Starting phenix.real_space_refine
on Mon May 19 20:43:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g8i_29856/05_2025/8g8i_29856.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g8i_29856/05_2025/8g8i_29856.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g8i_29856/05_2025/8g8i_29856.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g8i_29856/05_2025/8g8i_29856.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g8i_29856/05_2025/8g8i_29856.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g8i_29856/05_2025/8g8i_29856.cif"
  }
  resolution = 3.92
  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=   0.031
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      30      5.16       5
     C   12820      2.51       5
     N    2970      2.21       5
     O    3515      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 286 residue(s): 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 19335
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 465, 3867
          Classifications: {'peptide': 465}
          Link IDs: {'PTRANS': 12, 'TRANS': 452}
    Chain: "B"
      Number of atoms: 3867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 465, 3867
          Classifications: {'peptide': 465}
          Link IDs: {'PTRANS': 12, 'TRANS': 452}
    Chain: "C"
      Number of atoms: 3867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 465, 3867
          Classifications: {'peptide': 465}
          Link IDs: {'PTRANS': 12, 'TRANS': 452}
    Chain: "D"
      Number of atoms: 3867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 465, 3867
          Classifications: {'peptide': 465}
          Link IDs: {'PTRANS': 12, 'TRANS': 452}
    Chain: "E"
      Number of atoms: 3867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 465, 3867
          Classifications: {'peptide': 465}
          Link IDs: {'PTRANS': 12, 'TRANS': 452}
  Time building chain proxies: 11.08, per 1000 atoms: 0.57
  Number of scatterers: 19335
  At special positions: 0
  Unit cell: (83.19, 84.075, 238.95, 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      30     16.00
     O    3515      8.00
     N    2970      7.00
     C   12820      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: 4.63
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4440

  Finding SS restraints...
    Secondary structure from input PDB file:
      145 helices and 0 sheets defined
      96.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 12
    Processing helix  chain 'A' and resid 13 through 26
    Processing helix  chain 'A' and resid 28 through 47
      removed outlier: 3.960A  pdb=" N   VAL A  32 " --> pdb=" O   ARG A  28 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLU A  33 " --> pdb=" O   GLU A  29 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 60
    Processing helix  chain 'A' and resid 62 through 75
      removed outlier: 4.042A  pdb=" N   ILE A  75 " --> pdb=" O   LYS A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 96
      removed outlier: 3.599A  pdb=" N   VAL A  81 " --> pdb=" O   ARG A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 111
      removed outlier: 3.729A  pdb=" N   ASN A 111 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 124
      removed outlier: 3.572A  pdb=" N   ILE A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 145
      removed outlier: 3.659A  pdb=" N   VAL A 130 " --> pdb=" O   ARG A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 160
      removed outlier: 3.568A  pdb=" N   LEU A 151 " --> pdb=" O   ASN A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 173
    Processing helix  chain 'A' and resid 175 through 194
    Processing helix  chain 'A' and resid 196 through 208
    Processing helix  chain 'A' and resid 209 through 222
      removed outlier: 4.189A  pdb=" N   GLU A 222 " --> pdb=" O   GLU A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 243
      removed outlier: 3.808A  pdb=" N   GLY A 243 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 258
      removed outlier: 3.547A  pdb=" N   TYR A 249 " --> pdb=" O   ASN A 245 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   SER A 257 " --> pdb=" O   LYS A 253 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASN A 258 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 271
      removed outlier: 4.295A  pdb=" N   ILE A 271 " --> pdb=" O   GLU A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 292
    Processing helix  chain 'A' and resid 294 through 307
      removed outlier: 3.757A  pdb=" N   ASN A 307 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 320
      removed outlier: 3.950A  pdb=" N   ILE A 320 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 341
      removed outlier: 3.650A  pdb=" N   GLY A 341 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 354
      removed outlier: 3.636A  pdb=" N   LEU A 349 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 369
    Processing helix  chain 'A' and resid 371 through 390
      removed outlier: 3.628A  pdb=" N   VAL A 375 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   ASP A 388 " --> pdb=" O   TRP A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 404
      removed outlier: 3.617A  pdb=" N   ILE A 396 " --> pdb=" O   ASN A 392 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER A 404 " --> pdb=" O   ARG A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 418
    Processing helix  chain 'A' and resid 420 through 439
    Processing helix  chain 'A' and resid 441 through 453
      removed outlier: 3.653A  pdb=" N   ILE A 445 " --> pdb=" O   ASP A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 465
      removed outlier: 3.506A  pdb=" N   GLU A 460 " --> pdb=" O   GLU A 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 12
    Processing helix  chain 'B' and resid 13 through 26
    Processing helix  chain 'B' and resid 28 through 47
      removed outlier: 3.843A  pdb=" N   VAL B  32 " --> pdb=" O   ARG B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 62
      removed outlier: 3.645A  pdb=" N   ASN B  62 " --> pdb=" O   GLU B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 75
    Processing helix  chain 'B' and resid 77 through 96
      removed outlier: 3.557A  pdb=" N   VAL B  81 " --> pdb=" O   ARG B  77 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLY B  96 " --> pdb=" O   VAL B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 111
      removed outlier: 3.516A  pdb=" N   ASN B 111 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 124
      removed outlier: 3.585A  pdb=" N   ILE B 124 " --> pdb=" O   LEU B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 145
      removed outlier: 3.573A  pdb=" N   VAL B 130 " --> pdb=" O   ARG B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 160
    Processing helix  chain 'B' and resid 160 through 173
    Processing helix  chain 'B' and resid 175 through 194
    Processing helix  chain 'B' and resid 196 through 209
      removed outlier: 3.937A  pdb=" N   ASN B 209 " --> pdb=" O   GLU B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 221
    Processing helix  chain 'B' and resid 224 through 243
      removed outlier: 3.686A  pdb=" N   GLY B 243 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 258
    Processing helix  chain 'B' and resid 258 through 271
      removed outlier: 4.136A  pdb=" N   ILE B 271 " --> pdb=" O   GLU B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 292
      removed outlier: 3.530A  pdb=" N   VAL B 277 " --> pdb=" O   LYS B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 307
      removed outlier: 3.882A  pdb=" N   ASN B 307 " --> pdb=" O   LEU B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 320
      removed outlier: 3.901A  pdb=" N   ILE B 320 " --> pdb=" O   GLU B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 341
      removed outlier: 3.725A  pdb=" N   VAL B 326 " --> pdb=" O   ASN B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 356
      removed outlier: 3.508A  pdb=" N   SER B 355 " --> pdb=" O   GLU B 351 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ASN B 356 " --> pdb=" O   LEU B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 369
    Processing helix  chain 'B' and resid 371 through 390
      removed outlier: 3.568A  pdb=" N   GLY B 390 " --> pdb=" O   VAL B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 405
      removed outlier: 3.550A  pdb=" N   ILE B 396 " --> pdb=" O   ASN B 392 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ASN B 405 " --> pdb=" O   LYS B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 418
    Processing helix  chain 'B' and resid 420 through 439
    Processing helix  chain 'B' and resid 441 through 454
      removed outlier: 3.503A  pdb=" N   ASP B 454 " --> pdb=" O   GLU B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 465
    Processing helix  chain 'C' and resid 2 through 12
    Processing helix  chain 'C' and resid 13 through 26
    Processing helix  chain 'C' and resid 28 through 47
      removed outlier: 3.537A  pdb=" N   VAL C  32 " --> pdb=" O   ARG C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 49 through 62
      removed outlier: 3.545A  pdb=" N   ASN C  62 " --> pdb=" O   GLU C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 75
      removed outlier: 3.754A  pdb=" N   ILE C  75 " --> pdb=" O   LYS C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 77 through 96
      removed outlier: 3.595A  pdb=" N   VAL C  81 " --> pdb=" O   ARG C  77 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY C  96 " --> pdb=" O   VAL C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 98 through 109
    Processing helix  chain 'C' and resid 111 through 124
      removed outlier: 3.528A  pdb=" N   ILE C 124 " --> pdb=" O   LEU C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 145
      removed outlier: 3.636A  pdb=" N   VAL C 130 " --> pdb=" O   ARG C 126 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 160
      removed outlier: 3.544A  pdb=" N   LEU C 151 " --> pdb=" O   ASN C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 173
    Processing helix  chain 'C' and resid 175 through 194
      removed outlier: 4.019A  pdb=" N   GLU C 192 " --> pdb=" O   TYR C 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 207
    Processing helix  chain 'C' and resid 209 through 221
    Processing helix  chain 'C' and resid 224 through 243
      removed outlier: 3.922A  pdb=" N   GLY C 243 " --> pdb=" O   VAL C 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 258
      removed outlier: 3.510A  pdb=" N   TYR C 249 " --> pdb=" O   ASN C 245 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 258 through 271
      removed outlier: 3.858A  pdb=" N   ILE C 271 " --> pdb=" O   GLU C 267 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 273 through 291
    Processing helix  chain 'C' and resid 294 through 307
      removed outlier: 3.594A  pdb=" N   ASN C 307 " --> pdb=" O   LEU C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 320
      removed outlier: 3.776A  pdb=" N   ILE C 320 " --> pdb=" O   GLU C 316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 322 through 341
      removed outlier: 3.783A  pdb=" N   VAL C 326 " --> pdb=" O   ASN C 322 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 343 through 356
      removed outlier: 3.713A  pdb=" N   LEU C 349 " --> pdb=" O   VAL C 345 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASN C 356 " --> pdb=" O   LEU C 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 356 through 369
      removed outlier: 3.545A  pdb=" N   ILE C 369 " --> pdb=" O   LEU C 365 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 371 through 390
      removed outlier: 3.644A  pdb=" N   VAL C 375 " --> pdb=" O   ARG C 371 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ASP C 388 " --> pdb=" O   TRP C 384 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLY C 390 " --> pdb=" O   VAL C 386 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 392 through 405
      removed outlier: 3.627A  pdb=" N   ILE C 396 " --> pdb=" O   ASN C 392 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ASN C 405 " --> pdb=" O   LYS C 401 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 418
    Processing helix  chain 'C' and resid 420 through 439
    Processing helix  chain 'C' and resid 441 through 453
    Processing helix  chain 'C' and resid 454 through 465
      removed outlier: 3.550A  pdb=" N   VAL C 465 " --> pdb=" O   LEU C 461 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 13
      removed outlier: 3.813A  pdb=" N   ASN D  13 " --> pdb=" O   LEU D   9 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 13 through 26
    Processing helix  chain 'D' and resid 28 through 47
      removed outlier: 3.526A  pdb=" N   VAL D  32 " --> pdb=" O   ARG D  28 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 60
    Processing helix  chain 'D' and resid 62 through 75
      removed outlier: 3.717A  pdb=" N   ILE D  75 " --> pdb=" O   LYS D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 77 through 95
    Processing helix  chain 'D' and resid 98 through 111
      removed outlier: 3.522A  pdb=" N   ASN D 111 " --> pdb=" O   GLU D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 124
      removed outlier: 3.707A  pdb=" N   ILE D 124 " --> pdb=" O   LEU D 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 145
      removed outlier: 4.065A  pdb=" N   VAL D 130 " --> pdb=" O   ARG D 126 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LYS D 131 " --> pdb=" O   GLU D 127 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLY D 145 " --> pdb=" O   VAL D 141 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 147 through 160
      removed outlier: 3.575A  pdb=" N   LEU D 151 " --> pdb=" O   ASN D 147 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 160 through 173
    Processing helix  chain 'D' and resid 175 through 194
      removed outlier: 3.899A  pdb=" N   GLU D 192 " --> pdb=" O   TYR D 188 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 208
    Processing helix  chain 'D' and resid 209 through 222
      removed outlier: 3.969A  pdb=" N   GLU D 222 " --> pdb=" O   GLU D 218 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 224 through 243
      removed outlier: 3.500A  pdb=" N   VAL D 228 " --> pdb=" O   LYS D 224 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLY D 243 " --> pdb=" O   VAL D 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 245 through 256
      removed outlier: 3.570A  pdb=" N   LEU D 251 " --> pdb=" O   LYS D 247 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 258 through 271
      removed outlier: 3.679A  pdb=" N   ILE D 271 " --> pdb=" O   GLU D 267 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 273 through 292
      removed outlier: 3.600A  pdb=" N   VAL D 277 " --> pdb=" O   LYS D 273 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 294 through 306
    Processing helix  chain 'D' and resid 307 through 320
      removed outlier: 3.533A  pdb=" N   ILE D 320 " --> pdb=" O   GLU D 316 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 322 through 340
    Processing helix  chain 'D' and resid 343 through 354
    Processing helix  chain 'D' and resid 356 through 369
    Processing helix  chain 'D' and resid 371 through 390
      removed outlier: 3.687A  pdb=" N   LYS D 383 " --> pdb=" O   PHE D 379 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ASP D 388 " --> pdb=" O   TRP D 384 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 392 through 404
      removed outlier: 3.638A  pdb=" N   SER D 404 " --> pdb=" O   ARG D 400 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 405 through 418
    Processing helix  chain 'D' and resid 420 through 439
      removed outlier: 3.506A  pdb=" N   GLY D 439 " --> pdb=" O   VAL D 435 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 441 through 454
      removed outlier: 4.213A  pdb=" N   ASP D 454 " --> pdb=" O   GLU D 450 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 454 through 465
    Processing helix  chain 'E' and resid 2 through 13
      removed outlier: 3.810A  pdb=" N   ASN E  13 " --> pdb=" O   LEU E   9 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 13 through 26
    Processing helix  chain 'E' and resid 28 through 47
      removed outlier: 3.693A  pdb=" N   VAL E  32 " --> pdb=" O   ARG E  28 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 49 through 62
      removed outlier: 3.633A  pdb=" N   ASN E  62 " --> pdb=" O   GLU E  58 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 75
      removed outlier: 4.073A  pdb=" N   ILE E  75 " --> pdb=" O   LYS E  71 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 77 through 94
      removed outlier: 3.505A  pdb=" N   VAL E  81 " --> pdb=" O   ARG E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 98 through 109
    Processing helix  chain 'E' and resid 111 through 124
      removed outlier: 4.099A  pdb=" N   ILE E 117 " --> pdb=" O   GLU E 113 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE E 124 " --> pdb=" O   LEU E 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 126 through 145
      removed outlier: 3.827A  pdb=" N   VAL E 130 " --> pdb=" O   ARG E 126 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 147 through 160
      removed outlier: 3.584A  pdb=" N   ASN E 160 " --> pdb=" O   LEU E 156 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 173
    Processing helix  chain 'E' and resid 175 through 194
      removed outlier: 3.554A  pdb=" N   GLU E 192 " --> pdb=" O   TYR E 188 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 196 through 209
      removed outlier: 3.612A  pdb=" N   SER E 208 " --> pdb=" O   LYS E 204 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ASN E 209 " --> pdb=" O   GLU E 205 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 209 through 222
      removed outlier: 3.509A  pdb=" N   GLU E 222 " --> pdb=" O   GLU E 218 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 224 through 243
    Processing helix  chain 'E' and resid 245 through 258
    Processing helix  chain 'E' and resid 258 through 271
      removed outlier: 3.600A  pdb=" N   ILE E 271 " --> pdb=" O   GLU E 267 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 273 through 292
      removed outlier: 3.668A  pdb=" N   VAL E 277 " --> pdb=" O   LYS E 273 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 294 through 305
    Processing helix  chain 'E' and resid 307 through 320
    Processing helix  chain 'E' and resid 322 through 341
      removed outlier: 3.677A  pdb=" N   GLY E 341 " --> pdb=" O   VAL E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 343 through 356
      removed outlier: 3.712A  pdb=" N   ASN E 356 " --> pdb=" O   LEU E 352 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 356 through 369
    Processing helix  chain 'E' and resid 371 through 389
    Processing helix  chain 'E' and resid 392 through 404
    Processing helix  chain 'E' and resid 405 through 419
      removed outlier: 3.532A  pdb=" N   GLY E 419 " --> pdb=" O   TRP E 415 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 420 through 438
    Processing helix  chain 'E' and resid 441 through 453
    Processing helix  chain 'E' and resid 454 through 465

    1554 hydrogen bonds defined for protein.
    4662 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: 5.88

  Time building geometry restraints manager: 5.43 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 6075
        1.34 -     1.46: 3804
        1.46 -     1.58: 9771
        1.58 -     1.70: 0
        1.70 -     1.81: 60
  Bond restraints: 19710
  Sorted by residual:
  bond pdb=" CA  ASN C 223 "
       pdb=" C   ASN C 223 "
    ideal  model  delta    sigma   weight residual
    1.532  1.522  0.010 9.60e-03 1.09e+04 1.06e+00
  bond pdb=" C   GLY C 438 "
       pdb=" N   GLY C 439 "
    ideal  model  delta    sigma   weight residual
    1.331  1.316  0.014 1.46e-02 4.69e+03 9.53e-01
  bond pdb=" CA  ASN B 196 "
       pdb=" CB  ASN B 196 "
    ideal  model  delta    sigma   weight residual
    1.523  1.535 -0.012 1.35e-02 5.49e+03 7.41e-01
  bond pdb=" CG1 ILE A  53 "
       pdb=" CD1 ILE A  53 "
    ideal  model  delta    sigma   weight residual
    1.513  1.480  0.033 3.90e-02 6.57e+02 7.34e-01
  bond pdb=" N   ASN B 294 "
       pdb=" CA  ASN B 294 "
    ideal  model  delta    sigma   weight residual
    1.463  1.455  0.007 8.80e-03 1.29e+04 7.01e-01
  ... (remaining 19705 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 26018
        1.48 -     2.96: 506
        2.96 -     4.44: 79
        4.44 -     5.92: 11
        5.92 -     7.40: 6
  Bond angle restraints: 26620
  Sorted by residual:
  angle pdb=" N   ARG E 371 "
        pdb=" CA  ARG E 371 "
        pdb=" C   ARG E 371 "
      ideal   model   delta    sigma   weight residual
     112.97  109.88    3.09 1.06e+00 8.90e-01 8.52e+00
  angle pdb=" N   ILE E 271 "
        pdb=" CA  ILE E 271 "
        pdb=" C   ILE E 271 "
      ideal   model   delta    sigma   weight residual
     112.98  109.38    3.60 1.25e+00 6.40e-01 8.27e+00
  angle pdb=" N   LYS B 175 "
        pdb=" CA  LYS B 175 "
        pdb=" C   LYS B 175 "
      ideal   model   delta    sigma   weight residual
     112.97  110.23    2.74 1.06e+00 8.90e-01 6.67e+00
  angle pdb=" N   ILE B  26 "
        pdb=" CA  ILE B  26 "
        pdb=" C   ILE B  26 "
      ideal   model   delta    sigma   weight residual
     112.98  109.93    3.05 1.25e+00 6.40e-01 5.97e+00
  angle pdb=" N   ARG D 126 "
        pdb=" CA  ARG D 126 "
        pdb=" C   ARG D 126 "
      ideal   model   delta    sigma   weight residual
     110.44  107.71    2.73 1.20e+00 6.94e-01 5.17e+00
  ... (remaining 26615 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 10599
       17.97 -    35.94: 1013
       35.94 -    53.91: 162
       53.91 -    71.89: 84
       71.89 -    89.86: 52
  Dihedral angle restraints: 11910
    sinusoidal: 5120
      harmonic: 6790
  Sorted by residual:
  dihedral pdb=" CA  ASN A 147 "
           pdb=" C   ASN A 147 "
           pdb=" N   PRO A 148 "
           pdb=" CA  PRO A 148 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.25  -21.75     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  LEU C 452 "
           pdb=" C   LEU C 452 "
           pdb=" N   LEU C 453 "
           pdb=" CA  LEU C 453 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.00  -21.00     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  GLU A 270 "
           pdb=" C   GLU A 270 "
           pdb=" N   ILE A 271 "
           pdb=" CA  ILE A 271 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.17  -20.83     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 11907 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1568
       0.027 -    0.053: 981
       0.053 -    0.080: 397
       0.080 -    0.106: 80
       0.106 -    0.133: 34
  Chirality restraints: 3060
  Sorted by residual:
  chirality pdb=" CA  PRO A 148 "
            pdb=" N   PRO A 148 "
            pdb=" C   PRO A 148 "
            pdb=" CB  PRO A 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CB  ILE A  75 "
            pdb=" CA  ILE A  75 "
            pdb=" CG1 ILE A  75 "
            pdb=" CG2 ILE A  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.78   -0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CG  LEU D 349 "
            pdb=" CB  LEU D 349 "
            pdb=" CD1 LEU D 349 "
            pdb=" CD2 LEU D 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.72    0.13 2.00e-01 2.50e+01 4.26e-01
  ... (remaining 3057 not shown)

  Planarity restraints: 3315
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 258 "    0.037 5.00e-02 4.00e+02   5.70e-02 5.19e+00
        pdb=" N   PRO C 259 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO C 259 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 259 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 160 "    0.036 5.00e-02 4.00e+02   5.46e-02 4.78e+00
        pdb=" N   PRO A 161 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 161 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 161 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 454 "    0.033 5.00e-02 4.00e+02   5.12e-02 4.20e+00
        pdb=" N   PRO B 455 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO B 455 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 455 "    0.029 5.00e-02 4.00e+02
  ... (remaining 3312 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 3786
        2.78 -     3.31: 19764
        3.31 -     3.84: 31482
        3.84 -     4.37: 33985
        4.37 -     4.90: 59548
  Nonbonded interactions: 148565
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 351 "
            pdb=" OG  SER A 355 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   LYS A 302 "
            pdb=" OG  SER A 306 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   LYS D 204 "
            pdb=" OG  SER D 208 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   SER A  61 "
            pdb=" OG  SER A  61 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   SER E 110 "
            pdb=" OG  SER E 110 "
     model   vdw
     2.308 3.040
  ... (remaining 148560 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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=0.00 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:             2.920
  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:             0.010
  Extract box with map and model:          0.810
  Check model and map are aligned:         0.140
  Set scattering table:                    0.180
  Process input model:                     41.280
  Find NCS groups from input model:        0.720
  Set up NCS constraints:                  0.090
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
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   0.033  19710  Z= 0.154
  Angle     :  0.551   7.405  26620  Z= 0.308
  Chirality :  0.039   0.133   3060
  Planarity :  0.004   0.057   3315
  Dihedral  : 16.256  89.857   7470
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.15), residues: 2315
  helix:  0.22 (0.10), residues: 2105
  sheet:  None (None), residues: 0
  loop : -3.55 (0.34), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 415 
 HIS   0.004   0.001   HIS A 397 
 PHE   0.014   0.002   PHE A 379 
 TYR   0.010   0.001   TYR B 237 
 ARG   0.003   0.000   ARG E 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15133 ( 1554)
  hydrogen bonds       : angle       4.99941 ( 4662)
  covalent geometry    : bond        0.00355 (19710)
  covalent geometry    : angle       0.55105 (26620)

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

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

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  379 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 379
  time to evaluate  : 2.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7783 (tm-30)
REVERT: A  125 ASN cc_start: 0.7336 (m-40) cc_final: 0.7110 (m-40)
REVERT: A  156 LEU cc_start: 0.8386 (tp) cc_final: 0.8137 (tp)
REVERT: B    3 TYR cc_start: 0.6960 (t80) cc_final: 0.6655 (t80)
REVERT: B  162 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7045 (mm-30)
REVERT: C   16 ILE cc_start: 0.8639 (mm) cc_final: 0.8365 (mm)
REVERT: C  187 LEU cc_start: 0.8290 (tp) cc_final: 0.7931 (tt)
REVERT: D  257 SER cc_start: 0.7783 (p) cc_final: 0.7335 (t)
REVERT: E   89 LYS cc_start: 0.7495 (tmtt) cc_final: 0.7267 (tmtt)
REVERT: E  217 LEU cc_start: 0.8387 (mt) cc_final: 0.8087 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 379
  average time/residue: 0.3152
  time to fit residues: 178.4514
Evaluate side-chains
  190 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 2.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 194 optimal weight:    2.9990
   chunk 174 optimal weight:    3.9990
   chunk 96 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   chunk 117 optimal weight:    1.9990
   chunk 93 optimal weight:    5.9990
   chunk 180 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 109 optimal weight:    5.9990
   chunk 134 optimal weight:    1.9990
   chunk 208 optimal weight:    7.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  13 ASN
A 147 ASN
B 125 ASN
B 272 ASN
C  49 ASN
C 209 ASN
D  13 ASN
D 146 ASN
D 209 ASN
D 391 ASN
E  49 ASN
E 321 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.152235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.145891 restraints weight = 22844.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.145456 restraints weight = 37207.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.145799 restraints weight = 32332.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  19710  Z= 0.172
  Angle     :  0.590   9.983  26620  Z= 0.293
  Chirality :  0.040   0.178   3060
  Planarity :  0.004   0.039   3315
  Dihedral  :  4.027  22.257   2400
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  9.66 %
    Favored  : 88.78 %
  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:  1.78 (0.17), residues: 2315
  helix:  1.51 (0.10), residues: 2165
  sheet:  None (None), residues: 0
  loop : -3.34 (0.40), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 219 
 HIS   0.003   0.001   HIS A 368 
 PHE   0.013   0.001   PHE D 213 
 TYR   0.017   0.001   TYR C 188 
 ARG   0.004   0.000   ARG C 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04047 ( 1554)
  hydrogen bonds       : angle       3.50782 ( 4662)
  covalent geometry    : bond        0.00424 (19710)
  covalent geometry    : angle       0.59006 (26620)

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

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

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 227
  time to evaluate  : 2.161 
Fit side-chains
REVERT: B    3 TYR cc_start: 0.6763 (t80) cc_final: 0.6525 (t80)
REVERT: B   69 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6899 (mp)
REVERT: B  162 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6994 (mm-30)
REVERT: C   16 ILE cc_start: 0.8920 (mm) cc_final: 0.8469 (mm)
REVERT: C  355 SER cc_start: 0.8659 (p) cc_final: 0.8426 (m)
REVERT: C  452 LEU cc_start: 0.8530 (tp) cc_final: 0.8226 (tt)
REVERT: C  459 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8291 (tt0)
REVERT: D   12 GLU cc_start: 0.7237 (tp30) cc_final: 0.6985 (tp30)
REVERT: D  114 ILE cc_start: 0.9066 (mm) cc_final: 0.8855 (mt)
REVERT: D  125 ASN cc_start: 0.7804 (m-40) cc_final: 0.6382 (t0)
REVERT: D  146 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.7097 (p0)
REVERT: D  257 SER cc_start: 0.7680 (p) cc_final: 0.7287 (t)
REVERT: E   89 LYS cc_start: 0.7712 (tmtt) cc_final: 0.7431 (tmtt)
REVERT: E  200 LEU cc_start: 0.8494 (tt) cc_final: 0.7921 (mm)
REVERT: E  290 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8027 (tt0)
  outliers start: 34
  outliers final: 19
  residues processed: 252
  average time/residue: 0.2839
  time to fit residues: 112.4480
Evaluate side-chains
  186 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 165
  time to evaluate  : 2.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  445 ILE
Chi-restraints excluded: chain D residue  146 ASN
Chi-restraints excluded: chain D residue  207 LEU
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  374 VAL
Chi-restraints excluded: chain D residue  414 LEU
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain E residue  349 LEU
Chi-restraints excluded: chain E residue  431 VAL
Chi-restraints excluded: chain E residue  463 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 165 optimal weight:    3.9990
   chunk 215 optimal weight:    3.9990
   chunk 228 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9980
   chunk 176 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 159 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 197 optimal weight:    2.9990
   chunk 162 optimal weight:    4.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 391 ASN
B 272 ASN
D 294 ASN
D 392 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.150656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.144640 restraints weight = 22694.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.144364 restraints weight = 31958.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.144423 restraints weight = 29066.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  19710  Z= 0.158
  Angle     :  0.539   8.522  26620  Z= 0.266
  Chirality :  0.039   0.139   3060
  Planarity :  0.003   0.035   3315
  Dihedral  :  3.830  21.530   2400
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.38 %
    Favored  : 85.06 %
  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:  2.50 (0.17), residues: 2315
  helix:  1.96 (0.11), residues: 2170
  sheet:  None (None), residues: 0
  loop : -3.11 (0.41), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 219 
 HIS   0.003   0.001   HIS B 368 
 PHE   0.014   0.001   PHE E 458 
 TYR   0.012   0.001   TYR A 249 
 ARG   0.003   0.000   ARG B 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03803 ( 1554)
  hydrogen bonds       : angle       3.24580 ( 4662)
  covalent geometry    : bond        0.00389 (19710)
  covalent geometry    : angle       0.53868 (26620)

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

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

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 193
  time to evaluate  : 2.417 
Fit side-chains
REVERT: B   69 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6787 (mp)
REVERT: B  272 ASN cc_start: 0.6717 (m-40) cc_final: 0.6457 (t0)
REVERT: B  393 MET cc_start: 0.7109 (mmm) cc_final: 0.6843 (mmt)
REVERT: C   16 ILE cc_start: 0.8993 (mm) cc_final: 0.8466 (mm)
REVERT: C  208 SER cc_start: 0.8506 (p) cc_final: 0.8171 (m)
REVERT: C  355 SER cc_start: 0.8726 (p) cc_final: 0.8510 (m)
REVERT: D   37 GLU cc_start: 0.7462 (tm-30) cc_final: 0.6444 (tt0)
REVERT: D  114 ILE cc_start: 0.9069 (mm) cc_final: 0.8864 (mt)
REVERT: D  143 ARG cc_start: 0.7961 (tpp80) cc_final: 0.7635 (ttm170)
REVERT: D  146 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.7088 (p0)
REVERT: E   89 LYS cc_start: 0.7653 (tmtt) cc_final: 0.7338 (tmtt)
REVERT: E  123 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6685 (tm-30)
REVERT: E  200 LEU cc_start: 0.8524 (tt) cc_final: 0.7866 (mm)
  outliers start: 34
  outliers final: 21
  residues processed: 219
  average time/residue: 0.2866
  time to fit residues: 99.3913
Evaluate side-chains
  188 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 165
  time to evaluate  : 2.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain C residue  283 VAL
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain D residue  146 ASN
Chi-restraints excluded: chain D residue  207 LEU
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  414 LEU
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain E residue  349 LEU
Chi-restraints excluded: chain E residue  431 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 210 optimal weight:    4.9990
   chunk 229 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 151 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 95 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 116 optimal weight:    3.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 391 ASN
D 146 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.152399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.145319 restraints weight = 22785.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.144506 restraints weight = 34450.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.144873 restraints weight = 31902.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  19710  Z= 0.122
  Angle     :  0.481   9.658  26620  Z= 0.236
  Chirality :  0.037   0.180   3060
  Planarity :  0.003   0.033   3315
  Dihedral  :  3.585  19.305   2400
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.21 %
    Favored  : 83.82 %
  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:  3.04 (0.17), residues: 2315
  helix:  2.33 (0.10), residues: 2170
  sheet:  None (None), residues: 0
  loop : -3.42 (0.43), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 219 
 HIS   0.003   0.001   HIS A 368 
 PHE   0.008   0.001   PHE D 213 
 TYR   0.018   0.001   TYR E   3 
 ARG   0.004   0.000   ARG E 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03144 ( 1554)
  hydrogen bonds       : angle       2.91931 ( 4662)
  covalent geometry    : bond        0.00293 (19710)
  covalent geometry    : angle       0.48060 (26620)

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

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

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 175
  time to evaluate  : 2.201 
Fit side-chains
REVERT: B   69 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6791 (mp)
REVERT: B  352 LEU cc_start: 0.8139 (tp) cc_final: 0.7820 (tt)
REVERT: C   16 ILE cc_start: 0.8992 (mm) cc_final: 0.8454 (mm)
REVERT: C  208 SER cc_start: 0.8493 (p) cc_final: 0.8192 (m)
REVERT: C  355 SER cc_start: 0.8740 (p) cc_final: 0.8536 (m)
REVERT: D  125 ASN cc_start: 0.7967 (m-40) cc_final: 0.6476 (t0)
REVERT: D  143 ARG cc_start: 0.7935 (tpp80) cc_final: 0.7646 (ttm170)
REVERT: D  146 ASN cc_start: 0.7505 (OUTLIER) cc_final: 0.7162 (p0)
REVERT: E   89 LYS cc_start: 0.7676 (tmtt) cc_final: 0.7355 (tmtt)
REVERT: E  123 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6636 (tm-30)
REVERT: E  143 ARG cc_start: 0.7449 (tpt-90) cc_final: 0.7136 (ttt90)
REVERT: E  200 LEU cc_start: 0.8529 (tt) cc_final: 0.7903 (mm)
REVERT: E  344 MET cc_start: 0.5303 (tpp) cc_final: 0.5081 (tpp)
  outliers start: 43
  outliers final: 26
  residues processed: 209
  average time/residue: 0.2826
  time to fit residues: 93.1800
Evaluate side-chains
  179 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 2.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 TRP
Chi-restraints excluded: chain C residue   79 ASP
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain D residue  146 ASN
Chi-restraints excluded: chain D residue  207 LEU
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain E residue  349 LEU
Chi-restraints excluded: chain E residue  431 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 153 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 227 optimal weight:    4.9990
   chunk 128 optimal weight:    2.9990
   chunk 217 optimal weight:    0.9990
   chunk 197 optimal weight:    2.9990
   chunk 221 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 163 optimal weight:    0.0570
   overall best weight:    1.2102

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

Flipped N/Q/H residues before XYZ refinement:
A 391 ASN
D 146 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.152057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.146042 restraints weight = 22717.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.145781 restraints weight = 34045.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.146112 restraints weight = 28919.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.3247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  19710  Z= 0.120
  Angle     :  0.476  10.592  26620  Z= 0.231
  Chirality :  0.037   0.152   3060
  Planarity :  0.002   0.031   3315
  Dihedral  :  3.498  18.608   2400
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.85 %
    Favored  : 83.03 %
  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:  3.36 (0.17), residues: 2315
  helix:  2.53 (0.10), residues: 2165
  sheet:  None (None), residues: 0
  loop : -2.87 (0.49), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 219 
 HIS   0.002   0.001   HIS A 368 
 PHE   0.009   0.001   PHE A  25 
 TYR   0.012   0.001   TYR E   3 
 ARG   0.004   0.000   ARG B 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03108 ( 1554)
  hydrogen bonds       : angle       2.85197 ( 4662)
  covalent geometry    : bond        0.00291 (19710)
  covalent geometry    : angle       0.47562 (26620)

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

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

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 162
  time to evaluate  : 2.144 
Fit side-chains
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6768 (mp)
REVERT: C   16 ILE cc_start: 0.9009 (mm) cc_final: 0.8441 (mm)
REVERT: C  208 SER cc_start: 0.8423 (p) cc_final: 0.8094 (m)
REVERT: D   37 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6518 (tt0)
REVERT: D  125 ASN cc_start: 0.7938 (m-40) cc_final: 0.6443 (t0)
REVERT: D  146 ASN cc_start: 0.7309 (OUTLIER) cc_final: 0.7083 (p0)
REVERT: E   89 LYS cc_start: 0.7666 (tmtt) cc_final: 0.7340 (tmtt)
REVERT: E  123 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6600 (tm-30)
REVERT: E  200 LEU cc_start: 0.8539 (tt) cc_final: 0.7918 (mm)
  outliers start: 46
  outliers final: 35
  residues processed: 198
  average time/residue: 0.2814
  time to fit residues: 88.1954
Evaluate side-chains
  182 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 145
  time to evaluate  : 2.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 TRP
Chi-restraints excluded: chain C residue   79 ASP
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain C residue  283 VAL
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain D residue  146 ASN
Chi-restraints excluded: chain D residue  207 LEU
Chi-restraints excluded: chain D residue  332 VAL
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  414 LEU
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain E residue  349 LEU
Chi-restraints excluded: chain E residue  431 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 143 optimal weight:    0.9990
   chunk 215 optimal weight:    2.9990
   chunk 216 optimal weight:    5.9990
   chunk 206 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9980
   chunk 100 optimal weight:    0.7980
   chunk 169 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   chunk 115 optimal weight:    0.8980
   chunk 159 optimal weight:    0.9990
   chunk 223 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B 272 ASN
D 146 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.153283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.147579 restraints weight = 22619.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.147277 restraints weight = 29720.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.147319 restraints weight = 26175.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  19710  Z= 0.104
  Angle     :  0.460  10.518  26620  Z= 0.222
  Chirality :  0.036   0.141   3060
  Planarity :  0.002   0.029   3315
  Dihedral  :  3.380  17.044   2400
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.68 %
    Favored  : 82.39 %
  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:  3.63 (0.17), residues: 2315
  helix:  2.70 (0.10), residues: 2165
  sheet:  None (None), residues: 0
  loop : -2.74 (0.49), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 219 
 HIS   0.002   0.001   HIS A 368 
 PHE   0.018   0.001   PHE E 458 
 TYR   0.011   0.001   TYR E   3 
 ARG   0.004   0.000   ARG E 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02849 ( 1554)
  hydrogen bonds       : angle       2.69896 ( 4662)
  covalent geometry    : bond        0.00245 (19710)
  covalent geometry    : angle       0.45966 (26620)

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

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

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 165
  time to evaluate  : 2.240 
Fit side-chains
REVERT: B   69 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6672 (mp)
REVERT: B  352 LEU cc_start: 0.8200 (tp) cc_final: 0.7857 (tt)
REVERT: B  393 MET cc_start: 0.7066 (mmm) cc_final: 0.6726 (mmt)
REVERT: C   16 ILE cc_start: 0.9002 (mm) cc_final: 0.8415 (mm)
REVERT: C  208 SER cc_start: 0.8484 (p) cc_final: 0.8126 (m)
REVERT: D   37 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6474 (tt0)
REVERT: D  125 ASN cc_start: 0.7923 (m-40) cc_final: 0.6384 (t0)
REVERT: D  143 ARG cc_start: 0.8066 (tpp80) cc_final: 0.7760 (ttm170)
REVERT: E   89 LYS cc_start: 0.7699 (tmtt) cc_final: 0.7359 (tmtt)
REVERT: E  123 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6578 (tm-30)
REVERT: E  143 ARG cc_start: 0.7919 (tpp80) cc_final: 0.7358 (ttt90)
REVERT: E  344 MET cc_start: 0.5328 (tpp) cc_final: 0.5052 (tpp)
  outliers start: 42
  outliers final: 33
  residues processed: 196
  average time/residue: 0.2921
  time to fit residues: 91.2456
Evaluate side-chains
  184 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 150
  time to evaluate  : 2.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain C residue   72 TRP
Chi-restraints excluded: chain C residue   79 ASP
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain C residue  283 VAL
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain D residue  207 LEU
Chi-restraints excluded: chain D residue  332 VAL
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  414 LEU
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue  186 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain E residue  349 LEU
Chi-restraints excluded: chain E residue  431 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 115 optimal weight:    0.6980
   chunk 106 optimal weight:    9.9990
   chunk 69 optimal weight:    4.9990
   chunk 145 optimal weight:    3.9990
   chunk 156 optimal weight:    0.9990
   chunk 226 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   chunk 93 optimal weight:    0.7980
   chunk 210 optimal weight:    5.9990
   chunk 101 optimal weight:    0.7980
   chunk 133 optimal weight:    4.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 272 ASN
D 146 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.152389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.146492 restraints weight = 22312.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.146100 restraints weight = 33104.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.146305 restraints weight = 28841.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  19710  Z= 0.099
  Angle     :  0.463  10.745  26620  Z= 0.222
  Chirality :  0.036   0.137   3060
  Planarity :  0.002   0.027   3315
  Dihedral  :  3.273  15.636   2400
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.18 %
    Favored  : 81.61 %
  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:  3.85 (0.17), residues: 2315
  helix:  2.83 (0.10), residues: 2165
  sheet:  None (None), residues: 0
  loop : -2.63 (0.49), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 219 
 HIS   0.002   0.000   HIS B 368 
 PHE   0.013   0.001   PHE B  85 
 TYR   0.016   0.001   TYR C 188 
 ARG   0.005   0.000   ARG B 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02703 ( 1554)
  hydrogen bonds       : angle       2.59500 ( 4662)
  covalent geometry    : bond        0.00231 (19710)
  covalent geometry    : angle       0.46292 (26620)

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

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

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 164
  time to evaluate  : 2.349 
Fit side-chains
REVERT: A  143 ARG cc_start: 0.7597 (tpt-90) cc_final: 0.7388 (ttm170)
REVERT: A  393 MET cc_start: 0.6958 (mmm) cc_final: 0.6564 (tpt)
REVERT: B   69 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6798 (mp)
REVERT: B  393 MET cc_start: 0.7044 (mmm) cc_final: 0.6711 (mmt)
REVERT: C   16 ILE cc_start: 0.8993 (mm) cc_final: 0.8379 (mm)
REVERT: C  208 SER cc_start: 0.8433 (p) cc_final: 0.8085 (m)
REVERT: C  442 MET cc_start: 0.7141 (mmt) cc_final: 0.6909 (tpp)
REVERT: D   37 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6552 (tt0)
REVERT: D  143 ARG cc_start: 0.8032 (tpp80) cc_final: 0.7602 (ttm170)
REVERT: E   89 LYS cc_start: 0.7707 (tmtt) cc_final: 0.7418 (tmtt)
REVERT: E  123 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6544 (tm-30)
REVERT: E  344 MET cc_start: 0.5281 (tpp) cc_final: 0.5047 (tpp)
  outliers start: 48
  outliers final: 41
  residues processed: 200
  average time/residue: 0.2937
  time to fit residues: 92.7086
Evaluate side-chains
  195 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 153
  time to evaluate  : 2.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   99 MET
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 TRP
Chi-restraints excluded: chain C residue   79 ASP
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain C residue  283 VAL
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  435 VAL
Chi-restraints excluded: chain D residue  186 LEU
Chi-restraints excluded: chain D residue  207 LEU
Chi-restraints excluded: chain D residue  332 VAL
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  414 LEU
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue  186 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain E residue  349 LEU
Chi-restraints excluded: chain E residue  431 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 111 optimal weight:    4.9990
   chunk 194 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 149 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 135 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
D 146 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.154315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.148152 restraints weight = 22402.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.146331 restraints weight = 33061.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.145691 restraints weight = 29119.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.3619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  19710  Z= 0.103
  Angle     :  0.474  10.761  26620  Z= 0.227
  Chirality :  0.036   0.143   3060
  Planarity :  0.002   0.027   3315
  Dihedral  :  3.230  15.435   2400
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 17.29 %
    Favored  : 80.60 %
  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:  3.95 (0.17), residues: 2315
  helix:  2.90 (0.10), residues: 2165
  sheet:  None (None), residues: 0
  loop : -2.54 (0.50), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 219 
 HIS   0.002   0.001   HIS B 368 
 PHE   0.011   0.001   PHE B  85 
 TYR   0.009   0.001   TYR E   3 
 ARG   0.005   0.000   ARG B 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02713 ( 1554)
  hydrogen bonds       : angle       2.58719 ( 4662)
  covalent geometry    : bond        0.00245 (19710)
  covalent geometry    : angle       0.47424 (26620)

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

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

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 156
  time to evaluate  : 2.292 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 GLU cc_start: 0.6987 (tp30) cc_final: 0.6750 (tp30)
REVERT: A  143 ARG cc_start: 0.7632 (tpt-90) cc_final: 0.7383 (ttm170)
REVERT: A  393 MET cc_start: 0.7021 (mmm) cc_final: 0.6594 (tpt)
REVERT: B   69 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6879 (mp)
REVERT: B  352 LEU cc_start: 0.8151 (tp) cc_final: 0.7740 (tt)
REVERT: B  393 MET cc_start: 0.7129 (mmm) cc_final: 0.6824 (mmt)
REVERT: C   16 ILE cc_start: 0.8951 (mm) cc_final: 0.8350 (mm)
REVERT: C  208 SER cc_start: 0.8510 (p) cc_final: 0.8179 (m)
REVERT: D   37 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6559 (tt0)
REVERT: D  143 ARG cc_start: 0.7951 (tpp80) cc_final: 0.7612 (ttm170)
REVERT: E   89 LYS cc_start: 0.7735 (tmtt) cc_final: 0.7420 (tmtt)
REVERT: E  123 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6582 (tm-30)
REVERT: E  143 ARG cc_start: 0.8125 (tpp80) cc_final: 0.7535 (ttt90)
REVERT: E  344 MET cc_start: 0.5286 (tpp) cc_final: 0.5075 (tpp)
  outliers start: 46
  outliers final: 37
  residues processed: 192
  average time/residue: 0.2786
  time to fit residues: 86.0720
Evaluate side-chains
  184 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 146
  time to evaluate  : 2.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 TRP
Chi-restraints excluded: chain C residue   79 ASP
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  435 VAL
Chi-restraints excluded: chain D residue  207 LEU
Chi-restraints excluded: chain D residue  332 VAL
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue  186 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain E residue  349 LEU
Chi-restraints excluded: chain E residue  431 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 179 optimal weight:    0.0970
   chunk 39 optimal weight:    0.9980
   chunk 187 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 130 optimal weight:    3.9990
   chunk 112 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 181 optimal weight:    3.9990
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
D 146 ASN
E 245 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.155105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.148868 restraints weight = 22392.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.148488 restraints weight = 33154.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.148737 restraints weight = 29106.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.3707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  19710  Z= 0.098
  Angle     :  0.475  10.871  26620  Z= 0.225
  Chirality :  0.036   0.148   3060
  Planarity :  0.002   0.028   3315
  Dihedral  :  3.160  14.962   2400
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 17.61 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.06 (0.17), residues: 2315
  helix:  2.99 (0.10), residues: 2160
  sheet:  None (None), residues: 0
  loop : -2.75 (0.49), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 219 
 HIS   0.001   0.000   HIS B 368 
 PHE   0.012   0.001   PHE D 213 
 TYR   0.009   0.001   TYR E   3 
 ARG   0.005   0.000   ARG B 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02606 ( 1554)
  hydrogen bonds       : angle       2.53351 ( 4662)
  covalent geometry    : bond        0.00230 (19710)
  covalent geometry    : angle       0.47500 (26620)

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

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

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 165
  time to evaluate  : 2.440 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 GLU cc_start: 0.6876 (tp30) cc_final: 0.6650 (tp30)
REVERT: B   69 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6808 (mp)
REVERT: B  393 MET cc_start: 0.7050 (mmm) cc_final: 0.6769 (mmt)
REVERT: C   16 ILE cc_start: 0.8966 (mm) cc_final: 0.8329 (mm)
REVERT: C  208 SER cc_start: 0.8420 (p) cc_final: 0.8122 (m)
REVERT: D   37 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6482 (tt0)
REVERT: E   89 LYS cc_start: 0.7638 (tmtt) cc_final: 0.7341 (tmtt)
REVERT: E  123 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6531 (tm-30)
REVERT: E  143 ARG cc_start: 0.8160 (tpp80) cc_final: 0.7580 (ttt90)
  outliers start: 43
  outliers final: 36
  residues processed: 198
  average time/residue: 0.2808
  time to fit residues: 89.9217
Evaluate side-chains
  193 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 156
  time to evaluate  : 2.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 TRP
Chi-restraints excluded: chain C residue   79 ASP
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  435 VAL
Chi-restraints excluded: chain D residue  332 VAL
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue  186 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain E residue  349 LEU
Chi-restraints excluded: chain E residue  431 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 210 optimal weight:    5.9990
   chunk 214 optimal weight:    0.4980
   chunk 42 optimal weight:    2.9990
   chunk 92 optimal weight:    9.9990
   chunk 209 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 133 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 50 optimal weight:    7.9990
   chunk 106 optimal weight:    0.6980
   chunk 198 optimal weight:    6.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
D 146 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.153444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.147419 restraints weight = 22570.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.147083 restraints weight = 34303.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.147318 restraints weight = 29442.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.3755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  19710  Z= 0.117
  Angle     :  0.508  10.655  26620  Z= 0.242
  Chirality :  0.036   0.154   3060
  Planarity :  0.002   0.030   3315
  Dihedral  :  3.227  15.730   2400
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 17.98 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.02 (0.17), residues: 2315
  helix:  2.97 (0.10), residues: 2160
  sheet:  None (None), residues: 0
  loop : -2.74 (0.49), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 219 
 HIS   0.002   0.001   HIS B 368 
 PHE   0.015   0.001   PHE D 213 
 TYR   0.009   0.001   TYR E   3 
 ARG   0.005   0.000   ARG B 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02873 ( 1554)
  hydrogen bonds       : angle       2.65125 ( 4662)
  covalent geometry    : bond        0.00287 (19710)
  covalent geometry    : angle       0.50771 (26620)

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

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

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4630 Ramachandran restraints generated.
    2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 160
  time to evaluate  : 2.205 
Fit side-chains
REVERT: A   12 GLU cc_start: 0.6913 (tp30) cc_final: 0.6698 (tp30)
REVERT: A  125 ASN cc_start: 0.7128 (m-40) cc_final: 0.5806 (t0)
REVERT: B   15 GLU cc_start: 0.7530 (mp0) cc_final: 0.7264 (mp0)
REVERT: B   69 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6822 (mp)
REVERT: B  352 LEU cc_start: 0.8201 (tp) cc_final: 0.7865 (tt)
REVERT: B  393 MET cc_start: 0.7057 (mmm) cc_final: 0.6790 (mmt)
REVERT: C   16 ILE cc_start: 0.8976 (mm) cc_final: 0.8375 (mm)
REVERT: C   50 MET cc_start: 0.6849 (mmm) cc_final: 0.4864 (ttt)
REVERT: C  143 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7662 (ttm170)
REVERT: C  208 SER cc_start: 0.8390 (p) cc_final: 0.8122 (m)
REVERT: D   37 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6548 (tt0)
REVERT: D  143 ARG cc_start: 0.7756 (tpt-90) cc_final: 0.7248 (ttm170)
REVERT: E   89 LYS cc_start: 0.7719 (tmtt) cc_final: 0.7397 (tmtt)
REVERT: E  123 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6637 (tm-30)
REVERT: E  143 ARG cc_start: 0.8175 (tpp80) cc_final: 0.7596 (ttt90)
  outliers start: 42
  outliers final: 37
  residues processed: 195
  average time/residue: 0.2819
  time to fit residues: 89.2043
Evaluate side-chains
  185 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 147
  time to evaluate  : 2.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 TRP
Chi-restraints excluded: chain C residue   79 ASP
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain C residue  283 VAL
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  435 VAL
Chi-restraints excluded: chain D residue  332 VAL
Chi-restraints excluded: chain D residue  354 LEU
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue  186 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain E residue  349 LEU
Chi-restraints excluded: chain E residue  431 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 230
   random chunks:
   chunk 169 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 213 optimal weight:    5.9990
   chunk 196 optimal weight:    3.9990
   chunk 153 optimal weight:    1.9990
   chunk 185 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0040
   overall best weight:    1.1398

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.152859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.147177 restraints weight = 22728.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.146863 restraints weight = 31592.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.147173 restraints weight = 27961.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.3789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  19710  Z= 0.119
  Angle     :  0.512  10.917  26620  Z= 0.243
  Chirality :  0.037   0.195   3060
  Planarity :  0.002   0.030   3315
  Dihedral  :  3.254  16.314   2400
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 17.75 %
    Favored  : 80.32 %
  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:  4.00 (0.17), residues: 2315
  helix:  2.95 (0.10), residues: 2160
  sheet:  None (None), residues: 0
  loop : -2.79 (0.49), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  23 
 HIS   0.003   0.001   HIS B 368 
 PHE   0.016   0.001   PHE D 213 
 TYR   0.009   0.001   TYR C 188 
 ARG   0.005   0.000   ARG B 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02914 ( 1554)
  hydrogen bonds       : angle       2.68578 ( 4662)
  covalent geometry    : bond        0.00294 (19710)
  covalent geometry    : angle       0.51202 (26620)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4630.44 seconds
wall clock time: 82 minutes 20.95 seconds (4940.95 seconds total)