Starting phenix.real_space_refine
on Fri Mar 14 03:03:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6rvy_10018/03_2025/6rvy_10018.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6rvy_10018/03_2025/6rvy_10018.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6rvy_10018/03_2025/6rvy_10018.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6rvy_10018/03_2025/6rvy_10018.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6rvy_10018/03_2025/6rvy_10018.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6rvy_10018/03_2025/6rvy_10018.cif"
  }
  resolution = 4.13
  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=   0.005
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 33 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.00, per 1000 atoms: 0.62
  Number of scatterers: 9627
  At special positions: 0
  Unit cell: (119.416, 122.452, 85.008, 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: 2.50
  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
      78.6% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 51
      removed outlier: 3.831A  pdb=" N   CYS A  48 " --> pdb=" O   GLN A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 74
      removed outlier: 3.701A  pdb=" N   ALA A  64 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA A  67 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 90
    Processing helix  chain 'A' and resid 90 through 117
      removed outlier: 3.782A  pdb=" N   GLU A  94 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   MET A 102 " --> pdb=" O   ARG A  98 " (cutoff:3.500A)
      Proline residue:  A 106  - end of helix
    Processing helix  chain 'A' and resid 125 through 154
      removed outlier: 4.171A  pdb=" N   ALA A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 192
    Processing helix  chain 'A' and resid 197 through 200
    Processing helix  chain 'A' and resid 230 through 249
      removed outlier: 3.935A  pdb=" N   VAL A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   PHE A 237 " --> pdb=" O   GLY A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 293
      removed outlier: 3.596A  pdb=" N   SER A 261 " --> pdb=" O   ARG A 257 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU A 264 " --> pdb=" O   ASN A 260 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   VAL A 268 " --> pdb=" O   GLU A 264 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   LEU A 269 " --> pdb=" O   ALA A 265 " (cutoff:3.500A)
      Proline residue:  A 278  - end of helix
      removed outlier: 3.513A  pdb=" N   GLU A 293 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 327
      removed outlier: 4.453A  pdb=" N   ALA A 300 " --> pdb=" O   GLY A 296 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   LEU A 321 " --> pdb=" O   GLY A 317 " (cutoff:3.500A)
      Proline residue:  A 322  - end of helix
    Processing helix  chain 'A' and resid 332 through 340
      removed outlier: 3.659A  pdb=" N   PHE A 336 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 351
      removed outlier: 3.852A  pdb=" N   LEU A 344 " --> pdb=" O   ILE A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 367
      removed outlier: 3.602A  pdb=" N   GLU A 365 " --> pdb=" O   MET A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 386
      removed outlier: 4.175A  pdb=" N   LEU A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      Proline residue:  A 380  - end of helix
      removed outlier: 3.631A  pdb=" N   ALA A 383 " --> pdb=" O   LEU A 379 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   THR A 384 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 406
      removed outlier: 3.606A  pdb=" N   VAL A 399 " --> pdb=" O   CYS A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 424
      removed outlier: 3.731A  pdb=" N   THR A 420 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ALA A 421 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 445
      removed outlier: 3.636A  pdb=" N   LEU A 437 " --> pdb=" O   ALA A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 451
      No H-bonds generated for 'chain 'A' and resid 449 through 451'
    Processing helix  chain 'A' and resid 452 through 459
      removed outlier: 3.861A  pdb=" N   ILE A 456 " --> pdb=" O   HIS A 452 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 480
      removed outlier: 3.734A  pdb=" N   VAL A 463 " --> pdb=" O   VAL A 459 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   SER A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   VAL A 469 " --> pdb=" O   ARG A 465 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LEU A 470 " --> pdb=" O   SER A 466 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ASN A 471 " --> pdb=" O   ARG A 467 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL A 472 " --> pdb=" O   THR A 468 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ASP A 475 " --> pdb=" O   ASN A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 488
      removed outlier: 3.703A  pdb=" N   ASP A 487 " --> pdb=" O   GLN A 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 51
      removed outlier: 3.830A  pdb=" N   CYS B  48 " --> pdb=" O   GLN B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 74
      removed outlier: 3.701A  pdb=" N   ALA B  64 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA B  67 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 90
    Processing helix  chain 'B' and resid 90 through 117
      removed outlier: 3.783A  pdb=" N   GLU B  94 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   MET B 102 " --> pdb=" O   ARG B  98 " (cutoff:3.500A)
      Proline residue:  B 106  - end of helix
    Processing helix  chain 'B' and resid 125 through 154
      removed outlier: 4.171A  pdb=" N   ALA B 131 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 192
    Processing helix  chain 'B' and resid 197 through 200
    Processing helix  chain 'B' and resid 230 through 249
      removed outlier: 3.934A  pdb=" N   VAL B 236 " --> pdb=" O   LEU B 232 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   PHE B 237 " --> pdb=" O   GLY B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 293
      removed outlier: 3.596A  pdb=" N   SER B 261 " --> pdb=" O   ARG B 257 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU B 264 " --> pdb=" O   ASN B 260 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   VAL B 268 " --> pdb=" O   GLU B 264 " (cutoff:3.500A)
      removed outlier: 4.890A  pdb=" N   LEU B 269 " --> pdb=" O   ALA B 265 " (cutoff:3.500A)
      Proline residue:  B 278  - end of helix
      removed outlier: 3.513A  pdb=" N   GLU B 293 " --> pdb=" O   ILE B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 327
      removed outlier: 4.453A  pdb=" N   ALA B 300 " --> pdb=" O   GLY B 296 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   LEU B 321 " --> pdb=" O   GLY B 317 " (cutoff:3.500A)
      Proline residue:  B 322  - end of helix
    Processing helix  chain 'B' and resid 332 through 340
      removed outlier: 3.660A  pdb=" N   PHE B 336 " --> pdb=" O   ASN B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 351
      removed outlier: 3.852A  pdb=" N   LEU B 344 " --> pdb=" O   ILE B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 367
      removed outlier: 3.602A  pdb=" N   GLU B 365 " --> pdb=" O   MET B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 386
      removed outlier: 4.175A  pdb=" N   LEU B 379 " --> pdb=" O   SER B 375 " (cutoff:3.500A)
      Proline residue:  B 380  - end of helix
      removed outlier: 3.630A  pdb=" N   ALA B 383 " --> pdb=" O   LEU B 379 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   THR B 384 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 406
      removed outlier: 3.605A  pdb=" N   VAL B 399 " --> pdb=" O   CYS B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 424
      removed outlier: 3.731A  pdb=" N   THR B 420 " --> pdb=" O   THR B 416 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ALA B 421 " --> pdb=" O   ILE B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 445
      removed outlier: 3.636A  pdb=" N   LEU B 437 " --> pdb=" O   ALA B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 451
      No H-bonds generated for 'chain 'B' and resid 449 through 451'
    Processing helix  chain 'B' and resid 452 through 459
      removed outlier: 3.862A  pdb=" N   ILE B 456 " --> pdb=" O   HIS B 452 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL B 459 " --> pdb=" O   LEU B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 480
      removed outlier: 3.734A  pdb=" N   VAL B 463 " --> pdb=" O   VAL B 459 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   SER B 466 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   VAL B 469 " --> pdb=" O   ARG B 465 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LEU B 470 " --> pdb=" O   SER B 466 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ASN B 471 " --> pdb=" O   ARG B 467 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL B 472 " --> pdb=" O   THR B 468 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ASP B 475 " --> pdb=" O   ASN B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 488
      removed outlier: 3.704A  pdb=" N   ASP B 487 " --> pdb=" O   GLN B 483 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 51
      removed outlier: 3.830A  pdb=" N   CYS C  48 " --> pdb=" O   GLN C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 74
      removed outlier: 3.700A  pdb=" N   ALA C  64 " --> pdb=" O   VAL C  60 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA C  67 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 90
    Processing helix  chain 'C' and resid 90 through 117
      removed outlier: 3.782A  pdb=" N   GLU C  94 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   MET C 102 " --> pdb=" O   ARG C  98 " (cutoff:3.500A)
      Proline residue:  C 106  - end of helix
    Processing helix  chain 'C' and resid 125 through 154
      removed outlier: 4.171A  pdb=" N   ALA C 131 " --> pdb=" O   LEU C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 192
    Processing helix  chain 'C' and resid 197 through 200
    Processing helix  chain 'C' and resid 230 through 249
      removed outlier: 3.934A  pdb=" N   VAL C 236 " --> pdb=" O   LEU C 232 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   PHE C 237 " --> pdb=" O   GLY C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 293
      removed outlier: 3.597A  pdb=" N   SER C 261 " --> pdb=" O   ARG C 257 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU C 264 " --> pdb=" O   ASN C 260 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL C 268 " --> pdb=" O   GLU C 264 " (cutoff:3.500A)
      removed outlier: 4.890A  pdb=" N   LEU C 269 " --> pdb=" O   ALA C 265 " (cutoff:3.500A)
      Proline residue:  C 278  - end of helix
      removed outlier: 3.512A  pdb=" N   GLU C 293 " --> pdb=" O   ILE C 289 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 327
      removed outlier: 4.452A  pdb=" N   ALA C 300 " --> pdb=" O   GLY C 296 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   LEU C 321 " --> pdb=" O   GLY C 317 " (cutoff:3.500A)
      Proline residue:  C 322  - end of helix
    Processing helix  chain 'C' and resid 332 through 340
      removed outlier: 3.660A  pdb=" N   PHE C 336 " --> pdb=" O   ASN C 332 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 351
      removed outlier: 3.853A  pdb=" N   LEU C 344 " --> pdb=" O   ILE C 340 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 356 through 367
      removed outlier: 3.602A  pdb=" N   GLU C 365 " --> pdb=" O   MET C 361 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 373 through 386
      removed outlier: 4.175A  pdb=" N   LEU C 379 " --> pdb=" O   SER C 375 " (cutoff:3.500A)
      Proline residue:  C 380  - end of helix
      removed outlier: 3.631A  pdb=" N   ALA C 383 " --> pdb=" O   LEU C 379 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   THR C 384 " --> pdb=" O   PRO C 380 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 387 through 406
      removed outlier: 3.605A  pdb=" N   VAL C 399 " --> pdb=" O   CYS C 395 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 410 through 424
      removed outlier: 3.731A  pdb=" N   THR C 420 " --> pdb=" O   THR C 416 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ALA C 421 " --> pdb=" O   ILE C 417 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 433 through 445
      removed outlier: 3.636A  pdb=" N   LEU C 437 " --> pdb=" O   ALA C 433 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 449 through 451
      No H-bonds generated for 'chain 'C' and resid 449 through 451'
    Processing helix  chain 'C' and resid 452 through 459
      removed outlier: 3.862A  pdb=" N   ILE C 456 " --> pdb=" O   HIS C 452 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL C 459 " --> pdb=" O   LEU C 455 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 459 through 480
      removed outlier: 3.735A  pdb=" N   VAL C 463 " --> pdb=" O   VAL C 459 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   SER C 466 " --> pdb=" O   LEU C 462 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   VAL C 469 " --> pdb=" O   ARG C 465 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LEU C 470 " --> pdb=" O   SER C 466 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ASN C 471 " --> pdb=" O   ARG C 467 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL C 472 " --> pdb=" O   THR C 468 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ASP C 475 " --> pdb=" O   ASN C 471 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 483 through 488
      removed outlier: 3.704A  pdb=" N   ASP C 487 " --> pdb=" O   GLN C 483 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 210
    Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 210
    Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 210

    651 hydrogen bonds defined for protein.
    1944 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: 2.79

  Time building geometry restraints manager: 2.95 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: 2987
        1.34 -     1.46: 1399
        1.46 -     1.57: 5340
        1.57 -     1.69: 0
        1.69 -     1.80: 72
  Bond restraints: 9798
  Sorted by residual:
  bond pdb=" CG  LEU C 112 "
       pdb=" CD1 LEU C 112 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.09e+00
  bond pdb=" CG  LEU A 112 "
       pdb=" CD1 LEU A 112 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.07e+00
  bond pdb=" CG  LEU B 112 "
       pdb=" CD1 LEU B 112 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.00e+00
  bond pdb=" C   LEU C 105 "
       pdb=" N   PRO C 106 "
    ideal  model  delta    sigma   weight residual
    1.336  1.352 -0.017 1.23e-02 6.61e+03 1.88e+00
  bond pdb=" C   LEU B 105 "
       pdb=" N   PRO B 106 "
    ideal  model  delta    sigma   weight residual
    1.336  1.352 -0.017 1.23e-02 6.61e+03 1.84e+00
  ... (remaining 9793 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 12777
        2.16 -     4.31: 463
        4.31 -     6.47: 63
        6.47 -     8.62: 26
        8.62 -    10.78: 15
  Bond angle restraints: 13344
  Sorted by residual:
  angle pdb=" N   ALA C 277 "
        pdb=" CA  ALA C 277 "
        pdb=" C   ALA C 277 "
      ideal   model   delta    sigma   weight residual
     109.81  120.59  -10.78 2.21e+00 2.05e-01 2.38e+01
  angle pdb=" N   ALA B 277 "
        pdb=" CA  ALA B 277 "
        pdb=" C   ALA B 277 "
      ideal   model   delta    sigma   weight residual
     109.81  120.54  -10.73 2.21e+00 2.05e-01 2.36e+01
  angle pdb=" N   ALA A 277 "
        pdb=" CA  ALA A 277 "
        pdb=" C   ALA A 277 "
      ideal   model   delta    sigma   weight residual
     109.81  120.49  -10.68 2.21e+00 2.05e-01 2.34e+01
  angle pdb=" N   THR B 342 "
        pdb=" CA  THR B 342 "
        pdb=" C   THR B 342 "
      ideal   model   delta    sigma   weight residual
     109.81  118.00   -8.19 2.21e+00 2.05e-01 1.37e+01
  angle pdb=" N   THR A 342 "
        pdb=" CA  THR A 342 "
        pdb=" C   THR A 342 "
      ideal   model   delta    sigma   weight residual
     109.81  118.00   -8.19 2.21e+00 2.05e-01 1.37e+01
  ... (remaining 13339 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.03: 4963
       15.03 -    30.07: 599
       30.07 -    45.10: 159
       45.10 -    60.14: 39
       60.14 -    75.17: 6
  Dihedral angle restraints: 5766
    sinusoidal: 2127
      harmonic: 3639
  Sorted by residual:
  dihedral pdb=" CA  VAL A  90 "
           pdb=" C   VAL A  90 "
           pdb=" N   PHE A  91 "
           pdb=" CA  PHE A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.67  -26.33     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  VAL B  90 "
           pdb=" C   VAL B  90 "
           pdb=" N   PHE B  91 "
           pdb=" CA  PHE B  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.68  -26.32     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  VAL C  90 "
           pdb=" C   VAL C  90 "
           pdb=" N   PHE C  91 "
           pdb=" CA  PHE C  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.70  -26.30     0      5.00e+00 4.00e-02 2.77e+01
  ... (remaining 5763 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1220
       0.051 -    0.101: 327
       0.101 -    0.151: 79
       0.151 -    0.202: 33
       0.202 -    0.252: 9
  Chirality restraints: 1668
  Sorted by residual:
  chirality pdb=" CA  THR C 342 "
            pdb=" N   THR C 342 "
            pdb=" C   THR C 342 "
            pdb=" CB  THR C 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.27    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  THR B 342 "
            pdb=" N   THR B 342 "
            pdb=" C   THR B 342 "
            pdb=" CB  THR B 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CA  THR A 342 "
            pdb=" N   THR A 342 "
            pdb=" C   THR A 342 "
            pdb=" CB  THR A 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 1665 not shown)

  Planarity restraints: 1656
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 321 "    0.045 5.00e-02 4.00e+02   6.64e-02 7.06e+00
        pdb=" N   PRO C 322 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO C 322 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C 322 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 321 "    0.044 5.00e-02 4.00e+02   6.62e-02 7.02e+00
        pdb=" N   PRO A 322 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A 322 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 322 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 321 "    0.044 5.00e-02 4.00e+02   6.59e-02 6.95e+00
        pdb=" N   PRO B 322 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO B 322 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 322 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1653 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2841
        2.81 -     3.33: 9719
        3.33 -     3.86: 16133
        3.86 -     4.38: 18328
        4.38 -     4.90: 30139
  Nonbonded interactions: 77160
  Sorted by model distance:
  nonbonded pdb=" O   SER C 177 "
            pdb=" OG  SER C 177 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   SER A 177 "
            pdb=" OG  SER A 177 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   SER B 177 "
            pdb=" OG  SER B 177 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   GLY C  69 "
            pdb=" OG  SER C  73 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" O   GLY A  69 "
            pdb=" OG  SER A  73 "
     model   vdw
     2.328 3.040
  ... (remaining 77155 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: 0.07
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:             0.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.310
  Find NCS groups from input model:        0.190
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
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   0.057   9798  Z= 0.387
  Angle     :  1.030  10.778  13344  Z= 0.538
  Chirality :  0.056   0.252   1668
  Planarity :  0.008   0.066   1656
  Dihedral  : 14.692  75.172   3432
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 13.04 %
    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: -5.00 (0.17), residues: 1278
  helix: -3.03 (0.11), residues: 963
  sheet: -3.60 (0.57), residues: 42
  loop : -3.25 (0.34), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 461 
 HIS   0.003   0.001   HIS C 316 
 PHE   0.013   0.002   PHE A 258 
 TYR   0.006   0.002   TYR A 305 
 ARG   0.005   0.001   ARG C 465 

*********************** 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
  205 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 200
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 PHE cc_start: 0.8581 (p90) cc_final: 0.8375 (p90)
REVERT: A  279 VAL cc_start: 0.9209 (m) cc_final: 0.8901 (p)
REVERT: A  297 LEU cc_start: 0.8964 (tp) cc_final: 0.8706 (mp)
REVERT: A  325 TYR cc_start: 0.8860 (t80) cc_final: 0.8634 (t80)
REVERT: A  394 GLN cc_start: 0.8426 (mt0) cc_final: 0.8080 (mp10)
REVERT: A  439 LEU cc_start: 0.9410 (tp) cc_final: 0.9070 (tp)
REVERT: A  461 TRP cc_start: 0.8008 (p-90) cc_final: 0.7579 (p-90)
REVERT: A  473 GLU cc_start: 0.8720 (tt0) cc_final: 0.8270 (tt0)
REVERT: B   89 PHE cc_start: 0.7543 (t80) cc_final: 0.7338 (t80)
REVERT: B  178 LYS cc_start: 0.6864 (tptt) cc_final: 0.6525 (mppt)
REVERT: B  201 PHE cc_start: 0.8381 (p90) cc_final: 0.7916 (p90)
REVERT: B  279 VAL cc_start: 0.9119 (m) cc_final: 0.8919 (p)
REVERT: B  297 LEU cc_start: 0.8982 (tp) cc_final: 0.8738 (tp)
REVERT: B  305 TYR cc_start: 0.8954 (t80) cc_final: 0.8681 (t80)
REVERT: B  313 HIS cc_start: 0.8100 (m90) cc_final: 0.7794 (m90)
REVERT: B  325 TYR cc_start: 0.8723 (t80) cc_final: 0.8141 (t80)
REVERT: B  379 LEU cc_start: 0.9227 (tp) cc_final: 0.9017 (tp)
REVERT: B  439 LEU cc_start: 0.9379 (tp) cc_final: 0.9117 (tp)
REVERT: B  461 TRP cc_start: 0.8141 (p-90) cc_final: 0.7075 (p-90)
REVERT: B  473 GLU cc_start: 0.8796 (tt0) cc_final: 0.8408 (tt0)
REVERT: C   89 PHE cc_start: 0.7841 (t80) cc_final: 0.7449 (t80)
REVERT: C  100 LEU cc_start: 0.9130 (mt) cc_final: 0.8926 (mt)
REVERT: C  178 LYS cc_start: 0.6830 (tptt) cc_final: 0.6375 (mppt)
REVERT: C  201 PHE cc_start: 0.8345 (p90) cc_final: 0.7869 (p90)
REVERT: C  297 LEU cc_start: 0.8847 (tp) cc_final: 0.8584 (mp)
REVERT: C  313 HIS cc_start: 0.8158 (m90) cc_final: 0.7843 (m90)
REVERT: C  325 TYR cc_start: 0.8626 (t80) cc_final: 0.8330 (t80)
REVERT: C  395 CYS cc_start: 0.8202 (m) cc_final: 0.7891 (m)
REVERT: C  461 TRP cc_start: 0.8180 (p-90) cc_final: 0.6951 (p-90)
REVERT: C  473 GLU cc_start: 0.8812 (tt0) cc_final: 0.8400 (tt0)
  outliers start: 5
  outliers final: 0
  residues processed: 203
  average time/residue: 0.2071
  time to fit residues: 59.7029
Evaluate side-chains
  141 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 97 optimal weight:   20.0000
   chunk 54 optimal weight:   20.0000
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 101 optimal weight:    7.9990
   chunk 39 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   chunk 75 optimal weight:    0.0770
   chunk 117 optimal weight:    6.9990
   overall best weight:    2.0142

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

Flipped N/Q/H residues before XYZ refinement:
A 212 ASN
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 212 ASN
** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 212 ASN
** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 452 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.073389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.058422 restraints weight = 41037.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.059451 restraints weight = 26101.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.060067 restraints weight = 19539.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9798  Z= 0.195
  Angle     :  0.682   8.130  13344  Z= 0.342
  Chirality :  0.039   0.171   1668
  Planarity :  0.005   0.043   1656
  Dihedral  :  4.971  18.349   1365
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.65 (0.21), residues: 1278
  helix: -1.19 (0.15), residues: 990
  sheet: -2.97 (0.70), residues: 42
  loop : -3.16 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 461 
 HIS   0.004   0.001   HIS B 316 
 PHE   0.011   0.001   PHE C 237 
 TYR   0.013   0.002   TYR C 305 
 ARG   0.007   0.001   ARG B  47 

*********************** 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
  205 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9380 (m) cc_final: 0.9026 (p)
REVERT: A  282 MET cc_start: 0.8888 (tmm) cc_final: 0.8387 (tmm)
REVERT: A  297 LEU cc_start: 0.8967 (tp) cc_final: 0.8658 (mp)
REVERT: A  325 TYR cc_start: 0.8746 (t80) cc_final: 0.8414 (t80)
REVERT: A  394 GLN cc_start: 0.8722 (mt0) cc_final: 0.8283 (mp10)
REVERT: A  410 ASP cc_start: 0.8041 (t0) cc_final: 0.7776 (m-30)
REVERT: A  439 LEU cc_start: 0.9571 (tp) cc_final: 0.9210 (tt)
REVERT: A  461 TRP cc_start: 0.8442 (p-90) cc_final: 0.7708 (p-90)
REVERT: B   89 PHE cc_start: 0.7626 (t80) cc_final: 0.7412 (t80)
REVERT: B   91 PHE cc_start: 0.8419 (t80) cc_final: 0.7972 (t80)
REVERT: B  279 VAL cc_start: 0.9347 (m) cc_final: 0.9116 (p)
REVERT: B  282 MET cc_start: 0.8885 (tmm) cc_final: 0.8482 (tmm)
REVERT: B  297 LEU cc_start: 0.8872 (tp) cc_final: 0.8585 (mp)
REVERT: B  325 TYR cc_start: 0.8671 (t80) cc_final: 0.8096 (t80)
REVERT: B  439 LEU cc_start: 0.9566 (tp) cc_final: 0.9321 (tp)
REVERT: B  461 TRP cc_start: 0.8492 (p-90) cc_final: 0.7490 (p-90)
REVERT: B  473 GLU cc_start: 0.9032 (tt0) cc_final: 0.8572 (tt0)
REVERT: C   89 PHE cc_start: 0.7950 (t80) cc_final: 0.7436 (t80)
REVERT: C  178 LYS cc_start: 0.6721 (tptt) cc_final: 0.6360 (mppt)
REVERT: C  274 MET cc_start: 0.7740 (mtt) cc_final: 0.7506 (mtt)
REVERT: C  282 MET cc_start: 0.8880 (tmm) cc_final: 0.8352 (tmm)
REVERT: C  297 LEU cc_start: 0.8767 (tp) cc_final: 0.8473 (mp)
REVERT: C  313 HIS cc_start: 0.8375 (m90) cc_final: 0.8126 (m90)
REVERT: C  325 TYR cc_start: 0.8686 (t80) cc_final: 0.8405 (t80)
REVERT: C  395 CYS cc_start: 0.8327 (m) cc_final: 0.8001 (m)
REVERT: C  410 ASP cc_start: 0.7990 (t0) cc_final: 0.7750 (m-30)
REVERT: C  439 LEU cc_start: 0.9570 (tp) cc_final: 0.9247 (tp)
REVERT: C  473 GLU cc_start: 0.8977 (tt0) cc_final: 0.8572 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.1821
  time to fit residues: 54.4201
Evaluate side-chains
  143 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 102 optimal weight:   10.0000
   chunk 117 optimal weight:    8.9990
   chunk 109 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 76 optimal weight:    4.9990
   chunk 116 optimal weight:    3.9990
   chunk 115 optimal weight:    5.9990
   chunk 111 optimal weight:   20.0000
   chunk 113 optimal weight:   20.0000
   chunk 93 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 452 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.071903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.056764 restraints weight = 42286.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.057786 restraints weight = 27031.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.058447 restraints weight = 20216.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9798  Z= 0.255
  Angle     :  0.705   8.472  13344  Z= 0.348
  Chirality :  0.040   0.170   1668
  Planarity :  0.005   0.037   1656
  Dihedral  :  4.697  16.317   1365
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  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: -1.65 (0.23), residues: 1278
  helix: -0.51 (0.16), residues: 996
  sheet: -2.63 (0.75), residues: 42
  loop : -2.73 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 461 
 HIS   0.006   0.001   HIS B 316 
 PHE   0.013   0.001   PHE C  91 
 TYR   0.018   0.002   TYR C 305 
 ARG   0.003   0.000   ARG B 376 

*********************** 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
  194 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9409 (m) cc_final: 0.9061 (p)
REVERT: A  282 MET cc_start: 0.8858 (tmm) cc_final: 0.8456 (tmm)
REVERT: A  297 LEU cc_start: 0.8910 (tp) cc_final: 0.8528 (mp)
REVERT: A  325 TYR cc_start: 0.8566 (t80) cc_final: 0.8184 (t80)
REVERT: A  394 GLN cc_start: 0.8626 (mt0) cc_final: 0.8142 (mp10)
REVERT: A  410 ASP cc_start: 0.8068 (t0) cc_final: 0.7795 (m-30)
REVERT: A  461 TRP cc_start: 0.8494 (p-90) cc_final: 0.7670 (p-90)
REVERT: B   91 PHE cc_start: 0.8439 (t80) cc_final: 0.7983 (t80)
REVERT: B  201 PHE cc_start: 0.8440 (p90) cc_final: 0.8122 (p90)
REVERT: B  279 VAL cc_start: 0.9322 (m) cc_final: 0.9104 (p)
REVERT: B  282 MET cc_start: 0.8734 (tmm) cc_final: 0.8459 (tmm)
REVERT: B  297 LEU cc_start: 0.8895 (tp) cc_final: 0.8609 (tp)
REVERT: B  313 HIS cc_start: 0.8487 (m90) cc_final: 0.8235 (m90)
REVERT: B  325 TYR cc_start: 0.8717 (t80) cc_final: 0.8205 (t80)
REVERT: B  461 TRP cc_start: 0.8496 (p-90) cc_final: 0.7472 (p-90)
REVERT: B  473 GLU cc_start: 0.9069 (tt0) cc_final: 0.8552 (tt0)
REVERT: C   89 PHE cc_start: 0.8017 (t80) cc_final: 0.7574 (t80)
REVERT: C  178 LYS cc_start: 0.6816 (tptt) cc_final: 0.6415 (mppt)
REVERT: C  201 PHE cc_start: 0.8344 (p90) cc_final: 0.7974 (p90)
REVERT: C  208 TYR cc_start: 0.7527 (m-80) cc_final: 0.7287 (m-80)
REVERT: C  274 MET cc_start: 0.7703 (mtt) cc_final: 0.7498 (mtt)
REVERT: C  282 MET cc_start: 0.8767 (tmm) cc_final: 0.8336 (tmm)
REVERT: C  313 HIS cc_start: 0.8452 (m90) cc_final: 0.8201 (m90)
REVERT: C  325 TYR cc_start: 0.8673 (t80) cc_final: 0.8333 (t80)
REVERT: C  395 CYS cc_start: 0.8249 (m) cc_final: 0.7979 (m)
REVERT: C  439 LEU cc_start: 0.9480 (tp) cc_final: 0.9187 (tt)
REVERT: C  473 GLU cc_start: 0.8953 (tt0) cc_final: 0.8474 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.1746
  time to fit residues: 50.8573
Evaluate side-chains
  144 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 59 optimal weight:    8.9990
   chunk 0 optimal weight:   30.0000
   chunk 99 optimal weight:    1.9990
   chunk 70 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9980
   chunk 83 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 21 optimal weight:    0.7980
   chunk 26 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0170
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.9020

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.074064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.059126 restraints weight = 41082.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.060131 restraints weight = 25969.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.060866 restraints weight = 19553.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9798  Z= 0.163
  Angle     :  0.653   7.453  13344  Z= 0.317
  Chirality :  0.039   0.172   1668
  Planarity :  0.004   0.034   1656
  Dihedral  :  4.406  15.700   1365
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  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: -1.19 (0.24), residues: 1278
  helix: -0.20 (0.17), residues: 996
  sheet: -2.10 (0.84), residues: 42
  loop : -2.55 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP C 461 
 HIS   0.005   0.001   HIS C 452 
 PHE   0.012   0.001   PHE C 258 
 TYR   0.018   0.002   TYR C 305 
 ARG   0.003   0.000   ARG B  98 

*********************** 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
  202 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9440 (m) cc_final: 0.9101 (p)
REVERT: A  282 MET cc_start: 0.8783 (tmm) cc_final: 0.8363 (tmm)
REVERT: A  313 HIS cc_start: 0.8053 (m90) cc_final: 0.7630 (m90)
REVERT: A  316 HIS cc_start: 0.8664 (t-90) cc_final: 0.8422 (t-90)
REVERT: A  325 TYR cc_start: 0.8458 (t80) cc_final: 0.8117 (t80)
REVERT: A  379 LEU cc_start: 0.8945 (tp) cc_final: 0.8220 (tp)
REVERT: A  394 GLN cc_start: 0.8435 (mt0) cc_final: 0.8141 (mp10)
REVERT: A  461 TRP cc_start: 0.8491 (p-90) cc_final: 0.7680 (p-90)
REVERT: B   91 PHE cc_start: 0.8395 (t80) cc_final: 0.7878 (t80)
REVERT: B  201 PHE cc_start: 0.8491 (p90) cc_final: 0.7950 (p90)
REVERT: B  279 VAL cc_start: 0.9363 (m) cc_final: 0.9112 (p)
REVERT: B  282 MET cc_start: 0.8704 (tmm) cc_final: 0.8405 (tmm)
REVERT: B  297 LEU cc_start: 0.8943 (tp) cc_final: 0.8633 (tp)
REVERT: B  316 HIS cc_start: 0.8690 (t-90) cc_final: 0.8442 (t70)
REVERT: B  325 TYR cc_start: 0.8588 (t80) cc_final: 0.8129 (t80)
REVERT: B  395 CYS cc_start: 0.8461 (m) cc_final: 0.8159 (m)
REVERT: B  473 GLU cc_start: 0.9022 (tt0) cc_final: 0.8526 (tt0)
REVERT: C   89 PHE cc_start: 0.7986 (t80) cc_final: 0.7535 (t80)
REVERT: C  178 LYS cc_start: 0.6774 (tptt) cc_final: 0.6359 (mppt)
REVERT: C  282 MET cc_start: 0.8774 (tmm) cc_final: 0.8364 (tmm)
REVERT: C  325 TYR cc_start: 0.8543 (t80) cc_final: 0.8219 (t80)
REVERT: C  395 CYS cc_start: 0.8302 (m) cc_final: 0.8069 (m)
REVERT: C  439 LEU cc_start: 0.9479 (tp) cc_final: 0.9206 (tt)
REVERT: C  473 GLU cc_start: 0.9003 (tt0) cc_final: 0.8538 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.1966
  time to fit residues: 58.2131
Evaluate side-chains
  147 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 51 optimal weight:   30.0000
   chunk 89 optimal weight:    0.8980
   chunk 43 optimal weight:   30.0000
   chunk 18 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 52 optimal weight:   10.0000
   chunk 108 optimal weight:    0.9990
   chunk 23 optimal weight:    8.9990
   chunk 119 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 407 GLN
C  44 GLN
C 313 HIS
C 407 GLN
C 452 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.073191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.057934 restraints weight = 41294.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.058835 restraints weight = 26971.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.059496 restraints weight = 20731.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9798  Z= 0.192
  Angle     :  0.659   9.028  13344  Z= 0.321
  Chirality :  0.039   0.171   1668
  Planarity :  0.004   0.033   1656
  Dihedral  :  4.306  17.394   1365
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.24), residues: 1278
  helix:  0.10 (0.17), residues: 978
  sheet:  None (None), residues: 0
  loop : -2.64 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 461 
 HIS   0.004   0.001   HIS C 316 
 PHE   0.020   0.001   PHE B  89 
 TYR   0.021   0.002   TYR A 305 
 ARG   0.002   0.000   ARG A 376 

*********************** 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
  188 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 1.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9432 (m) cc_final: 0.9052 (p)
REVERT: A  282 MET cc_start: 0.8761 (tmm) cc_final: 0.8370 (tmm)
REVERT: A  309 CYS cc_start: 0.8205 (t) cc_final: 0.7588 (t)
REVERT: A  313 HIS cc_start: 0.8189 (m90) cc_final: 0.7780 (m90)
REVERT: A  325 TYR cc_start: 0.8476 (t80) cc_final: 0.8122 (t80)
REVERT: A  394 GLN cc_start: 0.8701 (mt0) cc_final: 0.8276 (mp10)
REVERT: A  439 LEU cc_start: 0.9541 (tp) cc_final: 0.9248 (tp)
REVERT: A  461 TRP cc_start: 0.8511 (p-90) cc_final: 0.7713 (p-90)
REVERT: A  475 ASP cc_start: 0.8402 (p0) cc_final: 0.8146 (p0)
REVERT: B   91 PHE cc_start: 0.8435 (t80) cc_final: 0.7918 (t80)
REVERT: B  201 PHE cc_start: 0.8534 (p90) cc_final: 0.7972 (p90)
REVERT: B  279 VAL cc_start: 0.9384 (m) cc_final: 0.9158 (p)
REVERT: B  297 LEU cc_start: 0.8952 (tp) cc_final: 0.8641 (tp)
REVERT: B  313 HIS cc_start: 0.8288 (m90) cc_final: 0.8062 (m90)
REVERT: B  325 TYR cc_start: 0.8583 (t80) cc_final: 0.8124 (t80)
REVERT: B  379 LEU cc_start: 0.8979 (tp) cc_final: 0.8466 (tp)
REVERT: B  439 LEU cc_start: 0.9564 (tp) cc_final: 0.9330 (tt)
REVERT: B  473 GLU cc_start: 0.9037 (tt0) cc_final: 0.8475 (tt0)
REVERT: C   89 PHE cc_start: 0.8046 (t80) cc_final: 0.7606 (t80)
REVERT: C  178 LYS cc_start: 0.6790 (tptt) cc_final: 0.6417 (mppt)
REVERT: C  190 ASN cc_start: 0.8844 (m-40) cc_final: 0.7926 (m110)
REVERT: C  316 HIS cc_start: 0.8775 (t-90) cc_final: 0.8462 (t-90)
REVERT: C  325 TYR cc_start: 0.8552 (t80) cc_final: 0.8219 (t80)
REVERT: C  387 MET cc_start: 0.8950 (mmm) cc_final: 0.8684 (mmt)
REVERT: C  473 GLU cc_start: 0.9022 (tt0) cc_final: 0.8523 (tt0)
REVERT: C  475 ASP cc_start: 0.8499 (p0) cc_final: 0.8279 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.2119
  time to fit residues: 58.5221
Evaluate side-chains
  148 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 66 optimal weight:    9.9990
   chunk 9 optimal weight:    9.9990
   chunk 128 optimal weight:    9.9990
   chunk 19 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9980
   chunk 30 optimal weight:   20.0000
   chunk 2 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    3.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.072494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.057339 restraints weight = 41635.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.058346 restraints weight = 26722.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.058892 restraints weight = 20171.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.3298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9798  Z= 0.235
  Angle     :  0.686   7.389  13344  Z= 0.332
  Chirality :  0.040   0.172   1668
  Planarity :  0.004   0.032   1656
  Dihedral  :  4.325  16.127   1365
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  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: -0.72 (0.24), residues: 1278
  helix:  0.15 (0.17), residues: 978
  sheet: -1.89 (0.86), residues: 42
  loop : -2.33 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 461 
 HIS   0.004   0.001   HIS B 316 
 PHE   0.011   0.001   PHE C  91 
 TYR   0.021   0.002   TYR C 305 
 ARG   0.006   0.000   ARG B 376 

*********************** 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
  182 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9386 (m) cc_final: 0.9062 (p)
REVERT: A  282 MET cc_start: 0.8775 (tmm) cc_final: 0.8439 (tmm)
REVERT: A  309 CYS cc_start: 0.8092 (t) cc_final: 0.7422 (t)
REVERT: A  313 HIS cc_start: 0.8250 (m90) cc_final: 0.7801 (m90)
REVERT: A  316 HIS cc_start: 0.8669 (t-90) cc_final: 0.8392 (t-90)
REVERT: A  325 TYR cc_start: 0.8468 (t80) cc_final: 0.8154 (t80)
REVERT: A  394 GLN cc_start: 0.8653 (mt0) cc_final: 0.8194 (mp10)
REVERT: A  439 LEU cc_start: 0.9527 (tp) cc_final: 0.9250 (tp)
REVERT: A  461 TRP cc_start: 0.8518 (p-90) cc_final: 0.7689 (p-90)
REVERT: A  475 ASP cc_start: 0.8403 (p0) cc_final: 0.8135 (p0)
REVERT: B   91 PHE cc_start: 0.8502 (t80) cc_final: 0.8075 (t80)
REVERT: B  201 PHE cc_start: 0.8498 (p90) cc_final: 0.8073 (p90)
REVERT: B  279 VAL cc_start: 0.9373 (m) cc_final: 0.9150 (p)
REVERT: B  282 MET cc_start: 0.8883 (tmm) cc_final: 0.8506 (tmm)
REVERT: B  313 HIS cc_start: 0.8355 (m90) cc_final: 0.7786 (m90)
REVERT: B  325 TYR cc_start: 0.8595 (t80) cc_final: 0.8115 (t80)
REVERT: B  473 GLU cc_start: 0.9027 (tt0) cc_final: 0.8477 (tt0)
REVERT: C   89 PHE cc_start: 0.8035 (t80) cc_final: 0.7575 (t80)
REVERT: C  178 LYS cc_start: 0.6742 (tptt) cc_final: 0.6395 (mmtm)
REVERT: C  190 ASN cc_start: 0.8724 (m-40) cc_final: 0.7814 (m110)
REVERT: C  201 PHE cc_start: 0.8438 (p90) cc_final: 0.7987 (p90)
REVERT: C  282 MET cc_start: 0.8821 (tmm) cc_final: 0.8290 (tmm)
REVERT: C  325 TYR cc_start: 0.8566 (t80) cc_final: 0.8269 (t80)
REVERT: C  395 CYS cc_start: 0.8396 (m) cc_final: 0.8142 (m)
REVERT: C  473 GLU cc_start: 0.9047 (tt0) cc_final: 0.8500 (tt0)
REVERT: C  475 ASP cc_start: 0.8545 (p0) cc_final: 0.8325 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1794
  time to fit residues: 49.2749
Evaluate side-chains
  141 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 120 optimal weight:    6.9990
   chunk 23 optimal weight:   10.0000
   chunk 79 optimal weight:    3.9990
   chunk 86 optimal weight:   20.0000
   chunk 118 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 37 optimal weight:    7.9990
   chunk 78 optimal weight:    6.9990
   overall best weight:    2.7786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.073502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.058370 restraints weight = 41459.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.059137 restraints weight = 28679.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.059365 restraints weight = 20828.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9798  Z= 0.216
  Angle     :  0.692   7.668  13344  Z= 0.332
  Chirality :  0.040   0.168   1668
  Planarity :  0.004   0.032   1656
  Dihedral  :  4.304  16.160   1365
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.24), residues: 1278
  helix:  0.23 (0.17), residues: 981
  sheet: -1.95 (0.84), residues: 42
  loop : -2.52 (0.38), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C 461 
 HIS   0.004   0.001   HIS B 316 
 PHE   0.011   0.001   PHE C  91 
 TYR   0.024   0.002   TYR A 276 
 ARG   0.003   0.000   ARG B 376 

*********************** 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
  185 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9439 (m) cc_final: 0.9082 (p)
REVERT: A  282 MET cc_start: 0.8794 (tmm) cc_final: 0.8465 (tmm)
REVERT: A  309 CYS cc_start: 0.8105 (t) cc_final: 0.7399 (t)
REVERT: A  313 HIS cc_start: 0.8239 (m90) cc_final: 0.7757 (m90)
REVERT: A  325 TYR cc_start: 0.8495 (t80) cc_final: 0.8195 (t80)
REVERT: A  394 GLN cc_start: 0.8603 (mt0) cc_final: 0.8161 (mp10)
REVERT: A  439 LEU cc_start: 0.9509 (tp) cc_final: 0.9219 (tp)
REVERT: A  461 TRP cc_start: 0.8581 (p-90) cc_final: 0.7713 (p-90)
REVERT: A  475 ASP cc_start: 0.8462 (p0) cc_final: 0.8206 (p0)
REVERT: B  201 PHE cc_start: 0.8538 (p90) cc_final: 0.8113 (p90)
REVERT: B  279 VAL cc_start: 0.9370 (m) cc_final: 0.9160 (p)
REVERT: B  282 MET cc_start: 0.8885 (tmm) cc_final: 0.8450 (tmm)
REVERT: B  309 CYS cc_start: 0.8455 (t) cc_final: 0.7802 (t)
REVERT: B  313 HIS cc_start: 0.8359 (m90) cc_final: 0.7782 (m90)
REVERT: B  325 TYR cc_start: 0.8685 (t80) cc_final: 0.8168 (t80)
REVERT: C   89 PHE cc_start: 0.7990 (t80) cc_final: 0.7582 (t80)
REVERT: C   91 PHE cc_start: 0.8568 (t80) cc_final: 0.8125 (t80)
REVERT: C  178 LYS cc_start: 0.6629 (tptt) cc_final: 0.6343 (mmtm)
REVERT: C  190 ASN cc_start: 0.8801 (m-40) cc_final: 0.8011 (m110)
REVERT: C  201 PHE cc_start: 0.8463 (p90) cc_final: 0.8000 (p90)
REVERT: C  316 HIS cc_start: 0.8751 (t-90) cc_final: 0.8533 (t-90)
REVERT: C  325 TYR cc_start: 0.8655 (t80) cc_final: 0.8280 (t80)
REVERT: C  395 CYS cc_start: 0.8333 (m) cc_final: 0.8104 (m)
REVERT: C  473 GLU cc_start: 0.9088 (tt0) cc_final: 0.8480 (tt0)
REVERT: C  475 ASP cc_start: 0.8609 (p0) cc_final: 0.8358 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1753
  time to fit residues: 48.4572
Evaluate side-chains
  150 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 50 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 12 optimal weight:    9.9990
   chunk 103 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0980
   chunk 59 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 75 optimal weight:    8.9990
   chunk 128 optimal weight:    0.7980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.075553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.060371 restraints weight = 41604.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.061379 restraints weight = 26443.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.062053 restraints weight = 19936.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.3752

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= 0.162
  Angle     :  0.673   8.942  13344  Z= 0.317
  Chirality :  0.039   0.168   1668
  Planarity :  0.004   0.030   1656
  Dihedral  :  4.122  16.447   1365
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.24), residues: 1278
  helix:  0.44 (0.17), residues: 978
  sheet: -1.50 (0.91), residues: 42
  loop : -2.21 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 461 
 HIS   0.004   0.001   HIS B 316 
 PHE   0.012   0.001   PHE C 258 
 TYR   0.018   0.002   TYR C 305 
 ARG   0.002   0.000   ARG B  98 

*********************** 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
  201 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9391 (m) cc_final: 0.9030 (p)
REVERT: A  282 MET cc_start: 0.8752 (tmm) cc_final: 0.8406 (tmm)
REVERT: A  288 LYS cc_start: 0.8478 (tppt) cc_final: 0.7811 (mtpp)
REVERT: A  309 CYS cc_start: 0.8082 (t) cc_final: 0.7240 (t)
REVERT: A  313 HIS cc_start: 0.8089 (m90) cc_final: 0.7741 (m90)
REVERT: A  325 TYR cc_start: 0.8383 (t80) cc_final: 0.8094 (t80)
REVERT: A  379 LEU cc_start: 0.8895 (tp) cc_final: 0.8524 (tp)
REVERT: A  394 GLN cc_start: 0.8556 (mt0) cc_final: 0.8098 (mp10)
REVERT: A  461 TRP cc_start: 0.8569 (p-90) cc_final: 0.7658 (p-90)
REVERT: A  475 ASP cc_start: 0.8401 (p0) cc_final: 0.8121 (p0)
REVERT: B  279 VAL cc_start: 0.9408 (m) cc_final: 0.9169 (p)
REVERT: B  282 MET cc_start: 0.8909 (tmm) cc_final: 0.8488 (tmm)
REVERT: B  309 CYS cc_start: 0.8356 (t) cc_final: 0.7709 (t)
REVERT: B  313 HIS cc_start: 0.8106 (m90) cc_final: 0.7581 (m90)
REVERT: B  325 TYR cc_start: 0.8487 (t80) cc_final: 0.8044 (t80)
REVERT: B  376 ARG cc_start: 0.8613 (mpt180) cc_final: 0.8251 (mmt-90)
REVERT: B  379 LEU cc_start: 0.8892 (tp) cc_final: 0.8569 (tp)
REVERT: B  439 LEU cc_start: 0.9542 (tp) cc_final: 0.9310 (tt)
REVERT: B  473 GLU cc_start: 0.9009 (tt0) cc_final: 0.8234 (tt0)
REVERT: C   89 PHE cc_start: 0.8025 (t80) cc_final: 0.7588 (t80)
REVERT: C   91 PHE cc_start: 0.8423 (t80) cc_final: 0.8054 (t80)
REVERT: C  178 LYS cc_start: 0.6700 (tptt) cc_final: 0.6349 (mppt)
REVERT: C  190 ASN cc_start: 0.8790 (m-40) cc_final: 0.7932 (m110)
REVERT: C  325 TYR cc_start: 0.8519 (t80) cc_final: 0.8155 (t80)
REVERT: C  387 MET cc_start: 0.8921 (mmm) cc_final: 0.8717 (mmt)
REVERT: C  395 CYS cc_start: 0.8404 (m) cc_final: 0.8119 (m)
REVERT: C  473 GLU cc_start: 0.9052 (tt0) cc_final: 0.8462 (tt0)
REVERT: C  475 ASP cc_start: 0.8583 (p0) cc_final: 0.8266 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.1634
  time to fit residues: 49.3670
Evaluate side-chains
  149 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 99 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 69 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9990
   chunk 98 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   overall best weight:    1.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.075551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.060578 restraints weight = 41601.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.061397 restraints weight = 29237.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.061838 restraints weight = 21075.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.3880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9798  Z= 0.185
  Angle     :  0.676   9.141  13344  Z= 0.322
  Chirality :  0.040   0.169   1668
  Planarity :  0.004   0.031   1656
  Dihedral  :  4.109  17.248   1365
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.24), residues: 1278
  helix:  0.47 (0.17), residues: 981
  sheet: -1.48 (0.89), residues: 42
  loop : -2.50 (0.36), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP C 461 
 HIS   0.005   0.001   HIS C 316 
 PHE   0.010   0.001   PHE B  91 
 TYR   0.027   0.002   TYR A 276 
 ARG   0.002   0.000   ARG A  98 

*********************** 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
  182 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9428 (m) cc_final: 0.9091 (p)
REVERT: A  282 MET cc_start: 0.8751 (tmm) cc_final: 0.8407 (tmm)
REVERT: A  309 CYS cc_start: 0.8022 (t) cc_final: 0.7223 (t)
REVERT: A  313 HIS cc_start: 0.8214 (m90) cc_final: 0.7799 (m90)
REVERT: A  325 TYR cc_start: 0.8387 (t80) cc_final: 0.8095 (t80)
REVERT: A  394 GLN cc_start: 0.8537 (mt0) cc_final: 0.8149 (mp10)
REVERT: A  461 TRP cc_start: 0.8576 (p-90) cc_final: 0.7662 (p-90)
REVERT: A  475 ASP cc_start: 0.8427 (p0) cc_final: 0.8121 (p0)
REVERT: B  279 VAL cc_start: 0.9361 (m) cc_final: 0.9160 (p)
REVERT: B  282 MET cc_start: 0.8880 (tmm) cc_final: 0.8472 (tmm)
REVERT: B  309 CYS cc_start: 0.8303 (t) cc_final: 0.7578 (t)
REVERT: B  313 HIS cc_start: 0.8191 (m90) cc_final: 0.7674 (m90)
REVERT: B  325 TYR cc_start: 0.8496 (t80) cc_final: 0.8014 (t80)
REVERT: B  376 ARG cc_start: 0.8509 (mpt180) cc_final: 0.8180 (mmt-90)
REVERT: B  439 LEU cc_start: 0.9497 (tp) cc_final: 0.9296 (tp)
REVERT: B  473 GLU cc_start: 0.9041 (tt0) cc_final: 0.8260 (tt0)
REVERT: C   89 PHE cc_start: 0.8009 (t80) cc_final: 0.7587 (t80)
REVERT: C   91 PHE cc_start: 0.8493 (t80) cc_final: 0.8084 (t80)
REVERT: C  178 LYS cc_start: 0.6582 (tptt) cc_final: 0.6290 (mmtm)
REVERT: C  190 ASN cc_start: 0.8772 (m-40) cc_final: 0.7958 (m110)
REVERT: C  325 TYR cc_start: 0.8524 (t80) cc_final: 0.8137 (t80)
REVERT: C  387 MET cc_start: 0.8978 (mmm) cc_final: 0.8747 (mmt)
REVERT: C  395 CYS cc_start: 0.8490 (m) cc_final: 0.8232 (m)
REVERT: C  473 GLU cc_start: 0.9060 (tt0) cc_final: 0.8441 (tt0)
REVERT: C  475 ASP cc_start: 0.8526 (p0) cc_final: 0.8315 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1758
  time to fit residues: 48.0780
Evaluate side-chains
  140 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 123 optimal weight:    0.3980
   chunk 5 optimal weight:    4.9990
   chunk 121 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0970
   chunk 65 optimal weight:   10.0000
   chunk 102 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.076619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.061456 restraints weight = 41694.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.062460 restraints weight = 28259.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.062777 restraints weight = 21111.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.4048

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= 0.167
  Angle     :  0.683   9.519  13344  Z= 0.323
  Chirality :  0.039   0.167   1668
  Planarity :  0.004   0.031   1656
  Dihedral  :  4.071  17.860   1365
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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: -0.24 (0.24), residues: 1278
  helix:  0.59 (0.17), residues: 963
  sheet: -2.10 (0.76), residues: 48
  loop : -2.32 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 461 
 HIS   0.004   0.001   HIS C 316 
 PHE   0.011   0.001   PHE C 258 
 TYR   0.028   0.002   TYR A 276 
 ARG   0.002   0.000   ARG B 376 

********************** 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
  188 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.9095 (m-40) cc_final: 0.8444 (m110)
REVERT: A  279 VAL cc_start: 0.9398 (m) cc_final: 0.9069 (p)
REVERT: A  282 MET cc_start: 0.8675 (tmm) cc_final: 0.8373 (tmm)
REVERT: A  309 CYS cc_start: 0.7929 (t) cc_final: 0.7065 (t)
REVERT: A  313 HIS cc_start: 0.8133 (m90) cc_final: 0.7781 (m90)
REVERT: A  325 TYR cc_start: 0.8239 (t80) cc_final: 0.7940 (t80)
REVERT: A  394 GLN cc_start: 0.8400 (mt0) cc_final: 0.8059 (mp10)
REVERT: A  461 TRP cc_start: 0.8562 (p-90) cc_final: 0.7632 (p-90)
REVERT: A  475 ASP cc_start: 0.8407 (p0) cc_final: 0.8107 (p0)
REVERT: B  279 VAL cc_start: 0.9364 (m) cc_final: 0.9139 (p)
REVERT: B  282 MET cc_start: 0.8848 (tmm) cc_final: 0.8443 (tmm)
REVERT: B  309 CYS cc_start: 0.8236 (t) cc_final: 0.7409 (t)
REVERT: B  313 HIS cc_start: 0.8208 (m90) cc_final: 0.7669 (m90)
REVERT: B  325 TYR cc_start: 0.8068 (t80) cc_final: 0.7757 (t80)
REVERT: B  376 ARG cc_start: 0.8558 (mpt180) cc_final: 0.8221 (mmt-90)
REVERT: B  394 GLN cc_start: 0.8474 (mt0) cc_final: 0.8111 (mt0)
REVERT: B  439 LEU cc_start: 0.9454 (tp) cc_final: 0.9223 (tp)
REVERT: B  473 GLU cc_start: 0.9027 (tt0) cc_final: 0.8343 (tt0)
REVERT: C   89 PHE cc_start: 0.7926 (t80) cc_final: 0.7532 (t80)
REVERT: C   91 PHE cc_start: 0.8358 (t80) cc_final: 0.7967 (t80)
REVERT: C  178 LYS cc_start: 0.6618 (tptt) cc_final: 0.6307 (mppt)
REVERT: C  190 ASN cc_start: 0.8697 (m-40) cc_final: 0.7868 (m110)
REVERT: C  309 CYS cc_start: 0.8204 (t) cc_final: 0.7778 (t)
REVERT: C  325 TYR cc_start: 0.8427 (t80) cc_final: 0.8021 (t80)
REVERT: C  387 MET cc_start: 0.8926 (mmm) cc_final: 0.8710 (mmt)
REVERT: C  395 CYS cc_start: 0.8431 (m) cc_final: 0.8211 (m)
REVERT: C  473 GLU cc_start: 0.9036 (tt0) cc_final: 0.8445 (tt0)
REVERT: C  475 ASP cc_start: 0.8516 (p0) cc_final: 0.8256 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1744
  time to fit residues: 49.1513
Evaluate side-chains
  139 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 122 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 72 optimal weight:   20.0000
   chunk 110 optimal weight:    9.9990
   chunk 62 optimal weight:    7.9990
   chunk 68 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   chunk 35 optimal weight:    4.9990
   chunk 126 optimal weight:    3.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** B 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 313 HIS ** 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 = 0.3342 r_free = 0.3342 target = 0.074777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.059163 restraints weight = 41725.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.060156 restraints weight = 26706.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.060808 restraints weight = 20371.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.4018

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= 0.207
  Angle     :  0.686   8.271  13344  Z= 0.327
  Chirality :  0.040   0.183   1668
  Planarity :  0.004   0.032   1656
  Dihedral  :  4.133  19.475   1365
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  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: -0.25 (0.24), residues: 1278
  helix:  0.53 (0.17), residues: 981
  sheet: -1.62 (0.82), residues: 42
  loop : -2.44 (0.36), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 461 
 HIS   0.004   0.001   HIS C 316 
 PHE   0.012   0.001   PHE B  91 
 TYR   0.027   0.002   TYR A 276 
 ARG   0.002   0.000   ARG B 376 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2668.86 seconds
wall clock time: 47 minutes 28.01 seconds (2848.01 seconds total)