Starting phenix.real_space_refine
on Thu Feb 13 22:08:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6rvx_10016/02_2025/6rvx_10016.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6rvx_10016/02_2025/6rvx_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_10016/02_2025/6rvx_10016.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6rvx_10016/02_2025/6rvx_10016.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6rvx_10016/02_2025/6rvx_10016.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6rvx_10016/02_2025/6rvx_10016.cif"
  }
  resolution = 3.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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:
    C, B
  Time building chain proxies: 5.32, per 1000 atoms: 0.55
  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: 2.64
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.82
  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: 2.50

  Time building geometry restraints manager: 3.02 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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:             2.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     22.940
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.060
-------------------------------------------------------------------------------
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= 0.398
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.46 (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
 TRP   0.013   0.002   TRP C 461 
 HIS   0.003   0.001   HIS A 373 
 PHE   0.018   0.002   PHE A  91 
 TYR   0.009   0.002   TYR B 334 
 ARG   0.002   0.000   ARG A  98 

*********************** 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  : 0.893 
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: 0.6733 (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: 0.7328 (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: 0.2338
  time to fit residues: 49.5785
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  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 97 optimal weight:    8.9990
   chunk 54 optimal weight:    9.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 101 optimal weight:    0.2980
   chunk 39 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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
C 386 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.159991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.124974 restraints weight = 10669.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.125365 restraints weight = 18781.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.126582 restraints weight = 15827.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1444

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= 0.180
  Angle     :  0.613   7.875  13344  Z= 0.319
  Chirality :  0.039   0.159   1668
  Planarity :  0.006   0.066   1656
  Dihedral  :  5.510  19.394   1365
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 12.06 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.41 (0.21), residues: 1278
  helix: -1.74 (0.15), residues: 933
  sheet: -3.34 (0.65), residues: 36
  loop : -3.20 (0.31), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 461 
 HIS   0.001   0.000   HIS A 373 
 PHE   0.022   0.001   PHE C 326 
 TYR   0.010   0.001   TYR C 208 
 ARG   0.004   0.000   ARG B 202 

*********************** 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
  163 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.6442 (mmt90) cc_final: 0.6095 (tmm160)
REVERT: A  208 TYR cc_start: 0.8169 (m-80) cc_final: 0.7292 (m-80)
REVERT: A  229 MET cc_start: 0.8135 (ptp) cc_final: 0.7794 (ptp)
REVERT: A  260 ASN cc_start: 0.7460 (t0) cc_final: 0.7095 (t0)
REVERT: A  307 LEU cc_start: 0.8515 (tp) cc_final: 0.8212 (tt)
REVERT: A  417 ILE cc_start: 0.8130 (tp) cc_final: 0.7859 (tt)
REVERT: A  457 LEU cc_start: 0.8807 (tp) cc_final: 0.8554 (tp)
REVERT: A  465 ARG cc_start: 0.7684 (mmt-90) cc_final: 0.7391 (mmt90)
REVERT: B  260 ASN cc_start: 0.7455 (t0) cc_final: 0.7075 (t0)
REVERT: B  417 ILE cc_start: 0.8370 (tp) cc_final: 0.8045 (tt)
REVERT: C  126 ARG cc_start: 0.6387 (mmt90) cc_final: 0.6108 (tpt-90)
REVERT: C  208 TYR cc_start: 0.8309 (m-80) cc_final: 0.8012 (m-10)
REVERT: C  260 ASN cc_start: 0.7377 (t0) cc_final: 0.6902 (t0)
REVERT: C  267 MET cc_start: 0.7475 (mmm) cc_final: 0.7046 (mmt)
REVERT: C  417 ILE cc_start: 0.8179 (tp) cc_final: 0.7881 (tt)
  outliers start: 15
  outliers final: 8
  residues processed: 157
  average time/residue: 0.2092
  time to fit residues: 47.4035
Evaluate side-chains
  138 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 130
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 102 optimal weight:    8.9990
   chunk 117 optimal weight:    0.5980
   chunk 109 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 116 optimal weight:    9.9990
   chunk 115 optimal weight:    0.4980
   chunk 111 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 120 optimal weight:    1.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.3682 r_free = 0.3682 target = 0.159789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.127153 restraints weight = 10778.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.127504 restraints weight = 18763.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.128373 restraints weight = 16270.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9798  Z= 0.173
  Angle     :  0.612   9.694  13344  Z= 0.308
  Chirality :  0.039   0.175   1668
  Planarity :  0.005   0.062   1656
  Dihedral  :  5.066  20.173   1365
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.20 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.23), residues: 1278
  helix: -0.90 (0.17), residues: 918
  sheet: -3.01 (0.69), residues: 36
  loop : -2.95 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 461 
 HIS   0.001   0.000   HIS A 373 
 PHE   0.022   0.001   PHE C 326 
 TYR   0.008   0.001   TYR C 208 
 ARG   0.003   0.000   ARG B 202 

*********************** 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: 26
    poor density    : 158
  time to evaluate  : 1.022 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.6372 (mmt90) cc_final: 0.6168 (tmm160)
REVERT: A  208 TYR cc_start: 0.7992 (m-80) cc_final: 0.7128 (m-80)
REVERT: A  229 MET cc_start: 0.8169 (ptp) cc_final: 0.7863 (ptp)
REVERT: A  260 ASN cc_start: 0.7249 (t0) cc_final: 0.7037 (t0)
REVERT: A  394 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8161 (mp-120)
REVERT: A  407 GLN cc_start: 0.7514 (mm110) cc_final: 0.7305 (mm-40)
REVERT: A  417 ILE cc_start: 0.8186 (tp) cc_final: 0.7963 (tt)
REVERT: A  437 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7980 (tt)
REVERT: A  465 ARG cc_start: 0.7735 (mmt-90) cc_final: 0.7434 (mmt90)
REVERT: B  126 ARG cc_start: 0.7473 (tpt170) cc_final: 0.7061 (tpt-90)
REVERT: B  186 ASP cc_start: 0.8232 (t70) cc_final: 0.8000 (t70)
REVERT: B  260 ASN cc_start: 0.7404 (t0) cc_final: 0.7094 (t0)
REVERT: B  394 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7043 (mp-120)
REVERT: B  417 ILE cc_start: 0.8373 (tp) cc_final: 0.8131 (tt)
REVERT: C  260 ASN cc_start: 0.7415 (t0) cc_final: 0.7114 (t0)
REVERT: C  394 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.7688 (mp-120)
REVERT: C  417 ILE cc_start: 0.8116 (tp) cc_final: 0.7897 (tt)
  outliers start: 26
  outliers final: 12
  residues processed: 174
  average time/residue: 0.1970
  time to fit residues: 50.1340
Evaluate side-chains
  153 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
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  282 MET
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  394 GLN
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  247 LYS
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 59 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 99 optimal weight:    0.0040
   chunk 70 optimal weight:    4.9990
   chunk 76 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   chunk 16 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:    8.9990
   chunk 11 optimal weight:    9.9990
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.8994

-------------------------------------------------------------------------------
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 = 0.3683 r_free = 0.3683 target = 0.159852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.126041 restraints weight = 10592.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.124519 restraints weight = 18184.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.125830 restraints weight = 16865.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.2182

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= 0.187
  Angle     :  0.627   9.421  13344  Z= 0.310
  Chirality :  0.040   0.191   1668
  Planarity :  0.005   0.059   1656
  Dihedral  :  4.886  19.445   1365
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.08 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.24), residues: 1278
  helix: -0.46 (0.18), residues: 912
  sheet: -2.76 (0.71), residues: 36
  loop : -2.84 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 461 
 HIS   0.001   0.000   HIS A 373 
 PHE   0.023   0.001   PHE C 326 
 TYR   0.012   0.001   TYR C 208 
 ARG   0.003   0.000   ARG B 202 

*********************** 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
  177 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 141
  time to evaluate  : 0.965 
Fit side-chains
REVERT: A  109 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8691 (p)
REVERT: A  126 ARG cc_start: 0.6359 (mmt90) cc_final: 0.6137 (tmm160)
REVERT: A  208 TYR cc_start: 0.7994 (m-80) cc_final: 0.7180 (m-80)
REVERT: A  229 MET cc_start: 0.8204 (ptp) cc_final: 0.7908 (ptp)
REVERT: A  260 ASN cc_start: 0.7356 (t0) cc_final: 0.7136 (t0)
REVERT: A  344 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7799 (mp)
REVERT: A  394 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8088 (mp-120)
REVERT: A  417 ILE cc_start: 0.8200 (tp) cc_final: 0.7950 (tt)
REVERT: A  437 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8018 (tt)
REVERT: A  465 ARG cc_start: 0.7771 (mmt-90) cc_final: 0.7558 (mmt90)
REVERT: B  109 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8502 (p)
REVERT: B  126 ARG cc_start: 0.7342 (tpt170) cc_final: 0.7051 (tpt-90)
REVERT: B  186 ASP cc_start: 0.8177 (t70) cc_final: 0.7948 (t70)
REVERT: B  260 ASN cc_start: 0.7444 (t0) cc_final: 0.7096 (t0)
REVERT: B  326 PHE cc_start: 0.7546 (t80) cc_final: 0.7279 (t80)
REVERT: B  344 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7385 (mp)
REVERT: B  394 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7007 (mp-120)
REVERT: C   52 ASN cc_start: 0.8597 (p0) cc_final: 0.8269 (p0)
REVERT: C  109 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8552 (p)
REVERT: C  260 ASN cc_start: 0.7463 (t0) cc_final: 0.7191 (t0)
REVERT: C  325 TYR cc_start: 0.7969 (t80) cc_final: 0.7544 (t80)
REVERT: C  394 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7665 (mp-120)
REVERT: C  417 ILE cc_start: 0.8141 (tp) cc_final: 0.7911 (tt)
  outliers start: 36
  outliers final: 12
  residues processed: 168
  average time/residue: 0.2015
  time to fit residues: 48.6743
Evaluate side-chains
  156 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
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  282 MET
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  422 THR
Chi-restraints excluded: chain A residue  437 LEU
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 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  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 51 optimal weight:    4.9990
   chunk 89 optimal weight:    0.0770
   chunk 43 optimal weight:   20.0000
   chunk 18 optimal weight:    0.7980
   chunk 69 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9990
   chunk 108 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 119 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   overall best weight:    0.7340

-------------------------------------------------------------------------------
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**
B 212 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.161522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.125847 restraints weight = 10550.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.124393 restraints weight = 16997.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.125926 restraints weight = 15460.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2380

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= 0.170
  Angle     :  0.608   9.481  13344  Z= 0.301
  Chirality :  0.040   0.181   1668
  Planarity :  0.005   0.060   1656
  Dihedral  :  4.682  19.139   1365
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 16.27 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.25), residues: 1278
  helix: -0.20 (0.18), residues: 912
  sheet: -2.58 (0.72), residues: 36
  loop : -2.73 (0.34), residues: 330

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

*********************** 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
  172 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 135
  time to evaluate  : 1.050 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.6432 (mmt90) cc_final: 0.6088 (tmm160)
REVERT: A  140 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8066 (mt)
REVERT: A  208 TYR cc_start: 0.7986 (m-80) cc_final: 0.7149 (m-80)
REVERT: A  229 MET cc_start: 0.8155 (ptp) cc_final: 0.7836 (ptp)
REVERT: A  260 ASN cc_start: 0.7472 (t0) cc_final: 0.7171 (t0)
REVERT: A  344 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7605 (mp)
REVERT: A  394 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8060 (mp-120)
REVERT: A  417 ILE cc_start: 0.8122 (tp) cc_final: 0.7840 (tt)
REVERT: A  418 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7661 (tt)
REVERT: B  109 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8507 (p)
REVERT: B  126 ARG cc_start: 0.7286 (tpt170) cc_final: 0.7052 (tpt-90)
REVERT: B  182 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6913 (m-30)
REVERT: B  260 ASN cc_start: 0.7473 (t0) cc_final: 0.7093 (t0)
REVERT: B  326 PHE cc_start: 0.7504 (t80) cc_final: 0.7285 (t80)
REVERT: B  340 ILE cc_start: 0.7681 (mt) cc_final: 0.7402 (mt)
REVERT: B  344 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7406 (mp)
REVERT: B  394 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.6979 (mp-120)
REVERT: B  437 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7850 (tt)
REVERT: C   52 ASN cc_start: 0.8582 (p0) cc_final: 0.8324 (p0)
REVERT: C  260 ASN cc_start: 0.7503 (t0) cc_final: 0.7250 (t0)
REVERT: C  394 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7571 (mp-120)
  outliers start: 37
  outliers final: 15
  residues processed: 166
  average time/residue: 0.2061
  time to fit residues: 49.0110
Evaluate side-chains
  153 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  282 MET
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  422 THR
Chi-restraints excluded: chain B residue  109 VAL
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  344 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  437 LEU
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  143 SER
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 128 optimal weight:    0.1980
   chunk 19 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0570
   chunk 14 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0020
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.3706

-------------------------------------------------------------------------------
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**
C 212 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.165922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.127067 restraints weight = 10555.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.124507 restraints weight = 15501.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.126143 restraints weight = 15037.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9798  Z= 0.148
  Angle     :  0.600   8.974  13344  Z= 0.295
  Chirality :  0.039   0.167   1668
  Planarity :  0.004   0.058   1656
  Dihedral  :  4.400  17.779   1365
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 16.96 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.25), residues: 1278
  helix:  0.11 (0.19), residues: 906
  sheet: -2.27 (0.71), residues: 36
  loop : -2.65 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 461 
 HIS   0.001   0.000   HIS A 373 
 PHE   0.025   0.001   PHE C 326 
 TYR   0.009   0.001   TYR C 208 
 ARG   0.001   0.000   ARG C 202 

*********************** 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
  178 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 144
  time to evaluate  : 0.784 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.6517 (mmt90) cc_final: 0.5949 (tmm160)
REVERT: A  140 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7960 (mt)
REVERT: A  208 TYR cc_start: 0.7886 (m-80) cc_final: 0.7001 (m-80)
REVERT: A  284 LEU cc_start: 0.7569 (tp) cc_final: 0.7204 (tp)
REVERT: A  394 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8104 (mp-120)
REVERT: B  109 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8522 (p)
REVERT: B  126 ARG cc_start: 0.7364 (tpt170) cc_final: 0.7094 (tpt-90)
REVERT: B  186 ASP cc_start: 0.8095 (t70) cc_final: 0.7860 (t70)
REVERT: B  260 ASN cc_start: 0.7457 (t0) cc_final: 0.7157 (t0)
REVERT: B  326 PHE cc_start: 0.7464 (t80) cc_final: 0.7257 (t80)
REVERT: B  340 ILE cc_start: 0.7551 (mt) cc_final: 0.7188 (mt)
REVERT: B  344 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7145 (mp)
REVERT: B  394 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.6959 (mp-120)
REVERT: B  437 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7824 (tt)
REVERT: C  126 ARG cc_start: 0.7222 (tpt-90) cc_final: 0.5383 (tmm160)
REVERT: C  325 TYR cc_start: 0.7981 (t80) cc_final: 0.7632 (t80)
REVERT: C  394 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.7459 (mp-120)
  outliers start: 34
  outliers final: 19
  residues processed: 173
  average time/residue: 0.1863
  time to fit residues: 47.5389
Evaluate side-chains
  158 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  140 LEU
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  378 ILE
Chi-restraints excluded: chain A residue  392 LEU
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  359 LEU
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  394 GLN
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  182 ASP
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 25 optimal weight:    7.9990
   chunk 99 optimal weight:    0.5980
   chunk 120 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 79 optimal weight:    8.9990
   chunk 86 optimal weight:   20.0000
   chunk 118 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   overall best weight:    1.0782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.161023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.125499 restraints weight = 10577.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.124742 restraints weight = 17645.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.126296 restraints weight = 15235.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9798  Z= 0.207
  Angle     :  0.646   9.312  13344  Z= 0.315
  Chirality :  0.043   0.277   1668
  Planarity :  0.004   0.058   1656
  Dihedral  :  4.530  18.443   1365
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.73 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.25), residues: 1278
  helix:  0.11 (0.18), residues: 912
  sheet: -2.20 (0.68), residues: 36
  loop : -2.68 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 461 
 HIS   0.001   0.000   HIS B 373 
 PHE   0.025   0.001   PHE C 326 
 TYR   0.009   0.001   TYR C 208 
 ARG   0.002   0.000   ARG C 202 

*********************** 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
  159 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 126
  time to evaluate  : 1.041 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.6517 (mmt90) cc_final: 0.6074 (tmm160)
REVERT: A  140 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8089 (mt)
REVERT: A  208 TYR cc_start: 0.7948 (m-80) cc_final: 0.7075 (m-80)
REVERT: A  229 MET cc_start: 0.8199 (ptp) cc_final: 0.7879 (ptp)
REVERT: A  394 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8064 (mp-120)
REVERT: A  418 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7667 (tt)
REVERT: B  109 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8492 (p)
REVERT: B  126 ARG cc_start: 0.7350 (tpt170) cc_final: 0.7046 (tpt-90)
REVERT: B  186 ASP cc_start: 0.8151 (t70) cc_final: 0.7924 (t70)
REVERT: B  260 ASN cc_start: 0.7407 (t0) cc_final: 0.7075 (t0)
REVERT: B  344 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7487 (mp)
REVERT: B  394 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.6984 (mp-120)
REVERT: C   52 ASN cc_start: 0.8589 (p0) cc_final: 0.8155 (p0)
REVERT: C  126 ARG cc_start: 0.7269 (tpt-90) cc_final: 0.5507 (tmm160)
REVERT: C  394 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7572 (mp-120)
  outliers start: 33
  outliers final: 18
  residues processed: 155
  average time/residue: 0.1962
  time to fit residues: 44.5259
Evaluate side-chains
  147 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  282 MET
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  422 THR
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  103 ILE
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  359 LEU
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  394 GLN
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  182 ASP
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 102 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 50 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   chunk 75 optimal weight:    5.9990
   chunk 128 optimal weight:    7.9990
   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 = 0.3657 r_free = 0.3657 target = 0.157880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.124749 restraints weight = 10739.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.124008 restraints weight = 20073.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.125309 restraints weight = 17704.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9798  Z= 0.245
  Angle     :  0.677   9.186  13344  Z= 0.329
  Chirality :  0.044   0.249   1668
  Planarity :  0.005   0.061   1656
  Dihedral  :  4.699  17.898   1365
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 19.12 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.25), residues: 1278
  helix:  0.06 (0.18), residues: 912
  sheet: -2.29 (0.67), residues: 36
  loop : -2.67 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 461 
 HIS   0.001   0.000   HIS A 373 
 PHE   0.027   0.001   PHE C 326 
 TYR   0.009   0.001   TYR C 208 
 ARG   0.003   0.000   ARG C 202 

*********************** 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
  160 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 0.966 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.6524 (mmt90) cc_final: 0.6316 (tpt-90)
REVERT: A  208 TYR cc_start: 0.7969 (m-80) cc_final: 0.7139 (m-80)
REVERT: A  394 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8104 (mp-120)
REVERT: A  418 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7331 (tt)
REVERT: B   85 ARG cc_start: 0.5724 (ttt180) cc_final: 0.5501 (ttt180)
REVERT: B  126 ARG cc_start: 0.7284 (tpt170) cc_final: 0.6938 (tpt-90)
REVERT: B  260 ASN cc_start: 0.7509 (t0) cc_final: 0.7096 (t0)
REVERT: B  394 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.7033 (mp-120)
REVERT: C  325 TYR cc_start: 0.7984 (t80) cc_final: 0.7764 (t80)
REVERT: C  394 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7704 (mp-120)
  outliers start: 30
  outliers final: 19
  residues processed: 154
  average time/residue: 0.1981
  time to fit residues: 44.5525
Evaluate side-chains
  148 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
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  282 MET
Chi-restraints excluded: chain A residue  363 CYS
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  422 THR
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  340 ILE
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  182 ASP
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 80 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9990
   chunk 4 optimal weight:    0.2980
   chunk 69 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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 = 0.3671 r_free = 0.3671 target = 0.159067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.126529 restraints weight = 10634.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.124842 restraints weight = 19076.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.125872 restraints weight = 18076.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9798  Z= 0.227
  Angle     :  0.670   9.081  13344  Z= 0.327
  Chirality :  0.044   0.263   1668
  Planarity :  0.005   0.061   1656
  Dihedral  :  4.659  18.585   1365
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 20.49 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.25), residues: 1278
  helix:  0.08 (0.18), residues: 915
  sheet: -2.32 (0.66), residues: 36
  loop : -2.60 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 461 
 HIS   0.001   0.000   HIS C 373 
 PHE   0.027   0.001   PHE C 326 
 TYR   0.009   0.001   TYR C 208 
 ARG   0.003   0.000   ARG C 202 

*********************** 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
  149 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 1.053 
Fit side-chains
REVERT: A  208 TYR cc_start: 0.7890 (m-80) cc_final: 0.7088 (m-80)
REVERT: A  260 ASN cc_start: 0.7481 (t0) cc_final: 0.7147 (t0)
REVERT: A  394 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8117 (mp-120)
REVERT: A  418 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7334 (tt)
REVERT: B   85 ARG cc_start: 0.5735 (ttt180) cc_final: 0.5496 (ttt180)
REVERT: B  126 ARG cc_start: 0.7263 (tpt170) cc_final: 0.6895 (tpt-90)
REVERT: B  394 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7054 (mp-120)
REVERT: C  325 TYR cc_start: 0.7866 (t80) cc_final: 0.7658 (t80)
REVERT: C  394 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7690 (mp-120)
  outliers start: 24
  outliers final: 18
  residues processed: 144
  average time/residue: 0.1897
  time to fit residues: 40.0451
Evaluate side-chains
  147 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
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  282 MET
Chi-restraints excluded: chain A residue  363 CYS
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  422 THR
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  103 ILE
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  451 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  182 ASP
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 123 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 121 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 70 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 102 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 ** 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 = 0.3659 r_free = 0.3659 target = 0.158200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.120760 restraints weight = 10665.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.116639 restraints weight = 14971.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.117669 restraints weight = 20680.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9798  Z= 0.242
  Angle     :  0.674   9.484  13344  Z= 0.327
  Chirality :  0.044   0.265   1668
  Planarity :  0.005   0.060   1656
  Dihedral  :  4.691  17.920   1365
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 20.98 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.25), residues: 1278
  helix:  0.04 (0.18), residues: 921
  sheet: -2.34 (0.66), residues: 36
  loop : -2.50 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 461 
 HIS   0.001   0.000   HIS B 373 
 PHE   0.027   0.001   PHE C 326 
 TYR   0.009   0.001   TYR C 208 
 ARG   0.003   0.000   ARG C 202 

********************** 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
  152 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 0.981 
Fit side-chains
REVERT: A  208 TYR cc_start: 0.7994 (m-80) cc_final: 0.7065 (m-80)
REVERT: A  260 ASN cc_start: 0.7542 (t0) cc_final: 0.7097 (t0)
REVERT: A  394 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8072 (mp-120)
REVERT: A  418 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7255 (tt)
REVERT: B   85 ARG cc_start: 0.5741 (ttt180) cc_final: 0.5470 (ttt180)
REVERT: B  126 ARG cc_start: 0.7255 (tpt170) cc_final: 0.5161 (ttp-110)
REVERT: B  394 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7019 (mp-120)
REVERT: C  394 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7631 (mp-120)
  outliers start: 24
  outliers final: 17
  residues processed: 147
  average time/residue: 0.1970
  time to fit residues: 42.0581
Evaluate side-chains
  146 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
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  282 MET
Chi-restraints excluded: chain A residue  363 CYS
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  422 THR
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  103 ILE
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  451 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  182 ASP
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 122 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 93 optimal weight:    0.1980
   chunk 77 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 126 optimal weight:    1.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 ** 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 = 0.3695 r_free = 0.3695 target = 0.161678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.125008 restraints weight = 10567.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.122772 restraints weight = 18168.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.124191 restraints weight = 18262.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9798  Z= 0.183
  Angle     :  0.658  11.020  13344  Z= 0.317
  Chirality :  0.042   0.239   1668
  Planarity :  0.004   0.057   1656
  Dihedral  :  4.496  17.642   1365
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 21.37 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.25), residues: 1278
  helix:  0.23 (0.19), residues: 924
  sheet: -2.19 (0.66), residues: 36
  loop : -2.45 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 338 
 HIS   0.001   0.000   HIS A 373 
 PHE   0.027   0.001   PHE C 326 
 TYR   0.011   0.001   TYR C 208 
 ARG   0.002   0.000   ARG C 202 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2563.73 seconds
wall clock time: 46 minutes 54.18 seconds (2814.18 seconds total)