Starting phenix.real_space_refine
on Mon Mar 11 02:19:21 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga0_29883/03_2024/8ga0_29883.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga0_29883/03_2024/8ga0_29883.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga0_29883/03_2024/8ga0_29883.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga0_29883/03_2024/8ga0_29883.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga0_29883/03_2024/8ga0_29883.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga0_29883/03_2024/8ga0_29883.pdb"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.052
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: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    4348      2.51       5
     N    1095      2.21       5
     O    1115      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   23": "NH1" <-> "NH2"
    Residue "A ARG   28": "NH1" <-> "NH2"
    Residue "A TYR   75": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  111": "OE1" <-> "OE2"
    Residue "A GLU  117": "OE1" <-> "OE2"
    Residue "A ARG  160": "NH1" <-> "NH2"
    Residue "A GLU  172": "OE1" <-> "OE2"
    Residue "A PHE  219": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  232": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  235": "OE1" <-> "OE2"
    Residue "A PHE  262": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  278": "OD1" <-> "OD2"
    Residue "A GLU  385": "OE1" <-> "OE2"
    Residue "A GLU  414": "OE1" <-> "OE2"
    Residue "A ASP  417": "OD1" <-> "OD2"
    Residue "B ARG   23": "NH1" <-> "NH2"
    Residue "B GLU   27": "OE1" <-> "OE2"
    Residue "B ARG   28": "NH1" <-> "NH2"
    Residue "B TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  205": "NH1" <-> "NH2"
    Residue "B TYR  255": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  278": "OD1" <-> "OD2"
    Residue "B GLU  377": "OE1" <-> "OE2"
    Residue "B TYR  419": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  438": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 6598
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3287
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 440, 3287
          Classifications: {'peptide': 440}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 19, 'TRANS': 420}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 3311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 442, 3311
          Classifications: {'peptide': 442}
          Link IDs: {'PTRANS': 19, 'TRANS': 422}
  Time building chain proxies: 3.97, per 1000 atoms: 0.60
  Number of scatterers: 6598
  At special positions: 0
  Unit cell: (72.092, 88.232, 114.056, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1115      8.00
     N    1095      7.00
     C    4348      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.21
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1536

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      66.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 28
      removed outlier: 3.520A  pdb=" N   GLU A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 38
    Processing helix  chain 'A' and resid 38 through 48
    Processing helix  chain 'A' and resid 50 through 55
    Processing helix  chain 'A' and resid 55 through 67
      removed outlier: 3.934A  pdb=" N   GLN A  61 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASN A  62 " --> pdb=" O   ALA A  58 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ARG A  64 " --> pdb=" O   LEU A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 71
      removed outlier: 3.549A  pdb=" N   THR A  71 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 68 through 71'
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 79 through 89
      removed outlier: 3.542A  pdb=" N   PHE A  83 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   CYS A  85 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   SER A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LEU A  89 " --> pdb=" O   CYS A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 93
    Processing helix  chain 'A' and resid 96 through 101
    Processing helix  chain 'A' and resid 109 through 114
    Processing helix  chain 'A' and resid 127 through 132
    Processing helix  chain 'A' and resid 133 through 141
      removed outlier: 3.502A  pdb=" N   GLY A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR A 138 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   LEU A 139 " --> pdb=" O   GLY A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 165
      removed outlier: 4.131A  pdb=" N   ILE A 154 " --> pdb=" O   PRO A 150 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   ARG A 160 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   LEU A 163 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE A 165 " --> pdb=" O   MET A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 188
      removed outlier: 3.884A  pdb=" N   LEU A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 202
      removed outlier: 3.671A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   TYR A 202 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 3.669A  pdb=" N   LYS A 216 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 231
      removed outlier: 4.026A  pdb=" N   MET A 228 " --> pdb=" O   MET A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 252
      removed outlier: 3.552A  pdb=" N   THR A 251 " --> pdb=" O   PRO A 248 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU A 252 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 248 through 252'
    Processing helix  chain 'A' and resid 253 through 274
      removed outlier: 3.933A  pdb=" N   GLY A 259 " --> pdb=" O   TYR A 255 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
    Processing helix  chain 'A' and resid 275 through 280
    Processing helix  chain 'A' and resid 281 through 284
      removed outlier: 3.856A  pdb=" N   HIS A 284 " --> pdb=" O   HIS A 281 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 281 through 284'
    Processing helix  chain 'A' and resid 287 through 292
      removed outlier: 4.028A  pdb=" N   VAL A 292 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 309
      removed outlier: 3.553A  pdb=" N   ALA A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   ILE A 298 " --> pdb=" O   MET A 294 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   PHE A 307 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.585A  pdb=" N   VAL A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   THR A 343 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 379
      removed outlier: 4.603A  pdb=" N   VAL A 366 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLU A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 383
      removed outlier: 3.777A  pdb=" N   HIS A 383 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 380 through 383'
    Processing helix  chain 'A' and resid 387 through 393
      removed outlier: 3.683A  pdb=" N   ILE A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ALA A 392 " --> pdb=" O   THR A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 402
    Processing helix  chain 'A' and resid 406 through 416
      removed outlier: 3.944A  pdb=" N   ILE A 410 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   VAL A 412 " --> pdb=" O   GLY A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 422
      removed outlier: 3.793A  pdb=" N   ILE A 422 " --> pdb=" O   TYR A 419 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 419 through 422'
    Processing helix  chain 'A' and resid 423 through 440
      removed outlier: 3.548A  pdb=" N   THR A 433 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ALA A 436 " --> pdb=" O   ALA A 432 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLN A 437 " --> pdb=" O   THR A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 461
      removed outlier: 4.347A  pdb=" N   LEU A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLU A 457 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLN A 460 " --> pdb=" O   GLN A 456 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU A 461 " --> pdb=" O   GLU A 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 26
      removed outlier: 3.612A  pdb=" N   LEU B  25 " --> pdb=" O   LEU B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 52
      removed outlier: 3.503A  pdb=" N   PHE B  37 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ALA B  39 " --> pdb=" O   ILE B  35 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLY B  43 " --> pdb=" O   ALA B  39 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   THR B  44 " --> pdb=" O   ALA B  40 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU B  45 " --> pdb=" O   VAL B  41 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL B  51 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 69
      removed outlier: 4.019A  pdb=" N   TRP B  59 " --> pdb=" O   LYS B  55 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASN B  62 " --> pdb=" O   ALA B  58 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   MET B  65 " --> pdb=" O   GLN B  61 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   GLY B  66 " --> pdb=" O   ASN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 82
      removed outlier: 3.507A  pdb=" N   THR B  80 " --> pdb=" O   PRO B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 98
      removed outlier: 3.631A  pdb=" N   PHE B  92 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   PHE B  95 " --> pdb=" O   MET B  91 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   VAL B  97 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 132
      removed outlier: 3.945A  pdb=" N   LEU B 128 " --> pdb=" O   TRP B 124 " (cutoff:3.500A)
      Proline residue:  B 129  - end of helix
    Processing helix  chain 'B' and resid 133 through 141
      removed outlier: 3.664A  pdb=" N   GLY B 137 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   THR B 138 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LEU B 139 " --> pdb=" O   GLY B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 160
      removed outlier: 4.143A  pdb=" N   ILE B 154 " --> pdb=" O   PRO B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 164
    Processing helix  chain 'B' and resid 177 through 187
      removed outlier: 3.694A  pdb=" N   LEU B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 201
      removed outlier: 3.637A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 231
      removed outlier: 3.557A  pdb=" N   GLY B 221 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   SER B 225 " --> pdb=" O   GLY B 221 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   MET B 228 " --> pdb=" O   MET B 224 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   TYR B 229 " --> pdb=" O   SER B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 277
      removed outlier: 3.837A  pdb=" N   ILE B 257 " --> pdb=" O   TRP B 253 " (cutoff:3.500A)
      Proline residue:  B 267  - end of helix
      removed outlier: 3.787A  pdb=" N   LEU B 274 " --> pdb=" O   ASN B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 297
    Processing helix  chain 'B' and resid 300 through 309
      removed outlier: 3.597A  pdb=" N   GLY B 306 " --> pdb=" O   CYS B 302 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   PHE B 307 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL B 308 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 313
      removed outlier: 4.032A  pdb=" N   SER B 313 " --> pdb=" O   PRO B 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 310 through 313'
    Processing helix  chain 'B' and resid 319 through 324
    Processing helix  chain 'B' and resid 329 through 334
      removed outlier: 3.562A  pdb=" N   VAL B 334 " --> pdb=" O   MET B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 345
      removed outlier: 4.750A  pdb=" N   ARG B 340 " --> pdb=" O   ILE B 336 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE B 342 " --> pdb=" O   VAL B 338 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   THR B 343 " --> pdb=" O   ALA B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 379
      removed outlier: 3.521A  pdb=" N   ALA B 362 " --> pdb=" O   ALA B 358 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   THR B 365 " --> pdb=" O   LEU B 361 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU B 367 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   VAL B 374 " --> pdb=" O   ALA B 370 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   GLU B 377 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 383
      removed outlier: 3.565A  pdb=" N   HIS B 383 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 380 through 383'
    Processing helix  chain 'B' and resid 393 through 397
      removed outlier: 3.657A  pdb=" N   ALA B 396 " --> pdb=" O   GLY B 393 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   LEU B 397 " --> pdb=" O   MET B 394 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 393 through 397'
    Processing helix  chain 'B' and resid 404 through 410
    Processing helix  chain 'B' and resid 412 through 417
    Processing helix  chain 'B' and resid 422 through 439
      removed outlier: 3.844A  pdb=" N   ILE B 426 " --> pdb=" O   ILE B 422 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA B 432 " --> pdb=" O   THR B 428 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU B 435 " --> pdb=" O   GLY B 431 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   GLN B 437 " --> pdb=" O   THR B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 448
    Processing helix  chain 'B' and resid 448 through 457
      removed outlier: 4.029A  pdb=" N   ALA B 454 " --> pdb=" O   ALA B 450 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LYS B 455 " --> pdb=" O   ARG B 451 " (cutoff:3.500A)

    251 hydrogen bonds defined for protein.
    747 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.84

  Time building geometry restraints manager: 2.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2059
        1.34 -     1.46: 1333
        1.46 -     1.58: 3278
        1.58 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 6744
  Sorted by residual:
  bond pdb=" C   ALA A 358 "
       pdb=" N   PRO A 359 "
    ideal  model  delta    sigma   weight residual
    1.334  1.379 -0.046 8.40e-03 1.42e+04 2.98e+01
  bond pdb=" N   GLU B 235 "
       pdb=" CA  GLU B 235 "
    ideal  model  delta    sigma   weight residual
    1.460  1.482 -0.022 1.54e-02 4.22e+03 2.01e+00
  bond pdb=" CA  THR A  31 "
       pdb=" C   THR A  31 "
    ideal  model  delta    sigma   weight residual
    1.524  1.539 -0.016 1.26e-02 6.30e+03 1.53e+00
  bond pdb=" C   LEU A 423 "
       pdb=" N   PRO A 424 "
    ideal  model  delta    sigma   weight residual
    1.336  1.351 -0.015 1.23e-02 6.61e+03 1.47e+00
  bond pdb=" C   LEU B 423 "
       pdb=" N   PRO B 424 "
    ideal  model  delta    sigma   weight residual
    1.336  1.351 -0.015 1.25e-02 6.40e+03 1.40e+00
  ... (remaining 6739 not shown)

  Histogram of bond angle deviations from ideal:
       99.95 -   106.77: 218
      106.77 -   113.60: 3655
      113.60 -   120.42: 2747
      120.42 -   127.25: 2469
      127.25 -   134.07: 71
  Bond angle restraints: 9160
  Sorted by residual:
  angle pdb=" N   ILE B 213 "
        pdb=" CA  ILE B 213 "
        pdb=" C   ILE B 213 "
      ideal   model   delta    sigma   weight residual
     113.71  104.51    9.20 9.50e-01 1.11e+00 9.38e+01
  angle pdb=" N   THR B 251 "
        pdb=" CA  THR B 251 "
        pdb=" C   THR B 251 "
      ideal   model   delta    sigma   weight residual
     114.56  106.62    7.94 1.27e+00 6.20e-01 3.91e+01
  angle pdb=" N   ILE B 336 "
        pdb=" CA  ILE B 336 "
        pdb=" C   ILE B 336 "
      ideal   model   delta    sigma   weight residual
     111.91  106.45    5.46 8.90e-01 1.26e+00 3.77e+01
  angle pdb=" N   ILE A  35 "
        pdb=" CA  ILE A  35 "
        pdb=" C   ILE A  35 "
      ideal   model   delta    sigma   weight residual
     112.29  108.55    3.74 9.40e-01 1.13e+00 1.59e+01
  angle pdb=" C   HIS A 234 "
        pdb=" N   GLU A 235 "
        pdb=" CA  GLU A 235 "
      ideal   model   delta    sigma   weight residual
     121.54  128.53   -6.99 1.91e+00 2.74e-01 1.34e+01
  ... (remaining 9155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 3458
       17.57 -    35.14: 380
       35.14 -    52.71: 52
       52.71 -    70.28: 5
       70.28 -    87.85: 3
  Dihedral angle restraints: 3898
    sinusoidal: 1462
      harmonic: 2436
  Sorted by residual:
  dihedral pdb=" CA  THR B 211 "
           pdb=" C   THR B 211 "
           pdb=" N   LEU B 212 "
           pdb=" CA  LEU B 212 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.54  -29.46     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  LEU B 212 "
           pdb=" C   LEU B 212 "
           pdb=" N   ILE B 213 "
           pdb=" CA  ILE B 213 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.74   20.26     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  ALA B 358 "
           pdb=" C   ALA B 358 "
           pdb=" N   PRO B 359 "
           pdb=" CA  PRO B 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.87   20.13     0      5.00e+00 4.00e-02 1.62e+01
  ... (remaining 3895 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 790
       0.051 -    0.102: 233
       0.102 -    0.153: 46
       0.153 -    0.204: 8
       0.204 -    0.255: 3
  Chirality restraints: 1080
  Sorted by residual:
  chirality pdb=" CB  ILE B 410 "
            pdb=" CA  ILE B 410 "
            pdb=" CG1 ILE B 410 "
            pdb=" CG2 ILE B 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.90   -0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CB  ILE B 336 "
            pdb=" CA  ILE B 336 "
            pdb=" CG1 ILE B 336 "
            pdb=" CG2 ILE B 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.89   -0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CB  ILE A 336 "
            pdb=" CA  ILE A 336 "
            pdb=" CG1 ILE A 336 "
            pdb=" CG2 ILE A 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.85   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 1077 not shown)

  Planarity restraints: 1146
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 358 "   -0.048 5.00e-02 4.00e+02   7.22e-02 8.34e+00
        pdb=" N   PRO B 359 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO B 359 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 359 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 109 "   -0.045 5.00e-02 4.00e+02   6.79e-02 7.37e+00
        pdb=" N   PRO A 110 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 110 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 110 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 149 "    0.045 5.00e-02 4.00e+02   6.78e-02 7.35e+00
        pdb=" N   PRO A 150 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "    0.038 5.00e-02 4.00e+02
  ... (remaining 1143 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1885
        2.80 -     3.32: 5441
        3.32 -     3.85: 10899
        3.85 -     4.37: 13154
        4.37 -     4.90: 22231
  Nonbonded interactions: 53610
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 345 "
            pdb=" OG  SER A 349 "
     model   vdw
     2.274 2.440
  nonbonded pdb=" O   VAL B 412 "
            pdb=" OG1 THR B 416 "
     model   vdw
     2.333 2.440
  nonbonded pdb=" O   ARG B 147 "
            pdb=" OG1 THR B 151 "
     model   vdw
     2.335 2.440
  nonbonded pdb=" O   VAL A 412 "
            pdb=" OG1 THR A 416 "
     model   vdw
     2.337 2.440
  nonbonded pdb=" OG  SER B  86 "
            pdb=" O   GLY B 299 "
     model   vdw
     2.346 2.440
  ... (remaining 53605 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 22 through 458 or (resid 459 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 460 or (resid 461 and (name N or name CA or \ 
 name C or name O or name CB ))))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          1.910
  Check model and map are aligned:         0.100
  Set scattering table:                    0.060
  Process input model:                     20.610
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
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   0.053   6744  Z= 0.246
  Angle     :  0.840   9.202   9160  Z= 0.460
  Chirality :  0.051   0.255   1080
  Planarity :  0.007   0.072   1146
  Dihedral  : 14.181  87.846   2362
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.86 (0.16), residues: 878
  helix: -4.82 (0.08), residues: 586
  sheet:  None (None), residues: 0
  loop : -3.41 (0.28), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 291 
 HIS   0.007   0.001   HIS A 284 
 PHE   0.015   0.001   PHE A 357 
 TYR   0.017   0.001   TYR B 419 
 ARG   0.003   0.000   ARG A 205 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.7827 (mt) cc_final: 0.7549 (mt)
REVERT: A  213 ILE cc_start: 0.7488 (tp) cc_final: 0.7076 (tp)
REVERT: A  276 MET cc_start: 0.5353 (mtt) cc_final: 0.5098 (mtt)
REVERT: B   38 MET cc_start: 0.7578 (mmt) cc_final: 0.7359 (mmt)
REVERT: B   55 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7921 (mtpp)
REVERT: B  201 ILE cc_start: 0.8935 (mt) cc_final: 0.8668 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2134
  time to fit residues: 40.3178
Evaluate side-chains
  117 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.0570
   chunk 66 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 22 optimal weight:    5.9990
   chunk 44 optimal weight:   20.0000
   chunk 35 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 26 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    1.1102

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

Flipped N/Q/H residues before XYZ refinement:
A 284 HIS
B  62 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6744  Z= 0.242
  Angle     :  0.607   6.098   9160  Z= 0.313
  Chirality :  0.041   0.113   1080
  Planarity :  0.006   0.058   1146
  Dihedral  :  5.608  23.313    936
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.50 %
    Favored  : 83.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.55 (0.20), residues: 878
  helix: -3.65 (0.14), residues: 618
  sheet:  None (None), residues: 0
  loop : -3.14 (0.31), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 124 
 HIS   0.001   0.000   HIS B 284 
 PHE   0.027   0.001   PHE A  95 
 TYR   0.008   0.001   TYR B 419 
 ARG   0.006   0.000   ARG B  98 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.689 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8011 (mt) cc_final: 0.7659 (mt)
REVERT: A  213 ILE cc_start: 0.7593 (tp) cc_final: 0.7106 (tp)
REVERT: A  256 LEU cc_start: 0.7876 (tp) cc_final: 0.7375 (tp)
REVERT: A  294 MET cc_start: 0.7961 (tmm) cc_final: 0.7605 (tpp)
REVERT: B   55 LYS cc_start: 0.8357 (mtpt) cc_final: 0.7985 (mtpp)
REVERT: B  201 ILE cc_start: 0.8948 (mt) cc_final: 0.8704 (mt)
REVERT: B  228 MET cc_start: 0.6970 (tpp) cc_final: 0.6540 (tpt)
REVERT: B  254 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7723 (mp)
REVERT: B  357 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.7047 (m-10)
  outliers start: 13
  outliers final: 9
  residues processed: 126
  average time/residue: 0.1680
  time to fit residues: 29.0813
Evaluate side-chains
  122 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  357 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 44 optimal weight:   20.0000
   chunk 24 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0170
   chunk 22 optimal weight:    0.0980
   chunk 80 optimal weight:    0.0050
   chunk 86 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.3832

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

Flipped N/Q/H residues before XYZ refinement:
B 233 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6744  Z= 0.147
  Angle     :  0.531   5.664   9160  Z= 0.273
  Chirality :  0.039   0.119   1080
  Planarity :  0.004   0.046   1146
  Dihedral  :  5.042  23.927    936
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.82 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.55 (0.24), residues: 878
  helix: -2.85 (0.17), residues: 628
  sheet:  None (None), residues: 0
  loop : -2.88 (0.32), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 291 
 HIS   0.001   0.000   HIS A  70 
 PHE   0.020   0.001   PHE A 208 
 TYR   0.006   0.001   TYR B  94 
 ARG   0.004   0.000   ARG B  98 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.685 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.7989 (tp) cc_final: 0.7558 (mm)
REVERT: A  213 ILE cc_start: 0.7364 (tp) cc_final: 0.7010 (tp)
REVERT: A  293 LEU cc_start: 0.8023 (mm) cc_final: 0.7660 (mm)
REVERT: A  294 MET cc_start: 0.7948 (tmm) cc_final: 0.7506 (tpp)
REVERT: B   55 LYS cc_start: 0.8455 (mtpt) cc_final: 0.8076 (mtpp)
REVERT: B  228 MET cc_start: 0.6867 (tpp) cc_final: 0.6587 (tpt)
  outliers start: 11
  outliers final: 6
  residues processed: 133
  average time/residue: 0.1767
  time to fit residues: 31.6812
Evaluate side-chains
  120 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  293 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0370
   chunk 38 optimal weight:    0.0470
   chunk 53 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6744  Z= 0.188
  Angle     :  0.554   5.825   9160  Z= 0.281
  Chirality :  0.041   0.221   1080
  Planarity :  0.004   0.045   1146
  Dihedral  :  4.921  22.967    936
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.98 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.91 (0.25), residues: 878
  helix: -2.38 (0.19), residues: 623
  sheet:  None (None), residues: 0
  loop : -2.65 (0.34), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 291 
 HIS   0.002   0.000   HIS A 284 
 PHE   0.028   0.001   PHE A  95 
 TYR   0.005   0.001   TYR B  94 
 ARG   0.007   0.000   ARG A 403 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.628 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8147 (mt) cc_final: 0.7806 (mp)
REVERT: A   84 LEU cc_start: 0.8030 (tp) cc_final: 0.7567 (mm)
REVERT: A  213 ILE cc_start: 0.7403 (tp) cc_final: 0.7044 (tp)
REVERT: A  293 LEU cc_start: 0.8169 (mm) cc_final: 0.7766 (mm)
REVERT: A  294 MET cc_start: 0.8154 (tmm) cc_final: 0.7605 (tpp)
REVERT: B   55 LYS cc_start: 0.8525 (mtpt) cc_final: 0.8147 (mtpp)
REVERT: B  357 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.7024 (m-10)
REVERT: B  384 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7275 (pp)
  outliers start: 19
  outliers final: 14
  residues processed: 132
  average time/residue: 0.1759
  time to fit residues: 31.2555
Evaluate side-chains
  130 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 35 optimal weight:    0.2980
   chunk 72 optimal weight:    0.6980
   chunk 58 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0030
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6744  Z= 0.164
  Angle     :  0.527   5.414   9160  Z= 0.266
  Chirality :  0.040   0.238   1080
  Planarity :  0.004   0.038   1146
  Dihedral  :  4.722  22.530    936
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.94 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.49 (0.26), residues: 878
  helix: -2.06 (0.20), residues: 625
  sheet:  None (None), residues: 0
  loop : -2.47 (0.35), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A 284 
 PHE   0.023   0.001   PHE A  95 
 TYR   0.006   0.001   TYR B  94 
 ARG   0.005   0.000   ARG B 282 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.621 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8144 (mt) cc_final: 0.7815 (mp)
REVERT: A   84 LEU cc_start: 0.8005 (tp) cc_final: 0.7516 (mm)
REVERT: A  213 ILE cc_start: 0.7349 (tp) cc_final: 0.7027 (tp)
REVERT: A  294 MET cc_start: 0.8228 (tmm) cc_final: 0.7831 (tpp)
REVERT: B   55 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8122 (mtpp)
REVERT: B  357 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6938 (m-10)
REVERT: B  384 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7250 (pp)
  outliers start: 21
  outliers final: 15
  residues processed: 129
  average time/residue: 0.1754
  time to fit residues: 30.4360
Evaluate side-chains
  130 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0040
   chunk 20 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 44 optimal weight:    9.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6744  Z= 0.177
  Angle     :  0.534   7.690   9160  Z= 0.266
  Chirality :  0.041   0.252   1080
  Planarity :  0.004   0.036   1146
  Dihedral  :  4.664  22.404    936
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 20.39 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.27), residues: 878
  helix: -1.84 (0.20), residues: 619
  sheet:  None (None), residues: 0
  loop : -2.35 (0.35), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A 284 
 PHE   0.021   0.001   PHE A  95 
 TYR   0.004   0.001   TYR A  94 
 ARG   0.006   0.000   ARG B 282 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.6675 (mtt) cc_final: 0.6444 (tpp)
REVERT: A   45 LEU cc_start: 0.8063 (mt) cc_final: 0.7663 (mp)
REVERT: A   84 LEU cc_start: 0.7906 (tp) cc_final: 0.7452 (mm)
REVERT: A  213 ILE cc_start: 0.7355 (tp) cc_final: 0.7014 (tp)
REVERT: A  294 MET cc_start: 0.8261 (tmm) cc_final: 0.7785 (tpp)
REVERT: B   55 LYS cc_start: 0.8481 (mtpt) cc_final: 0.8073 (mtpp)
REVERT: B  357 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.6922 (m-10)
REVERT: B  384 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7269 (pp)
  outliers start: 23
  outliers final: 17
  residues processed: 128
  average time/residue: 0.1805
  time to fit residues: 30.8369
Evaluate side-chains
  134 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0970
   chunk 51 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6744  Z= 0.182
  Angle     :  0.538   6.958   9160  Z= 0.266
  Chirality :  0.041   0.261   1080
  Planarity :  0.004   0.036   1146
  Dihedral  :  4.614  22.034    936
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 21.15 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.99 (0.27), residues: 878
  helix: -1.72 (0.21), residues: 624
  sheet:  None (None), residues: 0
  loop : -2.22 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A 284 
 PHE   0.031   0.001   PHE A  95 
 TYR   0.005   0.001   TYR B 100 
 ARG   0.006   0.000   ARG B 282 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.602 
Fit side-chains
REVERT: A   38 MET cc_start: 0.6720 (mtt) cc_final: 0.6508 (tpp)
REVERT: A   45 LEU cc_start: 0.8010 (mt) cc_final: 0.7628 (mp)
REVERT: A   84 LEU cc_start: 0.7907 (tp) cc_final: 0.7463 (mm)
REVERT: A  213 ILE cc_start: 0.7329 (tp) cc_final: 0.7052 (tp)
REVERT: A  294 MET cc_start: 0.8286 (tmm) cc_final: 0.7811 (tpp)
REVERT: B   55 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8084 (mtpp)
REVERT: B  207 GLN cc_start: 0.7665 (pm20) cc_final: 0.7392 (pm20)
REVERT: B  357 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6956 (m-10)
REVERT: B  384 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7258 (pp)
  outliers start: 24
  outliers final: 18
  residues processed: 128
  average time/residue: 0.1681
  time to fit residues: 29.2779
Evaluate side-chains
  130 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 25 optimal weight:    0.2980
   chunk 16 optimal weight:    1.9990
   chunk 53 optimal weight:    0.3980
   chunk 57 optimal weight:    0.5980
   chunk 41 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 77 optimal weight:    0.5980
   chunk 81 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6744  Z= 0.161
  Angle     :  0.532   6.722   9160  Z= 0.263
  Chirality :  0.041   0.269   1080
  Planarity :  0.004   0.036   1146
  Dihedral  :  4.510  21.603    936
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 21.45 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.27), residues: 878
  helix: -1.62 (0.21), residues: 629
  sheet:  None (None), residues: 0
  loop : -2.25 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A 284 
 PHE   0.027   0.001   PHE A  95 
 TYR   0.005   0.001   TYR B  94 
 ARG   0.007   0.000   ARG B 282 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.776 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.7970 (mt) cc_final: 0.7606 (mp)
REVERT: A   84 LEU cc_start: 0.7891 (tp) cc_final: 0.7452 (mm)
REVERT: A  213 ILE cc_start: 0.7261 (tp) cc_final: 0.7008 (tp)
REVERT: A  294 MET cc_start: 0.8298 (tmm) cc_final: 0.7813 (tpp)
REVERT: B   55 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8150 (mtpp)
REVERT: B  207 GLN cc_start: 0.7700 (pm20) cc_final: 0.7372 (pm20)
REVERT: B  357 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6928 (m-10)
REVERT: B  384 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7272 (pp)
  outliers start: 22
  outliers final: 17
  residues processed: 128
  average time/residue: 0.1741
  time to fit residues: 30.3046
Evaluate side-chains
  131 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 78 optimal weight:    0.0030
   chunk 51 optimal weight:    0.7980
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6744  Z= 0.176
  Angle     :  0.540   6.604   9160  Z= 0.265
  Chirality :  0.041   0.284   1080
  Planarity :  0.004   0.041   1146
  Dihedral  :  4.474  20.916    936
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 21.30 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.28), residues: 878
  helix: -1.49 (0.21), residues: 629
  sheet:  None (None), residues: 0
  loop : -2.23 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 291 
 HIS   0.002   0.000   HIS A 284 
 PHE   0.026   0.001   PHE A  95 
 TYR   0.005   0.001   TYR B 100 
 ARG   0.008   0.000   ARG B 282 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.620 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.7927 (mt) cc_final: 0.7613 (mp)
REVERT: A   84 LEU cc_start: 0.7903 (tp) cc_final: 0.7468 (mm)
REVERT: A  213 ILE cc_start: 0.7261 (tp) cc_final: 0.7030 (tp)
REVERT: B   55 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8106 (mtpp)
REVERT: B  207 GLN cc_start: 0.7846 (pm20) cc_final: 0.7563 (pm20)
REVERT: B  357 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6930 (m-10)
REVERT: B  384 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7234 (pp)
  outliers start: 20
  outliers final: 16
  residues processed: 128
  average time/residue: 0.1695
  time to fit residues: 29.6948
Evaluate side-chains
  132 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0470
   chunk 87 optimal weight:    2.9990
   chunk 80 optimal weight:    8.9990
   chunk 69 optimal weight:    0.4980
   chunk 7 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 55 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6744  Z= 0.169
  Angle     :  0.543   6.720   9160  Z= 0.266
  Chirality :  0.041   0.290   1080
  Planarity :  0.004   0.041   1146
  Dihedral  :  4.403  20.815    936
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 21.60 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.28), residues: 878
  helix: -1.31 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -2.12 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 291 
 HIS   0.002   0.000   HIS A 284 
 PHE   0.025   0.001   PHE A  95 
 TYR   0.005   0.001   TYR B  94 
 ARG   0.008   0.000   ARG B 282 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.727 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.7887 (mt) cc_final: 0.7566 (mp)
REVERT: A   84 LEU cc_start: 0.7941 (tp) cc_final: 0.7528 (mm)
REVERT: A  213 ILE cc_start: 0.7296 (tp) cc_final: 0.7024 (tp)
REVERT: A  294 MET cc_start: 0.8307 (tmm) cc_final: 0.8016 (tpp)
REVERT: B   55 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8107 (mtpp)
REVERT: B  203 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6650 (mt-10)
REVERT: B  207 GLN cc_start: 0.7843 (pm20) cc_final: 0.7510 (pm20)
REVERT: B  357 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6936 (m-10)
REVERT: B  384 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7189 (pp)
REVERT: B  407 THR cc_start: 0.7818 (m) cc_final: 0.7347 (m)
  outliers start: 19
  outliers final: 15
  residues processed: 126
  average time/residue: 0.1741
  time to fit residues: 29.6666
Evaluate side-chains
  133 residues out of total 664 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    0.0010
   chunk 64 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 69 optimal weight:    0.1980
   chunk 29 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.4586

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.206431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.182632 restraints weight = 8006.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.186228 restraints weight = 4658.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.188552 restraints weight = 3286.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.4099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6744  Z= 0.156
  Angle     :  0.537   6.592   9160  Z= 0.263
  Chirality :  0.041   0.285   1080
  Planarity :  0.004   0.037   1146
  Dihedral  :  4.290  20.811    936
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 21.90 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.28), residues: 878
  helix: -1.12 (0.21), residues: 624
  sheet:  None (None), residues: 0
  loop : -2.07 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 291 
 HIS   0.002   0.000   HIS A 284 
 PHE   0.025   0.001   PHE A  95 
 TYR   0.005   0.001   TYR B  94 
 ARG   0.008   0.000   ARG B 282 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1576.36 seconds
wall clock time: 29 minutes 7.97 seconds (1747.97 seconds total)