Starting phenix.real_space_refine
on Wed Mar  4 00:08:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6rvx_10016/03_2026/6rvx_10016.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6rvx_10016/03_2026/6rvx_10016.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6rvx_10016/03_2026/6rvx_10016.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6rvx_10016/03_2026/6rvx_10016.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6rvx_10016/03_2026/6rvx_10016.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6rvx_10016/03_2026/6rvx_10016.cif"
  }
  resolution = 3.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.001 sd=   0.011
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      45      5.16       5
     C    6300      2.51       5
     N    1602      2.21       5
     O    1680      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9627
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3209
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3209
          Classifications: {'peptide': 430}
          Link IDs: {'PTRANS': 16, 'TRANS': 413}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 1.83, per 1000 atoms: 0.19
  Number of scatterers: 9627
  At special positions: 0
  Unit cell: (117.392, 120.428, 81.972, 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      45     16.00
     O    1680      8.00
     N    1602      7.00
     C    6300      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: 0.76
  Conformation dependent library (CDL) restraints added in 407.8 milliseconds
  

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2334

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 3 sheets defined
      69.8% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 52 through 74
      removed outlier: 3.611A  pdb=" N   ALA A  67 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 90
      removed outlier: 4.321A  pdb=" N   SER A  87 " --> pdb=" O   PRO A  83 " (cutoff:3.500A)
      removed outlier: 5.583A  pdb=" N   ALA A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL A  90 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 117
      removed outlier: 4.185A  pdb=" N   LEU A  97 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   LEU A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
      Proline residue:  A 106  - end of helix
      removed outlier: 3.809A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU A 112 " --> pdb=" O   VAL A 108 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ILE A 113 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLY A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 127
      No H-bonds generated for 'chain 'A' and resid 125 through 127'
    Processing helix  chain 'A' and resid 128 through 153
    Processing helix  chain 'A' and resid 184 through 192
      removed outlier: 4.047A  pdb=" N   ASN A 190 " --> pdb=" O   ASP A 186 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   PHE A 192 " --> pdb=" O   ALA A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 248
      removed outlier: 3.812A  pdb=" N   VAL A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   PHE A 237 " --> pdb=" O   GLY A 233 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA A 238 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 251
      No H-bonds generated for 'chain 'A' and resid 249 through 251'
    Processing helix  chain 'A' and resid 252 through 262
      removed outlier: 3.800A  pdb=" N   ILE A 256 " --> pdb=" O   GLY A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 292
      removed outlier: 3.986A  pdb=" N   VAL A 268 " --> pdb=" O   GLU A 264 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   LEU A 269 " --> pdb=" O   ALA A 265 " (cutoff:3.500A)
      Proline residue:  A 278  - end of helix
      removed outlier: 3.781A  pdb=" N   MET A 292 " --> pdb=" O   LYS A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 320
    Processing helix  chain 'A' and resid 320 through 329
      removed outlier: 3.840A  pdb=" N   PHE A 328 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 340
      removed outlier: 3.949A  pdb=" N   PHE A 336 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 351
    Processing helix  chain 'A' and resid 356 through 367
      removed outlier: 4.288A  pdb=" N   GLU A 365 " --> pdb=" O   MET A 361 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLU A 366 " --> pdb=" O   LYS A 362 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ASN A 367 " --> pdb=" O   CYS A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 397
    Processing helix  chain 'A' and resid 400 through 404
    Processing helix  chain 'A' and resid 410 through 423
      removed outlier: 3.980A  pdb=" N   ILE A 415 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   THR A 420 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA A 421 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 445
      removed outlier: 3.675A  pdb=" N   LEU A 439 " --> pdb=" O   GLY A 435 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ILE A 442 " --> pdb=" O   THR A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 454
      removed outlier: 3.877A  pdb=" N   HIS A 452 " --> pdb=" O   PRO A 449 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   SER A 454 " --> pdb=" O   ASP A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 483
      removed outlier: 3.803A  pdb=" N   VAL A 463 " --> pdb=" O   VAL A 459 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   SER A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   VAL A 469 " --> pdb=" O   ARG A 465 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   LEU A 470 " --> pdb=" O   SER A 466 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ASN A 471 " --> pdb=" O   ARG A 467 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL A 472 " --> pdb=" O   THR A 468 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ASP A 475 " --> pdb=" O   ASN A 471 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLN A 483 " --> pdb=" O   ALA A 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 74
      removed outlier: 3.611A  pdb=" N   ALA B  67 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 90
      removed outlier: 4.321A  pdb=" N   SER B  87 " --> pdb=" O   PRO B  83 " (cutoff:3.500A)
      removed outlier: 5.583A  pdb=" N   ALA B  88 " --> pdb=" O   GLU B  84 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 117
      removed outlier: 4.184A  pdb=" N   LEU B  97 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LEU B 105 " --> pdb=" O   ARG B 101 " (cutoff:3.500A)
      Proline residue:  B 106  - end of helix
      removed outlier: 3.810A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU B 112 " --> pdb=" O   VAL B 108 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ILE B 113 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLY B 114 " --> pdb=" O   CYS B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 127
      No H-bonds generated for 'chain 'B' and resid 125 through 127'
    Processing helix  chain 'B' and resid 128 through 153
    Processing helix  chain 'B' and resid 184 through 192
      removed outlier: 4.047A  pdb=" N   ASN B 190 " --> pdb=" O   ASP B 186 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   PHE B 192 " --> pdb=" O   ALA B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 248
      removed outlier: 3.814A  pdb=" N   VAL B 236 " --> pdb=" O   LEU B 232 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   PHE B 237 " --> pdb=" O   GLY B 233 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA B 238 " --> pdb=" O   LEU B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 251
      No H-bonds generated for 'chain 'B' and resid 249 through 251'
    Processing helix  chain 'B' and resid 252 through 262
      removed outlier: 3.800A  pdb=" N   ILE B 256 " --> pdb=" O   GLY B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 292
      removed outlier: 3.987A  pdb=" N   VAL B 268 " --> pdb=" O   GLU B 264 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   LEU B 269 " --> pdb=" O   ALA B 265 " (cutoff:3.500A)
      Proline residue:  B 278  - end of helix
      removed outlier: 3.780A  pdb=" N   MET B 292 " --> pdb=" O   LYS B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 320
    Processing helix  chain 'B' and resid 320 through 329
      removed outlier: 3.839A  pdb=" N   PHE B 328 " --> pdb=" O   ILE B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 340
      removed outlier: 3.950A  pdb=" N   PHE B 336 " --> pdb=" O   ASN B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 351
    Processing helix  chain 'B' and resid 356 through 367
      removed outlier: 4.288A  pdb=" N   GLU B 365 " --> pdb=" O   MET B 361 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   GLU B 366 " --> pdb=" O   LYS B 362 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ASN B 367 " --> pdb=" O   CYS B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 397
    Processing helix  chain 'B' and resid 400 through 404
    Processing helix  chain 'B' and resid 410 through 423
      removed outlier: 3.981A  pdb=" N   ILE B 415 " --> pdb=" O   PHE B 411 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   THR B 420 " --> pdb=" O   THR B 416 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA B 421 " --> pdb=" O   ILE B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 445
      removed outlier: 3.675A  pdb=" N   LEU B 439 " --> pdb=" O   GLY B 435 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ILE B 442 " --> pdb=" O   THR B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 454
      removed outlier: 3.877A  pdb=" N   HIS B 452 " --> pdb=" O   PRO B 449 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   SER B 454 " --> pdb=" O   ASP B 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 483
      removed outlier: 3.803A  pdb=" N   VAL B 463 " --> pdb=" O   VAL B 459 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   SER B 466 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   VAL B 469 " --> pdb=" O   ARG B 465 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   LEU B 470 " --> pdb=" O   SER B 466 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ASN B 471 " --> pdb=" O   ARG B 467 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   VAL B 472 " --> pdb=" O   THR B 468 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ASP B 475 " --> pdb=" O   ASN B 471 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLN B 483 " --> pdb=" O   ALA B 479 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 74
      removed outlier: 3.610A  pdb=" N   ALA C  67 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 90
      removed outlier: 4.321A  pdb=" N   SER C  87 " --> pdb=" O   PRO C  83 " (cutoff:3.500A)
      removed outlier: 5.583A  pdb=" N   ALA C  88 " --> pdb=" O   GLU C  84 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL C  90 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 117
      removed outlier: 4.186A  pdb=" N   LEU C  97 " --> pdb=" O   GLY C  93 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LEU C 105 " --> pdb=" O   ARG C 101 " (cutoff:3.500A)
      Proline residue:  C 106  - end of helix
      removed outlier: 3.810A  pdb=" N   VAL C 109 " --> pdb=" O   LEU C 105 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   LEU C 112 " --> pdb=" O   VAL C 108 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ILE C 113 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLY C 114 " --> pdb=" O   CYS C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 127
      No H-bonds generated for 'chain 'C' and resid 125 through 127'
    Processing helix  chain 'C' and resid 128 through 153
    Processing helix  chain 'C' and resid 184 through 192
      removed outlier: 4.047A  pdb=" N   ASN C 190 " --> pdb=" O   ASP C 186 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   PHE C 192 " --> pdb=" O   ALA C 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 248
      removed outlier: 3.813A  pdb=" N   VAL C 236 " --> pdb=" O   LEU C 232 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   PHE C 237 " --> pdb=" O   GLY C 233 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA C 238 " --> pdb=" O   LEU C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 249 through 251
      No H-bonds generated for 'chain 'C' and resid 249 through 251'
    Processing helix  chain 'C' and resid 252 through 262
      removed outlier: 3.800A  pdb=" N   ILE C 256 " --> pdb=" O   GLY C 252 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 292
      removed outlier: 3.987A  pdb=" N   VAL C 268 " --> pdb=" O   GLU C 264 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   LEU C 269 " --> pdb=" O   ALA C 265 " (cutoff:3.500A)
      Proline residue:  C 278  - end of helix
      removed outlier: 3.780A  pdb=" N   MET C 292 " --> pdb=" O   LYS C 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 320
    Processing helix  chain 'C' and resid 320 through 329
      removed outlier: 3.839A  pdb=" N   PHE C 328 " --> pdb=" O   ILE C 324 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 340
      removed outlier: 3.950A  pdb=" N   PHE C 336 " --> pdb=" O   ASN C 332 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 351
    Processing helix  chain 'C' and resid 356 through 367
      removed outlier: 4.288A  pdb=" N   GLU C 365 " --> pdb=" O   MET C 361 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLU C 366 " --> pdb=" O   LYS C 362 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ASN C 367 " --> pdb=" O   CYS C 363 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 387 through 397
    Processing helix  chain 'C' and resid 400 through 404
    Processing helix  chain 'C' and resid 410 through 423
      removed outlier: 3.980A  pdb=" N   ILE C 415 " --> pdb=" O   PHE C 411 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   THR C 420 " --> pdb=" O   THR C 416 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA C 421 " --> pdb=" O   ILE C 417 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 433 through 445
      removed outlier: 3.674A  pdb=" N   LEU C 439 " --> pdb=" O   GLY C 435 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ILE C 442 " --> pdb=" O   THR C 438 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 449 through 454
      removed outlier: 3.876A  pdb=" N   HIS C 452 " --> pdb=" O   PRO C 449 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   SER C 454 " --> pdb=" O   ASP C 451 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 459 through 483
      removed outlier: 3.803A  pdb=" N   VAL C 463 " --> pdb=" O   VAL C 459 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   SER C 466 " --> pdb=" O   LEU C 462 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   VAL C 469 " --> pdb=" O   ARG C 465 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   LEU C 470 " --> pdb=" O   SER C 466 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ASN C 471 " --> pdb=" O   ARG C 467 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   VAL C 472 " --> pdb=" O   THR C 468 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ASP C 475 " --> pdb=" O   ASN C 471 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLN C 483 " --> pdb=" O   ALA C 479 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 210
      removed outlier: 3.659A  pdb=" N   VAL A 220 " --> pdb=" O   GLU A 209 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 210
      removed outlier: 3.659A  pdb=" N   VAL B 220 " --> pdb=" O   GLU B 209 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 210
      removed outlier: 3.658A  pdb=" N   VAL C 220 " --> pdb=" O   GLU C 209 " (cutoff:3.500A)

    546 hydrogen bonds defined for protein.
    1611 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.35

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2892
        1.34 -     1.46: 1438
        1.46 -     1.57: 5396
        1.57 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 9798
  Sorted by residual:
  bond pdb=" CG1 ILE B 273 "
       pdb=" CD1 ILE B 273 "
    ideal  model  delta    sigma   weight residual
    1.513  1.451  0.062 3.90e-02 6.57e+02 2.50e+00
  bond pdb=" CG1 ILE C 273 "
       pdb=" CD1 ILE C 273 "
    ideal  model  delta    sigma   weight residual
    1.513  1.452  0.061 3.90e-02 6.57e+02 2.48e+00
  bond pdb=" CG1 ILE A 273 "
       pdb=" CD1 ILE A 273 "
    ideal  model  delta    sigma   weight residual
    1.513  1.452  0.061 3.90e-02 6.57e+02 2.44e+00
  bond pdb=" CG  LEU A 112 "
       pdb=" CD1 LEU A 112 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.15e+00
  bond pdb=" CG  LEU C 112 "
       pdb=" CD1 LEU C 112 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.07e+00
  ... (remaining 9793 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 12672
        2.00 -     4.00: 535
        4.00 -     6.00: 98
        6.00 -     7.99: 30
        7.99 -     9.99: 9
  Bond angle restraints: 13344
  Sorted by residual:
  angle pdb=" N   VAL A 197 "
        pdb=" CA  VAL A 197 "
        pdb=" C   VAL A 197 "
      ideal   model   delta    sigma   weight residual
     112.96  107.26    5.70 1.00e+00 1.00e+00 3.25e+01
  angle pdb=" N   VAL C 197 "
        pdb=" CA  VAL C 197 "
        pdb=" C   VAL C 197 "
      ideal   model   delta    sigma   weight residual
     112.96  107.26    5.70 1.00e+00 1.00e+00 3.24e+01
  angle pdb=" N   VAL B 197 "
        pdb=" CA  VAL B 197 "
        pdb=" C   VAL B 197 "
      ideal   model   delta    sigma   weight residual
     112.96  107.30    5.66 1.00e+00 1.00e+00 3.20e+01
  angle pdb=" N   ILE B 456 "
        pdb=" CA  ILE B 456 "
        pdb=" C   ILE B 456 "
      ideal   model   delta    sigma   weight residual
     111.90  107.84    4.06 8.10e-01 1.52e+00 2.51e+01
  angle pdb=" N   ILE A 456 "
        pdb=" CA  ILE A 456 "
        pdb=" C   ILE A 456 "
      ideal   model   delta    sigma   weight residual
     111.90  107.86    4.04 8.10e-01 1.52e+00 2.49e+01
  ... (remaining 13339 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.69: 4846
       13.69 -    27.38: 689
       27.38 -    41.07: 195
       41.07 -    54.76: 27
       54.76 -    68.45: 9
  Dihedral angle restraints: 5766
    sinusoidal: 2127
      harmonic: 3639
  Sorted by residual:
  dihedral pdb=" CA  THR B 416 "
           pdb=" C   THR B 416 "
           pdb=" N   ILE B 417 "
           pdb=" CA  ILE B 417 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.57   23.43     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" CA  THR C 416 "
           pdb=" C   THR C 416 "
           pdb=" N   ILE C 417 "
           pdb=" CA  ILE C 417 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.59   23.41     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" CA  THR A 416 "
           pdb=" C   THR A 416 "
           pdb=" N   ILE A 417 "
           pdb=" CA  ILE A 417 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.63   23.37     0      5.00e+00 4.00e-02 2.18e+01
  ... (remaining 5763 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1411
       0.070 -    0.140: 218
       0.140 -    0.210: 30
       0.210 -    0.280: 6
       0.280 -    0.350: 3
  Chirality restraints: 1668
  Sorted by residual:
  chirality pdb=" CB  VAL B  90 "
            pdb=" CA  VAL B  90 "
            pdb=" CG1 VAL B  90 "
            pdb=" CG2 VAL B  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.06e+00
  chirality pdb=" CB  VAL C  90 "
            pdb=" CA  VAL C  90 "
            pdb=" CG1 VAL C  90 "
            pdb=" CG2 VAL C  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.00e+00
  chirality pdb=" CB  VAL A  90 "
            pdb=" CA  VAL A  90 "
            pdb=" CG1 VAL A  90 "
            pdb=" CG2 VAL A  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.34 2.00e-01 2.50e+01 2.94e+00
  ... (remaining 1665 not shown)

  Planarity restraints: 1656
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 277 "   -0.055 5.00e-02 4.00e+02   8.27e-02 1.10e+01
        pdb=" N   PRO C 278 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO C 278 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO C 278 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 277 "   -0.055 5.00e-02 4.00e+02   8.27e-02 1.09e+01
        pdb=" N   PRO B 278 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO B 278 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 278 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 277 "    0.055 5.00e-02 4.00e+02   8.26e-02 1.09e+01
        pdb=" N   PRO A 278 "   -0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO A 278 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 278 "    0.046 5.00e-02 4.00e+02
  ... (remaining 1653 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2391
        2.79 -     3.32: 8551
        3.32 -     3.84: 15658
        3.84 -     4.37: 17932
        4.37 -     4.90: 31395
  Nonbonded interactions: 75927
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 434 "
            pdb=" OG1 THR A 438 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   GLY C 434 "
            pdb=" OG1 THR C 438 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   GLY B 434 "
            pdb=" OG1 THR B 438 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   SER B 198 "
            pdb=" OG  SER B 198 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" O   SER A 198 "
            pdb=" OG  SER A 198 "
     model   vdw
     2.323 3.040
  ... (remaining 75922 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.830
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062   9798  Z= 0.261
  Angle     :  0.986   9.992  13344  Z= 0.541
  Chirality :  0.055   0.350   1668
  Planarity :  0.008   0.083   1656
  Dihedral  : 14.073  68.451   3432
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  7.94 %
    Favored  : 91.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.46 (0.16), residues: 1278
  helix: -3.44 (0.11), residues: 942
  sheet: -3.34 (0.67), residues: 30
  loop : -3.32 (0.30), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.009   0.002   TYR B 334 
 PHE   0.018   0.002   PHE A  91 
 TRP   0.013   0.002   TRP C 461 
 HIS   0.003   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00611 ( 9798)
  covalent geometry    : angle       0.98604 (13344)
  hydrogen bonds       : bond        0.14711 (  546)
  hydrogen bonds       : angle       7.18353 ( 1611)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 153
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  260 ASN cc_start: 0.7464 (t0) cc_final: 0.7097 (t0)
REVERT: A  267 MET cc_start: 0.7049 (mmt) cc_final: 0.6732 (mmm)
REVERT: A  417 ILE cc_start: 0.8505 (tp) cc_final: 0.8110 (tt)
REVERT: A  457 LEU cc_start: 0.8871 (tp) cc_final: 0.8584 (tp)
REVERT: B  260 ASN cc_start: 0.7329 (t0) cc_final: 0.6888 (t0)
REVERT: B  411 PHE cc_start: 0.8175 (t80) cc_final: 0.7826 (t80)
REVERT: B  417 ILE cc_start: 0.8732 (tp) cc_final: 0.8270 (tt)
REVERT: C   52 ASN cc_start: 0.8828 (p0) cc_final: 0.8316 (p0)
REVERT: C  260 ASN cc_start: 0.7405 (t0) cc_final: 0.6987 (t0)
REVERT: C  411 PHE cc_start: 0.8164 (t80) cc_final: 0.7920 (t80)
REVERT: C  417 ILE cc_start: 0.8570 (tp) cc_final: 0.8120 (tt)
  outliers start: 3
  outliers final: 0
  residues processed: 153
  average time/residue: 0.1032
  time to fit residues: 21.8260
Evaluate side-chains
  118 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.4980
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS
A 386 ASN
B 313 HIS
B 386 ASN
C 313 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.158571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 117)---------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.110082 restraints weight = 10673.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.110839 restraints weight = 8214.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.110940 restraints weight = 7631.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.111193 restraints weight = 7087.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.111260 restraints weight = 7050.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9798  Z= 0.127
  Angle     :  0.620   7.832  13344  Z= 0.324
  Chirality :  0.039   0.155   1668
  Planarity :  0.006   0.066   1656
  Dihedral  :  5.582  19.712   1365
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.86 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.48 (0.21), residues: 1278
  helix: -1.83 (0.15), residues: 951
  sheet: -3.34 (0.64), residues: 36
  loop : -3.13 (0.32), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 465 
 TYR   0.011   0.001   TYR C 208 
 PHE   0.022   0.001   PHE C 326 
 TRP   0.021   0.001   TRP B 461 
 HIS   0.001   0.000   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9798)
  covalent geometry    : angle       0.62047 (13344)
  hydrogen bonds       : bond        0.03615 (  546)
  hydrogen bonds       : angle       4.74825 ( 1611)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.6441 (mmt90) cc_final: 0.6065 (tpt90)
REVERT: A  186 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8246 (t70)
REVERT: A  208 TYR cc_start: 0.8220 (m-80) cc_final: 0.7318 (m-80)
REVERT: A  229 MET cc_start: 0.8304 (ptp) cc_final: 0.7973 (ptp)
REVERT: A  260 ASN cc_start: 0.7457 (t0) cc_final: 0.7135 (t0)
REVERT: A  307 LEU cc_start: 0.8327 (tp) cc_final: 0.8029 (tt)
REVERT: A  417 ILE cc_start: 0.8002 (tp) cc_final: 0.7687 (tt)
REVERT: A  457 LEU cc_start: 0.8804 (tp) cc_final: 0.8541 (tp)
REVERT: A  465 ARG cc_start: 0.7642 (mmt-90) cc_final: 0.7262 (mmt90)
REVERT: B  126 ARG cc_start: 0.6359 (mmt90) cc_final: 0.5871 (tpt170)
REVERT: B  222 VAL cc_start: 0.8350 (p) cc_final: 0.8135 (m)
REVERT: B  260 ASN cc_start: 0.7383 (t0) cc_final: 0.7089 (t0)
REVERT: B  417 ILE cc_start: 0.8303 (tp) cc_final: 0.7980 (tt)
REVERT: B  457 LEU cc_start: 0.8485 (tp) cc_final: 0.8277 (tp)
REVERT: B  465 ARG cc_start: 0.8191 (mmt90) cc_final: 0.7952 (mmt90)
REVERT: B  484 ASN cc_start: 0.8553 (m-40) cc_final: 0.8316 (m-40)
REVERT: C  126 ARG cc_start: 0.6313 (mmt90) cc_final: 0.5848 (tpt-90)
REVERT: C  208 TYR cc_start: 0.8396 (m-80) cc_final: 0.8064 (m-10)
REVERT: C  222 VAL cc_start: 0.8378 (p) cc_final: 0.8169 (m)
REVERT: C  260 ASN cc_start: 0.7271 (t0) cc_final: 0.6874 (t0)
REVERT: C  267 MET cc_start: 0.7341 (mmm) cc_final: 0.6904 (mmt)
REVERT: C  417 ILE cc_start: 0.8138 (tp) cc_final: 0.7846 (tt)
  outliers start: 16
  outliers final: 9
  residues processed: 154
  average time/residue: 0.0861
  time to fit residues: 19.0481
Evaluate side-chains
  140 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  247 LYS
Chi-restraints excluded: chain C residue  422 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 84 optimal weight:    0.5980
   chunk 111 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 74 optimal weight:    8.9990
   chunk 59 optimal weight:    0.2980
   chunk 27 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 117 optimal weight:   10.0000
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 316 HIS
** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 316 HIS
C 316 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.156415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 285)---------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.114807 restraints weight = 10736.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 76)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.110036 restraints weight = 15296.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.109668 restraints weight = 10599.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.109949 restraints weight = 10211.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.109934 restraints weight = 8632.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9798  Z= 0.138
  Angle     :  0.623   9.457  13344  Z= 0.315
  Chirality :  0.040   0.176   1668
  Planarity :  0.005   0.062   1656
  Dihedral  :  5.226  20.542   1365
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 16.08 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.47 (0.23), residues: 1278
  helix: -0.99 (0.17), residues: 918
  sheet: -3.08 (0.69), residues: 36
  loop : -2.98 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 202 
 TYR   0.009   0.001   TYR C 208 
 PHE   0.022   0.001   PHE C 326 
 TRP   0.013   0.001   TRP A 461 
 HIS   0.001   0.000   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9798)
  covalent geometry    : angle       0.62345 (13344)
  hydrogen bonds       : bond        0.03370 (  546)
  hydrogen bonds       : angle       4.42298 ( 1611)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A  109 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8742 (p)
REVERT: A  126 ARG cc_start: 0.6330 (mmt90) cc_final: 0.5618 (tmm160)
REVERT: A  208 TYR cc_start: 0.8170 (m-80) cc_final: 0.7265 (m-80)
REVERT: A  229 MET cc_start: 0.8337 (ptp) cc_final: 0.8041 (ptp)
REVERT: A  260 ASN cc_start: 0.7350 (t0) cc_final: 0.7052 (t0)
REVERT: A  307 LEU cc_start: 0.8437 (tp) cc_final: 0.8202 (tt)
REVERT: A  394 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8073 (mp-120)
REVERT: A  407 GLN cc_start: 0.7556 (mm110) cc_final: 0.7248 (mm-40)
REVERT: A  417 ILE cc_start: 0.7996 (tp) cc_final: 0.7771 (tt)
REVERT: A  420 THR cc_start: 0.8694 (t) cc_final: 0.8493 (t)
REVERT: A  457 LEU cc_start: 0.8756 (tp) cc_final: 0.8423 (tp)
REVERT: A  465 ARG cc_start: 0.7586 (mmt-90) cc_final: 0.7183 (mmt90)
REVERT: B   85 ARG cc_start: 0.5507 (ttt180) cc_final: 0.5185 (ttt180)
REVERT: B  126 ARG cc_start: 0.6401 (mmt90) cc_final: 0.5919 (tpt170)
REVERT: B  186 ASP cc_start: 0.8226 (t70) cc_final: 0.8001 (t70)
REVERT: B  222 VAL cc_start: 0.8299 (p) cc_final: 0.8096 (m)
REVERT: B  260 ASN cc_start: 0.7574 (t0) cc_final: 0.7202 (t0)
REVERT: B  394 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.7017 (mp-120)
REVERT: B  417 ILE cc_start: 0.8282 (tp) cc_final: 0.8011 (tt)
REVERT: C   52 ASN cc_start: 0.8834 (p0) cc_final: 0.8300 (p0)
REVERT: C  126 ARG cc_start: 0.6361 (mmt90) cc_final: 0.5920 (tpt-90)
REVERT: C  208 TYR cc_start: 0.8277 (m-80) cc_final: 0.8039 (m-10)
REVERT: C  260 ASN cc_start: 0.7447 (t0) cc_final: 0.7078 (t0)
REVERT: C  394 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.7683 (mp-120)
REVERT: C  417 ILE cc_start: 0.8057 (tp) cc_final: 0.7848 (tt)
  outliers start: 29
  outliers final: 14
  residues processed: 173
  average time/residue: 0.0807
  time to fit residues: 20.5556
Evaluate side-chains
  159 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  394 GLN
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  394 GLN
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  363 CYS
Chi-restraints excluded: chain C residue  394 GLN
Chi-restraints excluded: chain C residue  422 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 117 optimal weight:   20.0000
   chunk 121 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 109 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 98 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 212 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.159292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.124792 restraints weight = 10706.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.123667 restraints weight = 18557.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.125086 restraints weight = 17755.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.125222 restraints weight = 11764.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.125858 restraints weight = 11577.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9798  Z= 0.114
  Angle     :  0.606   9.460  13344  Z= 0.304
  Chirality :  0.040   0.175   1668
  Planarity :  0.005   0.060   1656
  Dihedral  :  4.888  19.350   1365
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 16.27 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.83 (0.24), residues: 1278
  helix: -0.47 (0.18), residues: 909
  sheet: -2.79 (0.72), residues: 36
  loop : -2.89 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 202 
 TYR   0.007   0.001   TYR C 208 
 PHE   0.023   0.001   PHE C 326 
 TRP   0.011   0.001   TRP B 461 
 HIS   0.001   0.000   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 9798)
  covalent geometry    : angle       0.60628 (13344)
  hydrogen bonds       : bond        0.03046 (  546)
  hydrogen bonds       : angle       4.23748 ( 1611)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 152
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.6408 (mmt90) cc_final: 0.6084 (tmm160)
REVERT: A  208 TYR cc_start: 0.8062 (m-80) cc_final: 0.7173 (m-80)
REVERT: A  229 MET cc_start: 0.8151 (ptp) cc_final: 0.7857 (ptp)
REVERT: A  260 ASN cc_start: 0.7431 (t0) cc_final: 0.7135 (t0)
REVERT: A  307 LEU cc_start: 0.8526 (tp) cc_final: 0.8315 (tt)
REVERT: A  344 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7644 (mp)
REVERT: A  394 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8073 (mp-120)
REVERT: A  417 ILE cc_start: 0.8084 (tp) cc_final: 0.7875 (tt)
REVERT: A  420 THR cc_start: 0.8750 (t) cc_final: 0.8496 (t)
REVERT: A  465 ARG cc_start: 0.7739 (mmt-90) cc_final: 0.7499 (mmt90)
REVERT: B  109 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8493 (p)
REVERT: B  260 ASN cc_start: 0.7541 (t0) cc_final: 0.7152 (t0)
REVERT: B  344 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7519 (mp)
REVERT: B  394 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.6961 (mp-120)
REVERT: B  417 ILE cc_start: 0.8289 (tp) cc_final: 0.8050 (tt)
REVERT: B  437 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7881 (tt)
REVERT: C   52 ASN cc_start: 0.8782 (p0) cc_final: 0.8266 (p0)
REVERT: C  109 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8420 (p)
REVERT: C  260 ASN cc_start: 0.7471 (t0) cc_final: 0.7179 (t0)
REVERT: C  325 TYR cc_start: 0.7952 (t80) cc_final: 0.7573 (t80)
REVERT: C  394 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7645 (mp-120)
REVERT: C  417 ILE cc_start: 0.8120 (tp) cc_final: 0.7901 (tt)
  outliers start: 35
  outliers final: 13
  residues processed: 178
  average time/residue: 0.0829
  time to fit residues: 21.7463
Evaluate side-chains
  162 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  394 GLN
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  394 GLN
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  363 CYS
Chi-restraints excluded: chain C residue  394 GLN
Chi-restraints excluded: chain C residue  422 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 31 optimal weight:    7.9990
   chunk 90 optimal weight:    7.9990
   chunk 95 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 66 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 102 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   chunk 113 optimal weight:    7.9990
   chunk 116 optimal weight:    9.9990
   chunk 110 optimal weight:    7.9990
   overall best weight:    2.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.153604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 149)---------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.106086 restraints weight = 10844.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.104163 restraints weight = 9311.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.104483 restraints weight = 9159.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.104593 restraints weight = 8571.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.104653 restraints weight = 8392.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   9798  Z= 0.252
  Angle     :  0.738   8.553  13344  Z= 0.364
  Chirality :  0.046   0.207   1668
  Planarity :  0.005   0.063   1656
  Dihedral  :  5.371  21.852   1365
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 16.27 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.01 (0.24), residues: 1278
  helix: -0.67 (0.18), residues: 894
  sheet: -2.84 (0.72), residues: 36
  loop : -2.64 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  98 
 TYR   0.010   0.001   TYR C 208 
 PHE   0.024   0.002   PHE C 326 
 TRP   0.011   0.001   TRP A 275 
 HIS   0.001   0.000   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00622 ( 9798)
  covalent geometry    : angle       0.73794 (13344)
  hydrogen bonds       : bond        0.03934 (  546)
  hydrogen bonds       : angle       4.54172 ( 1611)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 122
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  208 TYR cc_start: 0.8141 (m-80) cc_final: 0.7215 (m-80)
REVERT: A  344 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7220 (mp)
REVERT: A  394 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8014 (mp-120)
REVERT: A  407 GLN cc_start: 0.7771 (mm110) cc_final: 0.7375 (mm-40)
REVERT: A  417 ILE cc_start: 0.8023 (tp) cc_final: 0.7767 (tt)
REVERT: A  418 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7537 (tt)
REVERT: A  420 THR cc_start: 0.8721 (t) cc_final: 0.8502 (t)
REVERT: A  437 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7950 (tt)
REVERT: A  465 ARG cc_start: 0.7821 (mmt-90) cc_final: 0.7485 (mmt90)
REVERT: B   85 ARG cc_start: 0.5671 (ttt180) cc_final: 0.5374 (ttt180)
REVERT: B  186 ASP cc_start: 0.8334 (t70) cc_final: 0.8112 (t70)
REVERT: B  260 ASN cc_start: 0.7676 (t0) cc_final: 0.7178 (t0)
REVERT: B  394 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.7038 (mp-120)
REVERT: B  417 ILE cc_start: 0.8355 (tp) cc_final: 0.8094 (tt)
REVERT: C  109 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8812 (p)
REVERT: C  260 ASN cc_start: 0.7591 (t0) cc_final: 0.7080 (t0)
REVERT: C  325 TYR cc_start: 0.8090 (t80) cc_final: 0.7705 (t80)
REVERT: C  394 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.7774 (mp-120)
REVERT: C  417 ILE cc_start: 0.8104 (tp) cc_final: 0.7866 (tt)
  outliers start: 38
  outliers final: 14
  residues processed: 156
  average time/residue: 0.0863
  time to fit residues: 19.5392
Evaluate side-chains
  139 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  394 GLN
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  394 GLN
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  359 LEU
Chi-restraints excluded: chain C residue  394 GLN
Chi-restraints excluded: chain C residue  422 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 125 optimal weight:    1.9990
   chunk 89 optimal weight:   10.0000
   chunk 83 optimal weight:    0.5980
   chunk 43 optimal weight:   20.0000
   chunk 55 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 212 ASN
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.156391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 186)---------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.112783 restraints weight = 10737.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.110791 restraints weight = 11205.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 92)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.109416 restraints weight = 11449.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.109020 restraints weight = 8701.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.109261 restraints weight = 8790.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9798  Z= 0.144
  Angle     :  0.646   8.041  13344  Z= 0.320
  Chirality :  0.042   0.177   1668
  Planarity :  0.005   0.062   1656
  Dihedral  :  5.047  20.030   1365
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 17.84 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.24), residues: 1278
  helix: -0.38 (0.18), residues: 909
  sheet: -2.68 (0.70), residues: 36
  loop : -2.76 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 202 
 TYR   0.011   0.001   TYR C 208 
 PHE   0.024   0.001   PHE C 326 
 TRP   0.011   0.001   TRP A 461 
 HIS   0.001   0.000   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9798)
  covalent geometry    : angle       0.64620 (13344)
  hydrogen bonds       : bond        0.03278 (  546)
  hydrogen bonds       : angle       4.30851 ( 1611)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 127
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A  208 TYR cc_start: 0.8080 (m-80) cc_final: 0.7157 (m-80)
REVERT: A  260 ASN cc_start: 0.7437 (t0) cc_final: 0.7026 (t0)
REVERT: A  267 MET cc_start: 0.7598 (mmm) cc_final: 0.6856 (mmm)
REVERT: A  344 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7107 (mp)
REVERT: A  394 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8023 (mp-120)
REVERT: A  417 ILE cc_start: 0.8033 (tp) cc_final: 0.7798 (tt)
REVERT: A  418 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7206 (tt)
REVERT: A  420 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8493 (t)
REVERT: A  465 ARG cc_start: 0.7744 (mmt-90) cc_final: 0.7260 (mmt90)
REVERT: B   85 ARG cc_start: 0.5634 (ttt180) cc_final: 0.5393 (tpt170)
REVERT: B  186 ASP cc_start: 0.8231 (t70) cc_final: 0.8000 (t70)
REVERT: B  260 ASN cc_start: 0.7598 (t0) cc_final: 0.7184 (t0)
REVERT: B  394 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.6959 (mp-120)
REVERT: B  417 ILE cc_start: 0.8283 (tp) cc_final: 0.8020 (tt)
REVERT: C  109 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8728 (p)
REVERT: C  260 ASN cc_start: 0.7499 (t0) cc_final: 0.7093 (t0)
REVERT: C  325 TYR cc_start: 0.8001 (t80) cc_final: 0.7646 (t80)
REVERT: C  394 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7675 (mp-120)
  outliers start: 33
  outliers final: 16
  residues processed: 155
  average time/residue: 0.0858
  time to fit residues: 19.6570
Evaluate side-chains
  146 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  394 GLN
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  394 GLN
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  378 ILE
Chi-restraints excluded: chain C residue  394 GLN
Chi-restraints excluded: chain C residue  422 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 115 optimal weight:    4.9990
   chunk 110 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0020
   chunk 79 optimal weight:    3.9990
   chunk 75 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   overall best weight:    1.7392

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.154430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 169)---------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.108447 restraints weight = 10692.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.104957 restraints weight = 10745.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.105827 restraints weight = 9038.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.106492 restraints weight = 8207.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.107027 restraints weight = 7754.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9798  Z= 0.172
  Angle     :  0.678   9.287  13344  Z= 0.334
  Chirality :  0.043   0.181   1668
  Planarity :  0.005   0.063   1656
  Dihedral  :  5.064  21.018   1365
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.61 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.24), residues: 1278
  helix: -0.37 (0.18), residues: 918
  sheet: -2.70 (0.67), residues: 36
  loop : -2.62 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 202 
 TYR   0.009   0.001   TYR C 208 
 PHE   0.025   0.002   PHE B 326 
 TRP   0.009   0.001   TRP B 461 
 HIS   0.001   0.000   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 9798)
  covalent geometry    : angle       0.67816 (13344)
  hydrogen bonds       : bond        0.03475 (  546)
  hydrogen bonds       : angle       4.33008 ( 1611)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 127
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  208 TYR cc_start: 0.8051 (m-80) cc_final: 0.7091 (m-80)
REVERT: A  260 ASN cc_start: 0.7315 (t0) cc_final: 0.6985 (t0)
REVERT: A  267 MET cc_start: 0.7630 (mmm) cc_final: 0.6904 (mmm)
REVERT: A  344 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7248 (mp)
REVERT: A  394 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8014 (mp-120)
REVERT: A  417 ILE cc_start: 0.8019 (tp) cc_final: 0.7790 (tt)
REVERT: A  418 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7302 (tt)
REVERT: A  420 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8485 (t)
REVERT: A  465 ARG cc_start: 0.7804 (mmt-90) cc_final: 0.7294 (mmt90)
REVERT: B   85 ARG cc_start: 0.5679 (ttt180) cc_final: 0.5433 (tpt170)
REVERT: B  182 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7067 (m-30)
REVERT: B  186 ASP cc_start: 0.8271 (t70) cc_final: 0.8030 (t70)
REVERT: B  260 ASN cc_start: 0.7601 (t0) cc_final: 0.7174 (t0)
REVERT: B  394 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.6967 (mp-120)
REVERT: B  417 ILE cc_start: 0.8292 (tp) cc_final: 0.8032 (tt)
REVERT: C   52 ASN cc_start: 0.8770 (p0) cc_final: 0.8169 (p0)
REVERT: C  260 ASN cc_start: 0.7524 (t0) cc_final: 0.7100 (t0)
REVERT: C  325 TYR cc_start: 0.8022 (t80) cc_final: 0.7688 (t80)
REVERT: C  394 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.7703 (mp-120)
  outliers start: 31
  outliers final: 18
  residues processed: 154
  average time/residue: 0.0809
  time to fit residues: 18.4735
Evaluate side-chains
  143 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  394 GLN
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  394 GLN
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  229 MET
Chi-restraints excluded: chain C residue  378 ILE
Chi-restraints excluded: chain C residue  394 GLN
Chi-restraints excluded: chain C residue  422 THR
Chi-restraints excluded: chain C residue  470 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 19 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 97 optimal weight:   10.0000
   chunk 126 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.155531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 147)---------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.109588 restraints weight = 10712.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.106743 restraints weight = 10335.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.107598 restraints weight = 8811.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.108148 restraints weight = 8051.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.108148 restraints weight = 7653.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9798  Z= 0.157
  Angle     :  0.662   9.130  13344  Z= 0.327
  Chirality :  0.042   0.193   1668
  Planarity :  0.005   0.062   1656
  Dihedral  :  4.990  19.922   1365
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.20 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.49 (0.24), residues: 1278
  helix: -0.28 (0.18), residues: 918
  sheet: -2.65 (0.67), residues: 36
  loop : -2.59 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 202 
 TYR   0.010   0.001   TYR C 208 
 PHE   0.026   0.001   PHE C 326 
 TRP   0.009   0.001   TRP A 461 
 HIS   0.001   0.000   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 9798)
  covalent geometry    : angle       0.66191 (13344)
  hydrogen bonds       : bond        0.03370 (  546)
  hydrogen bonds       : angle       4.28255 ( 1611)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 124
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  208 TYR cc_start: 0.8027 (m-80) cc_final: 0.7089 (m-80)
REVERT: A  260 ASN cc_start: 0.7292 (t0) cc_final: 0.6973 (t0)
REVERT: A  267 MET cc_start: 0.7583 (mmm) cc_final: 0.6860 (mmm)
REVERT: A  344 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7265 (mp)
REVERT: A  394 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.7943 (mp-120)
REVERT: A  395 CYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7832 (m)
REVERT: A  418 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7358 (tt)
REVERT: A  465 ARG cc_start: 0.7612 (mmt-90) cc_final: 0.7168 (mmt90)
REVERT: B  182 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6926 (m-30)
REVERT: B  186 ASP cc_start: 0.8252 (t70) cc_final: 0.8015 (t70)
REVERT: B  260 ASN cc_start: 0.7580 (t0) cc_final: 0.7165 (t0)
REVERT: B  394 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.6964 (mp-120)
REVERT: B  395 CYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7674 (m)
REVERT: C  260 ASN cc_start: 0.7423 (t0) cc_final: 0.7060 (t0)
REVERT: C  325 TYR cc_start: 0.8010 (t80) cc_final: 0.7685 (t80)
REVERT: C  394 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7713 (mp-120)
  outliers start: 32
  outliers final: 17
  residues processed: 151
  average time/residue: 0.0758
  time to fit residues: 17.1638
Evaluate side-chains
  146 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  394 GLN
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  394 GLN
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  229 MET
Chi-restraints excluded: chain C residue  378 ILE
Chi-restraints excluded: chain C residue  394 GLN
Chi-restraints excluded: chain C residue  422 THR
Chi-restraints excluded: chain C residue  470 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 127 optimal weight:    0.6980
   chunk 122 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   chunk 103 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 212 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.156553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.119406 restraints weight = 10632.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.115113 restraints weight = 15244.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.116562 restraints weight = 19501.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.117094 restraints weight = 11443.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.117532 restraints weight = 9911.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9798  Z= 0.137
  Angle     :  0.656   8.949  13344  Z= 0.323
  Chirality :  0.042   0.190   1668
  Planarity :  0.005   0.061   1656
  Dihedral  :  4.847  19.710   1365
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 20.29 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.25), residues: 1278
  helix: -0.18 (0.18), residues: 924
  sheet: -2.56 (0.67), residues: 36
  loop : -2.48 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 202 
 TYR   0.011   0.001   TYR C 208 
 PHE   0.026   0.001   PHE C 326 
 TRP   0.010   0.001   TRP A 461 
 HIS   0.001   0.000   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9798)
  covalent geometry    : angle       0.65582 (13344)
  hydrogen bonds       : bond        0.03272 (  546)
  hydrogen bonds       : angle       4.20251 ( 1611)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 127
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  208 TYR cc_start: 0.7955 (m-80) cc_final: 0.7030 (m-80)
REVERT: A  260 ASN cc_start: 0.7271 (t0) cc_final: 0.6919 (t0)
REVERT: A  267 MET cc_start: 0.7573 (mmm) cc_final: 0.6845 (mmm)
REVERT: A  394 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8006 (mp-120)
REVERT: A  395 CYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7690 (m)
REVERT: A  418 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7384 (tt)
REVERT: B  182 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6839 (m-30)
REVERT: B  186 ASP cc_start: 0.8228 (t70) cc_final: 0.7977 (t70)
REVERT: B  260 ASN cc_start: 0.7500 (t0) cc_final: 0.7128 (t0)
REVERT: B  394 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.7017 (mp-120)
REVERT: B  395 CYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7757 (m)
REVERT: C   52 ASN cc_start: 0.8765 (p0) cc_final: 0.8559 (p0)
REVERT: C  260 ASN cc_start: 0.7442 (t0) cc_final: 0.7094 (t0)
REVERT: C  325 TYR cc_start: 0.7958 (t80) cc_final: 0.7680 (t80)
REVERT: C  394 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7632 (mp-120)
  outliers start: 33
  outliers final: 21
  residues processed: 155
  average time/residue: 0.0763
  time to fit residues: 17.6736
Evaluate side-chains
  148 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  394 GLN
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  394 GLN
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  229 MET
Chi-restraints excluded: chain C residue  378 ILE
Chi-restraints excluded: chain C residue  394 GLN
Chi-restraints excluded: chain C residue  422 THR
Chi-restraints excluded: chain C residue  470 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 84 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   chunk 116 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0470
   chunk 31 optimal weight:    0.0970
   chunk 59 optimal weight:    0.6980
   chunk 100 optimal weight:    0.4980
   chunk 17 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.3676

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 403 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.161919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.124875 restraints weight = 10432.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.122581 restraints weight = 16368.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.124336 restraints weight = 14534.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.124189 restraints weight = 10165.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.124466 restraints weight = 11863.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9798  Z= 0.112
  Angle     :  0.632   9.107  13344  Z= 0.312
  Chirality :  0.041   0.192   1668
  Planarity :  0.005   0.057   1656
  Dihedral  :  4.527  18.361   1365
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 20.98 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.25), residues: 1278
  helix:  0.08 (0.18), residues: 921
  sheet: -2.31 (0.68), residues: 36
  loop : -2.48 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 465 
 TYR   0.017   0.001   TYR C 208 
 PHE   0.028   0.001   PHE C 326 
 TRP   0.012   0.001   TRP A 461 
 HIS   0.001   0.000   HIS C 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9798)
  covalent geometry    : angle       0.63205 (13344)
  hydrogen bonds       : bond        0.02914 (  546)
  hydrogen bonds       : angle       4.02678 ( 1611)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A  208 TYR cc_start: 0.7805 (m-80) cc_final: 0.6924 (m-80)
REVERT: A  229 MET cc_start: 0.7973 (ptp) cc_final: 0.7687 (ptp)
REVERT: A  260 ASN cc_start: 0.7365 (t0) cc_final: 0.7040 (t0)
REVERT: A  394 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8054 (mp-120)
REVERT: A  395 CYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7719 (m)
REVERT: A  418 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7427 (tt)
REVERT: B  186 ASP cc_start: 0.8135 (t70) cc_final: 0.7903 (t70)
REVERT: B  394 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7013 (mp-120)
REVERT: B  395 CYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7673 (m)
REVERT: C  126 ARG cc_start: 0.7197 (tpt-90) cc_final: 0.5358 (tmm160)
REVERT: C  260 ASN cc_start: 0.7326 (t0) cc_final: 0.7081 (t0)
REVERT: C  394 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7532 (mp-120)
REVERT: C  395 CYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7580 (m)
  outliers start: 23
  outliers final: 10
  residues processed: 160
  average time/residue: 0.0778
  time to fit residues: 18.4599
Evaluate side-chains
  143 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  394 GLN
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  247 LYS
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  394 GLN
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain C residue  378 ILE
Chi-restraints excluded: chain C residue  394 GLN
Chi-restraints excluded: chain C residue  395 CYS
Chi-restraints excluded: chain C residue  422 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 119 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 87 optimal weight:    0.5980
   chunk 127 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 94 optimal weight:    0.0970
   chunk 45 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
C 403 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.160562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.125695 restraints weight = 10511.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.124332 restraints weight = 17727.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.125746 restraints weight = 16319.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.125631 restraints weight = 11391.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.125956 restraints weight = 12396.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.2867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9798  Z= 0.121
  Angle     :  0.654   9.386  13344  Z= 0.316
  Chirality :  0.042   0.246   1668
  Planarity :  0.004   0.058   1656
  Dihedral  :  4.480  19.001   1365
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 22.35 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.25), residues: 1278
  helix:  0.19 (0.18), residues: 921
  sheet: -2.17 (0.69), residues: 36
  loop : -2.45 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 202 
 TYR   0.009   0.001   TYR B 208 
 PHE   0.027   0.001   PHE C 326 
 TRP   0.015   0.001   TRP C 461 
 HIS   0.001   0.000   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9798)
  covalent geometry    : angle       0.65436 (13344)
  hydrogen bonds       : bond        0.02989 (  546)
  hydrogen bonds       : angle       4.00385 ( 1611)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1693.18 seconds
wall clock time: 29 minutes 44.96 seconds (1784.96 seconds total)