t0) cc_final: 0.7922 (t70)
REVERT: B  232 THR cc_start: 0.8667 (m) cc_final: 0.8353 (t)
REVERT: B  239 CYS cc_start: 0.9207 (m) cc_final: 0.8894 (m)
REVERT: B  417 ASP cc_start: 0.8346 (m-30) cc_final: 0.8041 (m-30)
REVERT: B  423 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8540 (tm-30)
REVERT: B  424 GLN cc_start: 0.8934 (tt0) cc_final: 0.8549 (tt0)
  outliers start: 24
  outliers final: 17
  residues processed: 241
  average time/residue: 0.2199
  time to fit residues: 74.9785
Evaluate side-chains
  240 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 222
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
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   42 GLN
Chi-restraints excluded: chain K residue   60 THR
Chi-restraints excluded: chain K residue   82 LEU
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  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   33 THR
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 55 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 1 optimal weight:    0.7980
   chunk 82 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0030
   chunk 91 optimal weight:    0.7980
   chunk 59 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.8792

-------------------------------------------------------------------------------
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**
A 186 ASN
B 190 HIS
B 291 GLN
** 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 = 0.3634 r_free = 0.3634 target = 0.122264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.095614 restraints weight = 14443.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 2.33
r_work: 0.3078 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2924
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2924
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.2441

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= 0.120
  Angle     :  0.561   7.271  13571  Z= 0.272
  Chirality :  0.044   0.238   1489
  Planarity :  0.004   0.075   1761
  Dihedral  :  8.929 145.117   1483
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.56 %
    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:  0.90 (0.24), residues: 1224
  helix:  2.04 (0.24), residues: 497
  sheet:  0.67 (0.36), residues: 238
  loop : -0.99 (0.26), residues: 489

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   0.012   0.001   PHE B 367 
 TYR   0.013   0.001   TYR K 177 
 ARG   0.009   0.000   ARG A 422 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03645 (  448)
  hydrogen bonds       : angle       3.83956 ( 1359)
  covalent geometry    : bond        0.00277 (10000)
  covalent geometry    : angle       0.56137 (13571)

*********************** 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
  246 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 223
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   31 SER cc_start: 0.7737 (t) cc_final: 0.7366 (p)
REVERT: K   42 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8032 (mp10)
REVERT: K  152 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7838 (mm-30)
REVERT: K  159 ASN cc_start: 0.8322 (t0) cc_final: 0.7908 (t0)
REVERT: K  322 ASN cc_start: 0.8278 (t0) cc_final: 0.7942 (t0)
REVERT: K  327 MET cc_start: 0.8717 (ttp) cc_final: 0.8472 (ttt)
REVERT: K  347 TYR cc_start: 0.8704 (t80) cc_final: 0.8153 (t80)
REVERT: A    3 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7512 (pt0)
REVERT: A   62 VAL cc_start: 0.8826 (t) cc_final: 0.8479 (m)
REVERT: A   69 ASP cc_start: 0.8350 (t0) cc_final: 0.7942 (t70)
REVERT: A   98 ASP cc_start: 0.6826 (t0) cc_final: 0.6552 (t0)
REVERT: A  108 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7557 (p90)
REVERT: B   67 ASP cc_start: 0.8279 (t0) cc_final: 0.7915 (t70)
REVERT: B  239 CYS cc_start: 0.9145 (m) cc_final: 0.8860 (m)
REVERT: B  417 ASP cc_start: 0.8338 (m-30) cc_final: 0.8041 (m-30)
REVERT: B  423 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8518 (tm-30)
REVERT: B  426 GLN cc_start: 0.8715 (tt0) cc_final: 0.8428 (tt0)
  outliers start: 23
  outliers final: 16
  residues processed: 237
  average time/residue: 0.2196
  time to fit residues: 74.4638
Evaluate side-chains
  234 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 216
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
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   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  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   33 THR
Chi-restraints excluded: chain B residue  322 SER
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:    5.9990
   chunk 14 optimal weight:   10.0000
   chunk 117 optimal weight:    0.4980
   chunk 56 optimal weight:    5.9990
   chunk 105 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   chunk 30 optimal weight:    0.5980
   chunk 120 optimal weight:    0.6980
   chunk 43 optimal weight:    0.0060
   overall best weight:    0.5396

-------------------------------------------------------------------------------
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 256 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.123576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.096641 restraints weight = 14558.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.43
r_work: 0.3112 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2945
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2945
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10000  Z= 0.102
  Angle     :  0.554   7.628  13571  Z= 0.266
  Chirality :  0.043   0.222   1489
  Planarity :  0.004   0.074   1761
  Dihedral  :  8.754 144.004   1483
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 17.12 %
    Favored  : 81.17 %
  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:  0.99 (0.25), residues: 1224
  helix:  2.06 (0.24), residues: 497
  sheet:  0.68 (0.36), residues: 237
  loop : -0.85 (0.27), 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   0.015   0.001   PHE A 255 
 TYR   0.016   0.001   TYR K 189 
 ARG   0.007   0.000   ARG A 422 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03311 (  448)
  hydrogen bonds       : angle       3.78424 ( 1359)
  covalent geometry    : bond        0.00228 (10000)
  covalent geometry    : angle       0.55386 (13571)

*********************** 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
  241 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 223
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   31 SER cc_start: 0.7677 (t) cc_final: 0.7301 (p)
REVERT: K  152 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7839 (mm-30)
REVERT: K  159 ASN cc_start: 0.8311 (t0) cc_final: 0.7895 (t0)
REVERT: K  174 LEU cc_start: 0.8951 (mt) cc_final: 0.8721 (mt)
REVERT: K  347 TYR cc_start: 0.8697 (t80) cc_final: 0.8056 (t80)
REVERT: A    3 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7553 (pt0)
REVERT: A   62 VAL cc_start: 0.8786 (t) cc_final: 0.8440 (m)
REVERT: A   69 ASP cc_start: 0.8410 (t0) cc_final: 0.8020 (t70)
REVERT: A   98 ASP cc_start: 0.6815 (t0) cc_final: 0.6564 (t0)
REVERT: A  108 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7638 (p90)
REVERT: B   67 ASP cc_start: 0.8279 (t0) cc_final: 0.7918 (t70)
REVERT: B  239 CYS cc_start: 0.9099 (m) cc_final: 0.8846 (m)
REVERT: B  417 ASP cc_start: 0.8362 (m-30) cc_final: 0.8027 (m-30)
REVERT: B  423 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8501 (tm-30)
REVERT: B  424 GLN cc_start: 0.8945 (tt0) cc_final: 0.8509 (tt0)
REVERT: B  426 GLN cc_start: 0.8704 (tt0) cc_final: 0.8433 (tt0)
  outliers start: 18
  outliers final: 11
  residues processed: 235
  average time/residue: 0.2063
  time to fit residues: 68.3298
Evaluate side-chains
  226 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 214
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    6 VAL
Chi-restraints excluded: chain K residue   60 THR
Chi-restraints excluded: chain K residue   82 LEU
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  295 CYS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 11 optimal weight:    0.0870
   chunk 48 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 85 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 114 optimal weight:    4.9990
   chunk 67 optimal weight:    0.5980
   chunk 108 optimal weight:    3.9990
   overall best weight:    1.6562

-------------------------------------------------------------------------------
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 184 ASN
B 190 HIS
** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 291 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.120376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.093596 restraints weight = 14691.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 2.33
r_work: 0.3053 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10000  Z= 0.176
  Angle     :  0.597  10.016  13571  Z= 0.290
  Chirality :  0.045   0.216   1489
  Planarity :  0.005   0.073   1761
  Dihedral  :  8.889 144.466   1483
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.56 %
    Favored  : 80.89 %
  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:  1.96 (0.24), residues: 498
  sheet:  0.56 (0.35), residues: 237
  loop : -0.92 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 344 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.014   0.001   PHE B 367 
 TYR   0.014   0.001   TYR A  24 
 ARG   0.008   0.000   ARG A 422 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04041 (  448)
  hydrogen bonds       : angle       3.88508 ( 1359)
  covalent geometry    : bond        0.00422 (10000)
  covalent geometry    : angle       0.59680 (13571)

*********************** 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
  255 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 228
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   42 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8030 (mp10)
REVERT: K  152 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7862 (mm-30)
REVERT: K  159 ASN cc_start: 0.8343 (t0) cc_final: 0.7920 (t0)
REVERT: K  174 LEU cc_start: 0.9017 (mt) cc_final: 0.8792 (mt)
REVERT: K  322 ASN cc_start: 0.8372 (t0) cc_final: 0.8011 (t0)
REVERT: K  347 TYR cc_start: 0.8662 (t80) cc_final: 0.8061 (t80)
REVERT: A    3 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7346 (pt0)
REVERT: A   62 VAL cc_start: 0.8813 (t) cc_final: 0.8477 (m)
REVERT: A   69 ASP cc_start: 0.8440 (t0) cc_final: 0.8058 (t70)
REVERT: A  398 MET cc_start: 0.8614 (ttp) cc_final: 0.8280 (ttm)
REVERT: B   67 ASP cc_start: 0.8254 (t0) cc_final: 0.7879 (t70)
REVERT: B  232 THR cc_start: 0.8649 (m) cc_final: 0.8365 (t)
REVERT: B  239 CYS cc_start: 0.9192 (m) cc_final: 0.8908 (m)
REVERT: B  282 ARG cc_start: 0.8944 (ttm-80) cc_final: 0.8454 (mtp85)
REVERT: B  312 THR cc_start: 0.8445 (m) cc_final: 0.8202 (p)
REVERT: B  417 ASP cc_start: 0.8378 (m-30) cc_final: 0.8109 (m-30)
REVERT: B  423 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8535 (tm-30)
REVERT: B  424 GLN cc_start: 0.8970 (tt0) cc_final: 0.8543 (tt0)
  outliers start: 27
  outliers final: 19
  residues processed: 245
  average time/residue: 0.2163
  time to fit residues: 74.1751
Evaluate side-chains
  239 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 219
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
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   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  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  234 ILE
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue  233 MET
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:    4.9990
   chunk 59 optimal weight:    0.0980
   chunk 65 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 98 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 117 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.6188

-------------------------------------------------------------------------------
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 = 0.3602 r_free = 0.3602 target = 0.120118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.093211 restraints weight = 14629.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 2.40
r_work: 0.3054 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2886
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2886
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10000  Z= 0.172
  Angle     :  0.609  14.816  13571  Z= 0.293
  Chirality :  0.045   0.211   1489
  Planarity :  0.005   0.073   1761
  Dihedral  :  8.860 144.751   1483
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.93 %
    Favored  : 80.89 %
  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:  1.91 (0.24), residues: 496
  sheet:  0.60 (0.36), residues: 230
  loop : -1.01 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  21 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.014   0.001   PHE B 367 
 TYR   0.015   0.001   TYR A  24 
 ARG   0.007   0.000   ARG A 422 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04024 (  448)
  hydrogen bonds       : angle       3.93520 ( 1359)
  covalent geometry    : bond        0.00415 (10000)
  covalent geometry    : angle       0.60860 (13571)

*********************** 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
  247 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 224
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
REVERT: K   31 SER cc_start: 0.7782 (t) cc_final: 0.7422 (p)
REVERT: K   42 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8105 (mp10)
REVERT: K  152 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7852 (mm-30)
REVERT: K  159 ASN cc_start: 0.8348 (t0) cc_final: 0.7971 (t0)
REVERT: K  174 LEU cc_start: 0.9028 (mt) cc_final: 0.8804 (mt)
REVERT: K  322 ASN cc_start: 0.8393 (t0) cc_final: 0.8051 (t0)
REVERT: A    3 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7481 (pt0)
REVERT: A   62 VAL cc_start: 0.8822 (t) cc_final: 0.8495 (m)
REVERT: A   69 ASP cc_start: 0.8433 (t0) cc_final: 0.8018 (t70)
REVERT: A   98 ASP cc_start: 0.6806 (t0) cc_final: 0.6549 (t0)
REVERT: B   67 ASP cc_start: 0.8314 (t0) cc_final: 0.7925 (t70)
REVERT: B  232 THR cc_start: 0.8654 (m) cc_final: 0.8355 (t)
REVERT: B  239 CYS cc_start: 0.9196 (m) cc_final: 0.8908 (m)
REVERT: B  282 ARG cc_start: 0.8971 (ttm-80) cc_final: 0.8482 (mtp85)
REVERT: B  417 ASP cc_start: 0.8391 (m-30) cc_final: 0.8128 (m-30)
REVERT: B  423 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8546 (tm-30)
REVERT: B  424 GLN cc_start: 0.8985 (tt0) cc_final: 0.8535 (tt0)
  outliers start: 23
  outliers final: 19
  residues processed: 238
  average time/residue: 0.2307
  time to fit residues: 78.0504
Evaluate side-chains
  240 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 220
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
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   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  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  234 ILE
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue  233 MET
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:    0.4980
   chunk 65 optimal weight:    0.0170
   chunk 6 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 90 optimal weight:    0.6980
   overall best weight:    0.5820

-------------------------------------------------------------------------------
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 = 0.3644 r_free = 0.3644 target = 0.123005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.096570 restraints weight = 14531.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.33
r_work: 0.3114 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2949
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2949 r_free = 0.2949    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2949 r_free = 0.2949    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2949
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10000  Z= 0.106
  Angle     :  0.578   8.416  13571  Z= 0.277
  Chirality :  0.043   0.220   1489
  Planarity :  0.004   0.073   1761
  Dihedral  :  8.653 144.714   1483
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.03 %
    Favored  : 81.17 %
  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:  0.91 (0.25), residues: 1224
  helix:  2.03 (0.24), residues: 497
  sheet:  0.62 (0.36), residues: 230
  loop : -0.89 (0.27), residues: 497

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   0.015   0.001   PHE A 255 
 TYR   0.012   0.001   TYR K 150 
 ARG   0.006   0.000   ARG A 422 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03352 (  448)
  hydrogen bonds       : angle       3.79532 ( 1359)
  covalent geometry    : bond        0.00240 (10000)
  covalent geometry    : angle       0.57833 (13571)

********************** 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
  234 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 215
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   31 SER cc_start: 0.7863 (t) cc_final: 0.7548 (p)
REVERT: K   42 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8040 (mp10)
REVERT: K   83 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8202 (mm-40)
REVERT: K  152 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7825 (mm-30)
REVERT: K  159 ASN cc_start: 0.8332 (t0) cc_final: 0.7910 (t0)
REVERT: K  174 LEU cc_start: 0.9002 (mt) cc_final: 0.8771 (mt)
REVERT: K  322 ASN cc_start: 0.8376 (t0) cc_final: 0.8015 (t0)
REVERT: A    3 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7511 (pt0)
REVERT: A   62 VAL cc_start: 0.8795 (t) cc_final: 0.8445 (m)
REVERT: A   69 ASP cc_start: 0.8460 (t0) cc_final: 0.8113 (t70)
REVERT: A   98 ASP cc_start: 0.6787 (t0) cc_final: 0.6545 (t0)
REVERT: A  108 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7733 (p90)
REVERT: A  398 MET cc_start: 0.8467 (ttp) cc_final: 0.8109 (ttm)
REVERT: B   67 ASP cc_start: 0.8249 (t0) cc_final: 0.7839 (t70)
REVERT: B  239 CYS cc_start: 0.9122 (m) cc_final: 0.8869 (m)
REVERT: B  282 ARG cc_start: 0.8908 (ttm-80) cc_final: 0.8421 (mtp85)
REVERT: B  312 THR cc_start: 0.8403 (m) cc_final: 0.8203 (p)
REVERT: B  323 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7559 (mtm)
REVERT: B  417 ASP cc_start: 0.8354 (m-30) cc_final: 0.8023 (m-30)
REVERT: B  423 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8521 (tm-30)
REVERT: B  424 GLN cc_start: 0.8953 (tt0) cc_final: 0.8527 (tt0)
REVERT: B  426 GLN cc_start: 0.8657 (tt0) cc_final: 0.8389 (tt0)
  outliers start: 19
  outliers final: 13
  residues processed: 227
  average time/residue: 0.2199
  time to fit residues: 70.3850
Evaluate side-chains
  232 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 216
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
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   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 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  295 CYS
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  323 MET
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:    4.9990
   chunk 120 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9980
   chunk 86 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 = 0.3616 r_free = 0.3616 target = 0.121188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.094471 restraints weight = 14658.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 2.37
r_work: 0.3057 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
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 = 0.40   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 = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2905
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2806

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= 0.154
  Angle     :  0.595   9.114  13571  Z= 0.287
  Chirality :  0.045   0.216   1489
  Planarity :  0.004   0.072   1761
  Dihedral  :  8.722 144.966   1483
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.65 %
    Favored  : 81.55 %
  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:  2.00 (0.24), residues: 495
  sheet:  0.58 (0.36), residues: 230
  loop : -0.94 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  21 
 HIS   0.006   0.001   HIS B 190 
 PHE   0.013   0.001   PHE B 367 
 TYR   0.014   0.001   TYR A  24 
 ARG   0.007   0.000   ARG A 422 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03818 (  448)
  hydrogen bonds       : angle       3.85223 ( 1359)
  covalent geometry    : bond        0.00366 (10000)
  covalent geometry    : angle       0.59494 (13571)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5461.31 seconds
wall clock time: 96 minutes 5.15 seconds (5765.15 seconds total)