Starting phenix.real_space_refine
on Wed Mar  4 00:22:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6rvy_10018/03_2026/6rvy_10018.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6rvy_10018/03_2026/6rvy_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6rvy_10018/03_2026/6rvy_10018.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6rvy_10018/03_2026/6rvy_10018.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6rvy_10018/03_2026/6rvy_10018.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6rvy_10018/03_2026/6rvy_10018.map"
  }
  resolution = 4.13
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.005
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9627
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3209
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3209
          Classifications: {'peptide': 430}
          Link IDs: {'PTRANS': 16, 'TRANS': 413}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.21, per 1000 atoms: 0.23
  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: 0.76
  Conformation dependent library (CDL) restraints added in 529.0 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 3 sheets defined
      78.6% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 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: 1.26

  Time building geometry restraints manager: 0.96 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.410
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.440
-------------------------------------------------------------------------------
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= 0.278
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.00 (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
 ARG   0.005   0.001   ARG C 465 
 TYR   0.006   0.002   TYR A 305 
 PHE   0.013   0.002   PHE A 258 
 TRP   0.011   0.001   TRP A 461 
 HIS   0.003   0.001   HIS C 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00598 ( 9798)
  covalent geometry    : angle       1.02983 (13344)
  hydrogen bonds       : bond        0.16403 (  651)
  hydrogen bonds       : angle       7.33192 ( 1944)

*********************** 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  : 0.348 
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: 0.8079 (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: 0.8918 (p)
REVERT: B  297 LEU cc_start: 0.8981 (tp) cc_final: 0.8737 (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: 0.8583 (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: 0.0871
  time to fit residues: 25.5002
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  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:   10.0000
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 212 ASN
** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 212 ASN
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 = 0.3327 r_free = 0.3327 target = 0.073703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.058694 restraints weight = 41164.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.059738 restraints weight = 26245.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.060335 restraints weight = 19565.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.060621 restraints weight = 16595.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.061050 restraints weight = 15243.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9798  Z= 0.140
  Angle     :  0.675   8.092  13344  Z= 0.339
  Chirality :  0.039   0.171   1668
  Planarity :  0.005   0.042   1656
  Dihedral  :  4.933  18.252   1365
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.60 (0.21), residues: 1278
  helix: -1.16 (0.15), residues: 990
  sheet: -2.94 (0.71), residues: 42
  loop : -3.16 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 217 
 TYR   0.014   0.002   TYR C 305 
 PHE   0.011   0.001   PHE C 237 
 TRP   0.005   0.001   TRP B 130 
 HIS   0.004   0.001   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9798)
  covalent geometry    : angle       0.67454 (13344)
  hydrogen bonds       : bond        0.04152 (  651)
  hydrogen bonds       : angle       4.98239 ( 1944)

*********************** 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
  208 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9375 (m) cc_final: 0.9010 (p)
REVERT: A  282 MET cc_start: 0.8862 (tmm) cc_final: 0.8371 (tmm)
REVERT: A  297 LEU cc_start: 0.8945 (tp) cc_final: 0.8650 (mp)
REVERT: A  313 HIS cc_start: 0.8168 (m90) cc_final: 0.7473 (m90)
REVERT: A  325 TYR cc_start: 0.8695 (t80) cc_final: 0.8372 (t80)
REVERT: A  394 GLN cc_start: 0.8714 (mt0) cc_final: 0.8287 (mp10)
REVERT: A  410 ASP cc_start: 0.8015 (t0) cc_final: 0.7786 (m-30)
REVERT: A  439 LEU cc_start: 0.9574 (tp) cc_final: 0.9215 (tt)
REVERT: A  461 TRP cc_start: 0.8429 (p-90) cc_final: 0.7762 (p-90)
REVERT: B   89 PHE cc_start: 0.7603 (t80) cc_final: 0.7394 (t80)
REVERT: B   91 PHE cc_start: 0.8411 (t80) cc_final: 0.7923 (t80)
REVERT: B  279 VAL cc_start: 0.9344 (m) cc_final: 0.9129 (p)
REVERT: B  282 MET cc_start: 0.8867 (tmm) cc_final: 0.8528 (tmm)
REVERT: B  297 LEU cc_start: 0.8861 (tp) cc_final: 0.8566 (mp)
REVERT: B  325 TYR cc_start: 0.8619 (t80) cc_final: 0.8069 (t80)
REVERT: B  439 LEU cc_start: 0.9572 (tp) cc_final: 0.9330 (tp)
REVERT: B  461 TRP cc_start: 0.8461 (p-90) cc_final: 0.7435 (p-90)
REVERT: B  473 GLU cc_start: 0.8985 (tt0) cc_final: 0.8466 (tt0)
REVERT: C   89 PHE cc_start: 0.7902 (t80) cc_final: 0.7392 (t80)
REVERT: C  178 LYS cc_start: 0.6715 (tptt) cc_final: 0.6343 (mppt)
REVERT: C  208 TYR cc_start: 0.7521 (m-80) cc_final: 0.7281 (m-80)
REVERT: C  274 MET cc_start: 0.7725 (mtt) cc_final: 0.7492 (mtt)
REVERT: C  282 MET cc_start: 0.8815 (tmm) cc_final: 0.8252 (tmm)
REVERT: C  288 LYS cc_start: 0.8722 (tppt) cc_final: 0.8354 (mmtt)
REVERT: C  297 LEU cc_start: 0.8747 (tp) cc_final: 0.8418 (mp)
REVERT: C  313 HIS cc_start: 0.8284 (m90) cc_final: 0.8056 (m90)
REVERT: C  325 TYR cc_start: 0.8640 (t80) cc_final: 0.8360 (t80)
REVERT: C  395 CYS cc_start: 0.8326 (m) cc_final: 0.8009 (m)
REVERT: C  410 ASP cc_start: 0.8003 (t0) cc_final: 0.7761 (m-30)
REVERT: C  439 LEU cc_start: 0.9577 (tp) cc_final: 0.9273 (tp)
REVERT: C  473 GLU cc_start: 0.8920 (tt0) cc_final: 0.8529 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.0780
  time to fit residues: 24.1130
Evaluate side-chains
  145 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 82 optimal weight:    8.9990
   chunk 84 optimal weight:    5.9990
   chunk 111 optimal weight:   20.0000
   chunk 103 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 59 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 71 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9990
   chunk 87 optimal weight:    8.9990
   chunk 117 optimal weight:    4.9990
   overall best weight:    4.5990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.071382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.056182 restraints weight = 42162.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.057132 restraints weight = 27218.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.057767 restraints weight = 20660.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.057979 restraints weight = 17439.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.057979 restraints weight = 16118.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   9798  Z= 0.214
  Angle     :  0.728   8.912  13344  Z= 0.359
  Chirality :  0.041   0.172   1668
  Planarity :  0.005   0.038   1656
  Dihedral  :  4.758  16.658   1365
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.23), residues: 1278
  helix: -0.53 (0.16), residues: 996
  sheet: -2.59 (0.76), residues: 42
  loop : -2.75 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  85 
 TYR   0.016   0.002   TYR C 305 
 PHE   0.012   0.001   PHE B  91 
 TRP   0.005   0.001   TRP B 461 
 HIS   0.005   0.001   HIS C 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 9798)
  covalent geometry    : angle       0.72823 (13344)
  hydrogen bonds       : bond        0.04067 (  651)
  hydrogen bonds       : angle       4.84545 ( 1944)

*********************** 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
  188 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9389 (m) cc_final: 0.9069 (p)
REVERT: A  282 MET cc_start: 0.8892 (tmm) cc_final: 0.8484 (tmm)
REVERT: A  297 LEU cc_start: 0.8901 (tp) cc_final: 0.8526 (mp)
REVERT: A  309 CYS cc_start: 0.8148 (t) cc_final: 0.7544 (t)
REVERT: A  313 HIS cc_start: 0.8362 (m90) cc_final: 0.7651 (m90)
REVERT: A  325 TYR cc_start: 0.8605 (t80) cc_final: 0.8217 (t80)
REVERT: A  394 GLN cc_start: 0.8665 (mt0) cc_final: 0.8230 (mp10)
REVERT: A  395 CYS cc_start: 0.8303 (m) cc_final: 0.8070 (m)
REVERT: A  410 ASP cc_start: 0.8135 (t0) cc_final: 0.7838 (m-30)
REVERT: A  439 LEU cc_start: 0.9570 (tp) cc_final: 0.9314 (tp)
REVERT: A  461 TRP cc_start: 0.8464 (p-90) cc_final: 0.7674 (p-90)
REVERT: B   91 PHE cc_start: 0.8442 (t80) cc_final: 0.7985 (t80)
REVERT: B  201 PHE cc_start: 0.8483 (p90) cc_final: 0.8202 (p90)
REVERT: B  279 VAL cc_start: 0.9334 (m) cc_final: 0.9110 (p)
REVERT: B  282 MET cc_start: 0.8743 (tmm) cc_final: 0.8463 (tmm)
REVERT: B  297 LEU cc_start: 0.8931 (tp) cc_final: 0.8632 (tp)
REVERT: B  313 HIS cc_start: 0.8565 (m90) cc_final: 0.8287 (m90)
REVERT: B  325 TYR cc_start: 0.8784 (t80) cc_final: 0.8248 (t80)
REVERT: B  461 TRP cc_start: 0.8516 (p-90) cc_final: 0.7484 (p-90)
REVERT: B  473 GLU cc_start: 0.9012 (tt0) cc_final: 0.8502 (tt0)
REVERT: C   89 PHE cc_start: 0.8013 (t80) cc_final: 0.7635 (t80)
REVERT: C  178 LYS cc_start: 0.6828 (tptt) cc_final: 0.6427 (mppt)
REVERT: C  201 PHE cc_start: 0.8356 (p90) cc_final: 0.7992 (p90)
REVERT: C  208 TYR cc_start: 0.7534 (m-80) cc_final: 0.7298 (m-80)
REVERT: C  274 MET cc_start: 0.7748 (mtt) cc_final: 0.7533 (mtt)
REVERT: C  282 MET cc_start: 0.8774 (tmm) cc_final: 0.8353 (tmm)
REVERT: C  313 HIS cc_start: 0.8506 (m90) cc_final: 0.8214 (m90)
REVERT: C  325 TYR cc_start: 0.8702 (t80) cc_final: 0.8378 (t80)
REVERT: C  395 CYS cc_start: 0.8240 (m) cc_final: 0.8019 (m)
REVERT: C  473 GLU cc_start: 0.8972 (tt0) cc_final: 0.8481 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.0753
  time to fit residues: 21.4773
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  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 117 optimal weight:   30.0000
   chunk 121 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 109 optimal weight:    8.9990
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0570
   chunk 49 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.9902

-------------------------------------------------------------------------------
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 = 0.3349 r_free = 0.3349 target = 0.074147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.059310 restraints weight = 41372.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.060316 restraints weight = 25897.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.061023 restraints weight = 19364.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.061492 restraints weight = 16212.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.061672 restraints weight = 14610.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9798  Z= 0.123
  Angle     :  0.662   7.723  13344  Z= 0.320
  Chirality :  0.039   0.172   1668
  Planarity :  0.004   0.034   1656
  Dihedral  :  4.430  15.696   1365
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.24), residues: 1278
  helix: -0.23 (0.16), residues: 996
  sheet: -2.16 (0.84), residues: 42
  loop : -2.55 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  98 
 TYR   0.021   0.002   TYR C 305 
 PHE   0.011   0.001   PHE C 258 
 TRP   0.021   0.001   TRP C 461 
 HIS   0.003   0.001   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9798)
  covalent geometry    : angle       0.66178 (13344)
  hydrogen bonds       : bond        0.03623 (  651)
  hydrogen bonds       : angle       4.43299 ( 1944)

*********************** 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  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9359 (m) cc_final: 0.8984 (p)
REVERT: A  282 MET cc_start: 0.8792 (tmm) cc_final: 0.8355 (tmm)
REVERT: A  297 LEU cc_start: 0.8930 (tp) cc_final: 0.8511 (mp)
REVERT: A  309 CYS cc_start: 0.7996 (t) cc_final: 0.7496 (t)
REVERT: A  313 HIS cc_start: 0.7996 (m90) cc_final: 0.7564 (m90)
REVERT: A  316 HIS cc_start: 0.8624 (t-90) cc_final: 0.8379 (t-90)
REVERT: A  325 TYR cc_start: 0.8415 (t80) cc_final: 0.8073 (t80)
REVERT: A  379 LEU cc_start: 0.8963 (tp) cc_final: 0.8209 (tp)
REVERT: A  394 GLN cc_start: 0.8530 (mt0) cc_final: 0.8203 (mp10)
REVERT: A  395 CYS cc_start: 0.8489 (m) cc_final: 0.8173 (m)
REVERT: A  461 TRP cc_start: 0.8491 (p-90) cc_final: 0.7675 (p-90)
REVERT: B   91 PHE cc_start: 0.8390 (t80) cc_final: 0.7885 (t80)
REVERT: B  279 VAL cc_start: 0.9363 (m) cc_final: 0.9106 (p)
REVERT: B  282 MET cc_start: 0.8669 (tmm) cc_final: 0.8383 (tmm)
REVERT: B  297 LEU cc_start: 0.8887 (tp) cc_final: 0.8592 (tp)
REVERT: B  325 TYR cc_start: 0.8583 (t80) cc_final: 0.8133 (t80)
REVERT: B  395 CYS cc_start: 0.8468 (m) cc_final: 0.8174 (m)
REVERT: B  473 GLU cc_start: 0.9058 (tt0) cc_final: 0.8548 (tt0)
REVERT: C   89 PHE cc_start: 0.7939 (t80) cc_final: 0.7550 (t80)
REVERT: C  178 LYS cc_start: 0.6773 (tptt) cc_final: 0.6383 (mppt)
REVERT: C  282 MET cc_start: 0.8732 (tmm) cc_final: 0.8321 (tmm)
REVERT: C  325 TYR cc_start: 0.8532 (t80) cc_final: 0.8219 (t80)
REVERT: C  395 CYS cc_start: 0.8288 (m) cc_final: 0.8028 (m)
REVERT: C  439 LEU cc_start: 0.9471 (tp) cc_final: 0.9243 (tt)
REVERT: C  473 GLU cc_start: 0.8991 (tt0) cc_final: 0.8511 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.0767
  time to fit residues: 23.0306
Evaluate side-chains
  153 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 95 optimal weight:    9.9990
   chunk 36 optimal weight:    0.5980
   chunk 66 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 102 optimal weight:   10.0000
   chunk 83 optimal weight:    8.9990
   chunk 113 optimal weight:   10.0000
   chunk 116 optimal weight:   20.0000
   chunk 110 optimal weight:   10.0000
   overall best weight:    3.3188

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.071867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.056578 restraints weight = 41760.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.057482 restraints weight = 27319.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.058086 restraints weight = 20986.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.058454 restraints weight = 17922.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.058454 restraints weight = 16111.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9798  Z= 0.167
  Angle     :  0.686   8.648  13344  Z= 0.335
  Chirality :  0.040   0.171   1668
  Planarity :  0.004   0.034   1656
  Dihedral  :  4.410  17.676   1365
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.24), residues: 1278
  helix:  0.03 (0.17), residues: 978
  sheet:  None (None), residues: 0
  loop : -2.72 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 376 
 TYR   0.022   0.002   TYR A 305 
 PHE   0.021   0.001   PHE B  89 
 TRP   0.015   0.001   TRP C 461 
 HIS   0.004   0.001   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 9798)
  covalent geometry    : angle       0.68625 (13344)
  hydrogen bonds       : bond        0.03761 (  651)
  hydrogen bonds       : angle       4.44601 ( 1944)

*********************** 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
  179 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9371 (m) cc_final: 0.9034 (p)
REVERT: A  282 MET cc_start: 0.8794 (tmm) cc_final: 0.8417 (tmm)
REVERT: A  309 CYS cc_start: 0.8137 (t) cc_final: 0.7542 (t)
REVERT: A  313 HIS cc_start: 0.8224 (m90) cc_final: 0.7698 (m90)
REVERT: A  325 TYR cc_start: 0.8507 (t80) cc_final: 0.8142 (t80)
REVERT: A  394 GLN cc_start: 0.8741 (mt0) cc_final: 0.8254 (mp10)
REVERT: A  439 LEU cc_start: 0.9528 (tp) cc_final: 0.9253 (tp)
REVERT: A  461 TRP cc_start: 0.8473 (p-90) cc_final: 0.7602 (p-90)
REVERT: A  475 ASP cc_start: 0.8360 (p0) cc_final: 0.8092 (p0)
REVERT: B   91 PHE cc_start: 0.8404 (t80) cc_final: 0.7960 (t80)
REVERT: B  201 PHE cc_start: 0.8526 (p90) cc_final: 0.8124 (p90)
REVERT: B  279 VAL cc_start: 0.9377 (m) cc_final: 0.9152 (p)
REVERT: B  297 LEU cc_start: 0.8899 (tp) cc_final: 0.8561 (tp)
REVERT: B  313 HIS cc_start: 0.8409 (m90) cc_final: 0.8183 (m90)
REVERT: B  325 TYR cc_start: 0.8655 (t80) cc_final: 0.8209 (t80)
REVERT: B  439 LEU cc_start: 0.9565 (tp) cc_final: 0.9310 (tt)
REVERT: C   89 PHE cc_start: 0.7979 (t80) cc_final: 0.7572 (t80)
REVERT: C  178 LYS cc_start: 0.6722 (tptt) cc_final: 0.6414 (mppt)
REVERT: C  190 ASN cc_start: 0.8821 (m-40) cc_final: 0.7817 (m110)
REVERT: C  201 PHE cc_start: 0.8421 (p90) cc_final: 0.7907 (p90)
REVERT: C  282 MET cc_start: 0.8738 (tmm) cc_final: 0.8387 (tmm)
REVERT: C  316 HIS cc_start: 0.8711 (t-90) cc_final: 0.8409 (t-90)
REVERT: C  325 TYR cc_start: 0.8576 (t80) cc_final: 0.8206 (t80)
REVERT: C  473 GLU cc_start: 0.9012 (tt0) cc_final: 0.8479 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.0727
  time to fit residues: 19.8050
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  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 88 optimal weight:    0.2980
   chunk 125 optimal weight:    0.9990
   chunk 89 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9980
   chunk 43 optimal weight:   30.0000
   chunk 55 optimal weight:    1.9990
   chunk 41 optimal weight:    8.9990
   chunk 96 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9980
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.074967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.059834 restraints weight = 41349.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.060952 restraints weight = 25576.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.061574 restraints weight = 18749.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.062075 restraints weight = 15746.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.062259 restraints weight = 14112.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9798  Z= 0.121
  Angle     :  0.665   7.988  13344  Z= 0.318
  Chirality :  0.039   0.165   1668
  Planarity :  0.004   0.032   1656
  Dihedral  :  4.241  16.179   1365
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.24), residues: 1278
  helix:  0.19 (0.17), residues: 978
  sheet: -1.99 (0.85), residues: 42
  loop : -2.26 (0.41), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.021   0.002   TYR C 305 
 PHE   0.018   0.001   PHE B  89 
 TRP   0.010   0.001   TRP C 461 
 HIS   0.004   0.001   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 9798)
  covalent geometry    : angle       0.66548 (13344)
  hydrogen bonds       : bond        0.03509 (  651)
  hydrogen bonds       : angle       4.23070 ( 1944)

*********************** 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
  197 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9406 (m) cc_final: 0.9102 (p)
REVERT: A  309 CYS cc_start: 0.7999 (t) cc_final: 0.7339 (t)
REVERT: A  313 HIS cc_start: 0.8015 (m90) cc_final: 0.7640 (m90)
REVERT: A  325 TYR cc_start: 0.8395 (t80) cc_final: 0.8126 (t80)
REVERT: A  394 GLN cc_start: 0.8610 (mt0) cc_final: 0.8163 (mp10)
REVERT: A  461 TRP cc_start: 0.8510 (p-90) cc_final: 0.7621 (p-90)
REVERT: A  475 ASP cc_start: 0.8362 (p0) cc_final: 0.8025 (p0)
REVERT: B   91 PHE cc_start: 0.8426 (t80) cc_final: 0.7956 (t80)
REVERT: B  279 VAL cc_start: 0.9360 (m) cc_final: 0.9146 (p)
REVERT: B  282 MET cc_start: 0.8855 (tmm) cc_final: 0.8517 (tmm)
REVERT: B  325 TYR cc_start: 0.8505 (t80) cc_final: 0.7983 (t80)
REVERT: B  379 LEU cc_start: 0.8930 (tp) cc_final: 0.8233 (tp)
REVERT: B  473 GLU cc_start: 0.9031 (tt0) cc_final: 0.8328 (tt0)
REVERT: C   89 PHE cc_start: 0.7969 (t80) cc_final: 0.7511 (t80)
REVERT: C   91 PHE cc_start: 0.8463 (t80) cc_final: 0.7956 (t80)
REVERT: C  178 LYS cc_start: 0.6662 (tptt) cc_final: 0.6359 (mppt)
REVERT: C  190 ASN cc_start: 0.8813 (m-40) cc_final: 0.7935 (m110)
REVERT: C  325 TYR cc_start: 0.8467 (t80) cc_final: 0.8180 (t80)
REVERT: C  387 MET cc_start: 0.8941 (mmm) cc_final: 0.8733 (mmt)
REVERT: C  395 CYS cc_start: 0.8381 (m) cc_final: 0.8120 (m)
REVERT: C  473 GLU cc_start: 0.8976 (tt0) cc_final: 0.8479 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.0711
  time to fit residues: 21.3542
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  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 115 optimal weight:    3.9990
   chunk 110 optimal weight:   20.0000
   chunk 29 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 79 optimal weight:    0.0970
   chunk 75 optimal weight:    0.0770
   chunk 3 optimal weight:   20.0000
   chunk 1 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 101 optimal weight:    3.9990
   overall best weight:    1.8340

-------------------------------------------------------------------------------
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 = 0.3341 r_free = 0.3341 target = 0.073956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.059072 restraints weight = 41658.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.059886 restraints weight = 27866.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.060123 restraints weight = 20211.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.060160 restraints weight = 19230.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.060238 restraints weight = 18603.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.3584

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= 0.131
  Angle     :  0.689   8.327  13344  Z= 0.329
  Chirality :  0.040   0.167   1668
  Planarity :  0.004   0.032   1656
  Dihedral  :  4.221  17.272   1365
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.24), residues: 1278
  helix:  0.28 (0.17), residues: 978
  sheet:  None (None), residues: 0
  loop : -2.49 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 376 
 TYR   0.021   0.002   TYR B 305 
 PHE   0.015   0.001   PHE B  89 
 TRP   0.017   0.001   TRP C 461 
 HIS   0.003   0.001   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9798)
  covalent geometry    : angle       0.68852 (13344)
  hydrogen bonds       : bond        0.03534 (  651)
  hydrogen bonds       : angle       4.22939 ( 1944)

*********************** 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
  189 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.9199 (m-40) cc_final: 0.8485 (m110)
REVERT: A  279 VAL cc_start: 0.9415 (m) cc_final: 0.9109 (p)
REVERT: A  282 MET cc_start: 0.8849 (tmm) cc_final: 0.8105 (tmm)
REVERT: A  309 CYS cc_start: 0.8276 (t) cc_final: 0.7558 (t)
REVERT: A  313 HIS cc_start: 0.8205 (m90) cc_final: 0.7766 (m90)
REVERT: A  325 TYR cc_start: 0.8404 (t80) cc_final: 0.8121 (t80)
REVERT: A  394 GLN cc_start: 0.8548 (mt0) cc_final: 0.8119 (mp10)
REVERT: A  461 TRP cc_start: 0.8548 (p-90) cc_final: 0.7624 (p-90)
REVERT: A  475 ASP cc_start: 0.8406 (p0) cc_final: 0.8103 (p0)
REVERT: B  201 PHE cc_start: 0.8489 (p90) cc_final: 0.7952 (p90)
REVERT: B  279 VAL cc_start: 0.9356 (m) cc_final: 0.9148 (p)
REVERT: B  282 MET cc_start: 0.8848 (tmm) cc_final: 0.8455 (tmm)
REVERT: B  325 TYR cc_start: 0.8261 (t80) cc_final: 0.7912 (t80)
REVERT: B  473 GLU cc_start: 0.9121 (tt0) cc_final: 0.8354 (tt0)
REVERT: C   89 PHE cc_start: 0.7999 (t80) cc_final: 0.7546 (t80)
REVERT: C   91 PHE cc_start: 0.8497 (t80) cc_final: 0.8115 (t80)
REVERT: C  178 LYS cc_start: 0.6705 (tptt) cc_final: 0.6330 (mppt)
REVERT: C  190 ASN cc_start: 0.8806 (m-40) cc_final: 0.8011 (m110)
REVERT: C  282 MET cc_start: 0.8821 (tmm) cc_final: 0.8343 (tmm)
REVERT: C  316 HIS cc_start: 0.8696 (t-90) cc_final: 0.8442 (t-90)
REVERT: C  325 TYR cc_start: 0.8529 (t80) cc_final: 0.8204 (t80)
REVERT: C  395 CYS cc_start: 0.8451 (m) cc_final: 0.8195 (m)
REVERT: C  473 GLU cc_start: 0.9074 (tt0) cc_final: 0.8474 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.0766
  time to fit residues: 21.5158
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  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 46 optimal weight:   20.0000
   chunk 24 optimal weight:   20.0000
   chunk 61 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 97 optimal weight:    0.4980
   chunk 126 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0770
   chunk 6 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    2.1144

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

Flipped N/Q/H residues before XYZ refinement:
B 313 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.074746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.059364 restraints weight = 41569.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.060390 restraints weight = 26611.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.060952 restraints weight = 20109.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.061391 restraints weight = 17179.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.061447 restraints weight = 15467.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.3699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9798  Z= 0.135
  Angle     :  0.691   7.951  13344  Z= 0.328
  Chirality :  0.040   0.170   1668
  Planarity :  0.004   0.031   1656
  Dihedral  :  4.235  17.103   1365
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.24), residues: 1278
  helix:  0.38 (0.17), residues: 978
  sheet:  None (None), residues: 0
  loop : -2.49 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 217 
 TYR   0.020   0.002   TYR C 305 
 PHE   0.014   0.001   PHE B  89 
 TRP   0.023   0.001   TRP C 461 
 HIS   0.005   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9798)
  covalent geometry    : angle       0.69076 (13344)
  hydrogen bonds       : bond        0.03536 (  651)
  hydrogen bonds       : angle       4.18181 ( 1944)

*********************** 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
  185 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.9154 (m-40) cc_final: 0.8551 (m110)
REVERT: A  279 VAL cc_start: 0.9438 (m) cc_final: 0.9113 (p)
REVERT: A  282 MET cc_start: 0.8840 (tmm) cc_final: 0.8122 (tmm)
REVERT: A  309 CYS cc_start: 0.8062 (t) cc_final: 0.7321 (t)
REVERT: A  313 HIS cc_start: 0.8156 (m90) cc_final: 0.7746 (m90)
REVERT: A  325 TYR cc_start: 0.8383 (t80) cc_final: 0.8100 (t80)
REVERT: A  379 LEU cc_start: 0.8952 (tp) cc_final: 0.8741 (tp)
REVERT: A  394 GLN cc_start: 0.8553 (mt0) cc_final: 0.8219 (mp10)
REVERT: A  461 TRP cc_start: 0.8527 (p-90) cc_final: 0.7610 (p-90)
REVERT: A  475 ASP cc_start: 0.8386 (p0) cc_final: 0.8118 (p0)
REVERT: B  201 PHE cc_start: 0.8457 (p90) cc_final: 0.8008 (p90)
REVERT: B  279 VAL cc_start: 0.9368 (m) cc_final: 0.9150 (p)
REVERT: B  282 MET cc_start: 0.8878 (tmm) cc_final: 0.8477 (tmm)
REVERT: B  313 HIS cc_start: 0.8232 (m90) cc_final: 0.7772 (m-70)
REVERT: B  325 TYR cc_start: 0.8206 (t80) cc_final: 0.7919 (t80)
REVERT: B  361 MET cc_start: 0.7412 (tpt) cc_final: 0.6934 (tpt)
REVERT: B  376 ARG cc_start: 0.8725 (mpt180) cc_final: 0.8365 (mmt-90)
REVERT: B  473 GLU cc_start: 0.9021 (tt0) cc_final: 0.8315 (tt0)
REVERT: C   89 PHE cc_start: 0.7972 (t80) cc_final: 0.7500 (t80)
REVERT: C   91 PHE cc_start: 0.8474 (t80) cc_final: 0.8086 (t80)
REVERT: C  178 LYS cc_start: 0.6717 (tptt) cc_final: 0.6392 (mppt)
REVERT: C  190 ASN cc_start: 0.8865 (m-40) cc_final: 0.8002 (m110)
REVERT: C  282 MET cc_start: 0.8810 (tmm) cc_final: 0.8284 (tmm)
REVERT: C  309 CYS cc_start: 0.8151 (t) cc_final: 0.7884 (t)
REVERT: C  316 HIS cc_start: 0.8619 (t-90) cc_final: 0.8358 (t-90)
REVERT: C  325 TYR cc_start: 0.8497 (t80) cc_final: 0.8152 (t80)
REVERT: C  395 CYS cc_start: 0.8386 (m) cc_final: 0.8145 (m)
REVERT: C  473 GLU cc_start: 0.9017 (tt0) cc_final: 0.8431 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.0771
  time to fit residues: 21.2581
Evaluate side-chains
  146 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 127 optimal weight:   10.0000
   chunk 122 optimal weight:    0.0970
   chunk 68 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 60 optimal weight:    0.8980
   chunk 41 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9980
   chunk 51 optimal weight:   30.0000
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B 313 HIS
** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.076576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.061442 restraints weight = 41604.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.062418 restraints weight = 29890.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.062515 restraints weight = 21141.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.062549 restraints weight = 21806.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.062619 restraints weight = 20494.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.3952

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= 0.119
  Angle     :  0.684   8.227  13344  Z= 0.321
  Chirality :  0.039   0.169   1668
  Planarity :  0.004   0.032   1656
  Dihedral  :  4.088  17.027   1365
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.24), residues: 1278
  helix:  0.50 (0.17), residues: 975
  sheet: -1.45 (0.84), residues: 42
  loop : -2.20 (0.39), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.020   0.002   TYR A 305 
 PHE   0.012   0.001   PHE A  91 
 TRP   0.022   0.001   TRP C 461 
 HIS   0.003   0.001   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9798)
  covalent geometry    : angle       0.68351 (13344)
  hydrogen bonds       : bond        0.03383 (  651)
  hydrogen bonds       : angle       4.07507 ( 1944)

*********************** 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
  192 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.9091 (m-40) cc_final: 0.8579 (m110)
REVERT: A  279 VAL cc_start: 0.9419 (m) cc_final: 0.9090 (p)
REVERT: A  282 MET cc_start: 0.8836 (tmm) cc_final: 0.8103 (tmm)
REVERT: A  309 CYS cc_start: 0.8053 (t) cc_final: 0.7143 (t)
REVERT: A  313 HIS cc_start: 0.8027 (m90) cc_final: 0.7700 (m90)
REVERT: A  325 TYR cc_start: 0.8351 (t80) cc_final: 0.8076 (t80)
REVERT: A  379 LEU cc_start: 0.8874 (tp) cc_final: 0.8462 (tp)
REVERT: A  461 TRP cc_start: 0.8557 (p-90) cc_final: 0.7635 (p-90)
REVERT: B  279 VAL cc_start: 0.9344 (m) cc_final: 0.9137 (p)
REVERT: B  282 MET cc_start: 0.8900 (tmm) cc_final: 0.8485 (tmm)
REVERT: B  325 TYR cc_start: 0.8217 (t80) cc_final: 0.7903 (t80)
REVERT: B  376 ARG cc_start: 0.8790 (mpt180) cc_final: 0.8346 (mmt-90)
REVERT: B  473 GLU cc_start: 0.9023 (tt0) cc_final: 0.8353 (tt0)
REVERT: C   89 PHE cc_start: 0.7998 (t80) cc_final: 0.7536 (t80)
REVERT: C   91 PHE cc_start: 0.8403 (t80) cc_final: 0.8058 (t80)
REVERT: C  178 LYS cc_start: 0.6724 (tptt) cc_final: 0.6336 (mppt)
REVERT: C  190 ASN cc_start: 0.8721 (m-40) cc_final: 0.7896 (m110)
REVERT: C  282 MET cc_start: 0.8855 (tmm) cc_final: 0.8296 (tmm)
REVERT: C  325 TYR cc_start: 0.8480 (t80) cc_final: 0.8067 (t80)
REVERT: C  395 CYS cc_start: 0.8433 (m) cc_final: 0.8191 (m)
REVERT: C  439 LEU cc_start: 0.9476 (tp) cc_final: 0.9263 (tp)
REVERT: C  473 GLU cc_start: 0.9085 (tt0) cc_final: 0.8573 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.0757
  time to fit residues: 21.6424
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  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 84 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 116 optimal weight:    0.6980
   chunk 36 optimal weight:   10.0000
   chunk 31 optimal weight:    0.0030
   chunk 59 optimal weight:    0.7980
   chunk 100 optimal weight:    9.9990
   chunk 17 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
B 407 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.076675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.061247 restraints weight = 41080.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.062263 restraints weight = 26706.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.062814 restraints weight = 20359.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.063265 restraints weight = 17502.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.063404 restraints weight = 15911.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.4138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9798  Z= 0.119
  Angle     :  0.691   8.212  13344  Z= 0.325
  Chirality :  0.040   0.173   1668
  Planarity :  0.004   0.031   1656
  Dihedral  :  4.097  18.839   1365
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.24), residues: 1278
  helix:  0.57 (0.17), residues: 960
  sheet:  None (None), residues: 0
  loop : -2.54 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.021   0.001   TYR A 305 
 PHE   0.012   0.001   PHE A  91 
 TRP   0.022   0.001   TRP C 461 
 HIS   0.003   0.001   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9798)
  covalent geometry    : angle       0.69062 (13344)
  hydrogen bonds       : bond        0.03426 (  651)
  hydrogen bonds       : angle       4.02387 ( 1944)

********************** 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
  184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 ASN cc_start: 0.9034 (m-40) cc_final: 0.8655 (m110)
REVERT: A  279 VAL cc_start: 0.9402 (m) cc_final: 0.9098 (p)
REVERT: A  282 MET cc_start: 0.8778 (tmm) cc_final: 0.8012 (tmm)
REVERT: A  309 CYS cc_start: 0.7938 (t) cc_final: 0.7002 (t)
REVERT: A  325 TYR cc_start: 0.8225 (t80) cc_final: 0.7921 (t80)
REVERT: A  461 TRP cc_start: 0.8455 (p-90) cc_final: 0.7416 (p-90)
REVERT: B  190 ASN cc_start: 0.8806 (m-40) cc_final: 0.7930 (m110)
REVERT: B  282 MET cc_start: 0.8815 (tmm) cc_final: 0.8393 (tmm)
REVERT: B  325 TYR cc_start: 0.8048 (t80) cc_final: 0.7769 (t80)
REVERT: B  376 ARG cc_start: 0.8603 (mpt180) cc_final: 0.8343 (mmt-90)
REVERT: B  473 GLU cc_start: 0.8920 (tt0) cc_final: 0.8273 (tt0)
REVERT: C   89 PHE cc_start: 0.7900 (t80) cc_final: 0.7438 (t80)
REVERT: C   91 PHE cc_start: 0.8295 (t80) cc_final: 0.7936 (t80)
REVERT: C  178 LYS cc_start: 0.6644 (tptt) cc_final: 0.6308 (mppt)
REVERT: C  190 ASN cc_start: 0.8781 (m-40) cc_final: 0.7877 (m110)
REVERT: C  282 MET cc_start: 0.8804 (tmm) cc_final: 0.8218 (tmm)
REVERT: C  309 CYS cc_start: 0.7986 (t) cc_final: 0.7538 (t)
REVERT: C  325 TYR cc_start: 0.8327 (t80) cc_final: 0.7954 (t80)
REVERT: C  395 CYS cc_start: 0.8450 (m) cc_final: 0.8198 (m)
REVERT: C  439 LEU cc_start: 0.9454 (tp) cc_final: 0.9240 (tp)
REVERT: C  473 GLU cc_start: 0.8994 (tt0) cc_final: 0.8442 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.0730
  time to fit residues: 20.2087
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  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 119 optimal weight:    5.9990
   chunk 75 optimal weight:   20.0000
   chunk 87 optimal weight:    5.9990
   chunk 127 optimal weight:    7.9990
   chunk 22 optimal weight:    0.7980
   chunk 94 optimal weight:   30.0000
   chunk 45 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    2.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 407 GLN
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.075861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.060216 restraints weight = 42008.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.061190 restraints weight = 27452.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.061762 restraints weight = 21025.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.062187 restraints weight = 18099.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.062358 restraints weight = 16521.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.4092

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= 0.140
  Angle     :  0.694   7.903  13344  Z= 0.330
  Chirality :  0.040   0.172   1668
  Planarity :  0.004   0.032   1656
  Dihedral  :  4.120  17.066   1365
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.24), residues: 1278
  helix:  0.57 (0.17), residues: 960
  sheet:  None (None), residues: 0
  loop : -2.51 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 217 
 TYR   0.025   0.002   TYR A 276 
 PHE   0.016   0.001   PHE B  91 
 TRP   0.023   0.001   TRP C 461 
 HIS   0.005   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9798)
  covalent geometry    : angle       0.69436 (13344)
  hydrogen bonds       : bond        0.03510 (  651)
  hydrogen bonds       : angle       4.06675 ( 1944)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1377.26 seconds
wall clock time: 24 minutes 34.07 seconds (1474.07 seconds total)