Starting phenix.real_space_refine
on Thu Feb 13 23:18:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6rvy_10018/02_2025/6rvy_10018.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6rvy_10018/02_2025/6rvy_10018.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6rvy_10018/02_2025/6rvy_10018.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6rvy_10018/02_2025/6rvy_10018.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6rvy_10018/02_2025/6rvy_10018.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6rvy_10018/02_2025/6rvy_10018.cif"
  }
  resolution = 4.13
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      45      5.16       5
     C    6300      2.51       5
     N    1602      2.21       5
     O    1680      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9627
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3209
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3209
          Classifications: {'peptide': 430}
          Link IDs: {'PTRANS': 16, 'TRANS': 413}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 5.16, per 1000 atoms: 0.54
  Number of scatterers: 9627
  At special positions: 0
  Unit cell: (119.416, 122.452, 85.008, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      45     16.00
     O    1680      8.00
     N    1602      7.00
     C    6300      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.45
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 3 sheets defined
      78.6% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 51
      removed outlier: 3.831A  pdb=" N   CYS A  48 " --> pdb=" O   GLN A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 74
      removed outlier: 3.701A  pdb=" N   ALA A  64 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA A  67 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 90
    Processing helix  chain 'A' and resid 90 through 117
      removed outlier: 3.782A  pdb=" N   GLU A  94 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   MET A 102 " --> pdb=" O   ARG A  98 " (cutoff:3.500A)
      Proline residue:  A 106  - end of helix
    Processing helix  chain 'A' and resid 125 through 154
      removed outlier: 4.171A  pdb=" N   ALA A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 192
    Processing helix  chain 'A' and resid 197 through 200
    Processing helix  chain 'A' and resid 230 through 249
      removed outlier: 3.935A  pdb=" N   VAL A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   PHE A 237 " --> pdb=" O   GLY A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 293
      removed outlier: 3.596A  pdb=" N   SER A 261 " --> pdb=" O   ARG A 257 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU A 264 " --> pdb=" O   ASN A 260 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   VAL A 268 " --> pdb=" O   GLU A 264 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   LEU A 269 " --> pdb=" O   ALA A 265 " (cutoff:3.500A)
      Proline residue:  A 278  - end of helix
      removed outlier: 3.513A  pdb=" N   GLU A 293 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 327
      removed outlier: 4.453A  pdb=" N   ALA A 300 " --> pdb=" O   GLY A 296 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   LEU A 321 " --> pdb=" O   GLY A 317 " (cutoff:3.500A)
      Proline residue:  A 322  - end of helix
    Processing helix  chain 'A' and resid 332 through 340
      removed outlier: 3.659A  pdb=" N   PHE A 336 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 351
      removed outlier: 3.852A  pdb=" N   LEU A 344 " --> pdb=" O   ILE A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 367
      removed outlier: 3.602A  pdb=" N   GLU A 365 " --> pdb=" O   MET A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 386
      removed outlier: 4.175A  pdb=" N   LEU A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      Proline residue:  A 380  - end of helix
      removed outlier: 3.631A  pdb=" N   ALA A 383 " --> pdb=" O   LEU A 379 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   THR A 384 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 406
      removed outlier: 3.606A  pdb=" N   VAL A 399 " --> pdb=" O   CYS A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 424
      removed outlier: 3.731A  pdb=" N   THR A 420 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ALA A 421 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 445
      removed outlier: 3.636A  pdb=" N   LEU A 437 " --> pdb=" O   ALA A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 451
      No H-bonds generated for 'chain 'A' and resid 449 through 451'
    Processing helix  chain 'A' and resid 452 through 459
      removed outlier: 3.861A  pdb=" N   ILE A 456 " --> pdb=" O   HIS A 452 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 480
      removed outlier: 3.734A  pdb=" N   VAL A 463 " --> pdb=" O   VAL A 459 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   SER A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   VAL A 469 " --> pdb=" O   ARG A 465 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LEU A 470 " --> pdb=" O   SER A 466 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ASN A 471 " --> pdb=" O   ARG A 467 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL A 472 " --> pdb=" O   THR A 468 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ASP A 475 " --> pdb=" O   ASN A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 488
      removed outlier: 3.703A  pdb=" N   ASP A 487 " --> pdb=" O   GLN A 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 51
      removed outlier: 3.830A  pdb=" N   CYS B  48 " --> pdb=" O   GLN B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 74
      removed outlier: 3.701A  pdb=" N   ALA B  64 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA B  67 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 90
    Processing helix  chain 'B' and resid 90 through 117
      removed outlier: 3.783A  pdb=" N   GLU B  94 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   MET B 102 " --> pdb=" O   ARG B  98 " (cutoff:3.500A)
      Proline residue:  B 106  - end of helix
    Processing helix  chain 'B' and resid 125 through 154
      removed outlier: 4.171A  pdb=" N   ALA B 131 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 192
    Processing helix  chain 'B' and resid 197 through 200
    Processing helix  chain 'B' and resid 230 through 249
      removed outlier: 3.934A  pdb=" N   VAL B 236 " --> pdb=" O   LEU B 232 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   PHE B 237 " --> pdb=" O   GLY B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 293
      removed outlier: 3.596A  pdb=" N   SER B 261 " --> pdb=" O   ARG B 257 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU B 264 " --> pdb=" O   ASN B 260 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   VAL B 268 " --> pdb=" O   GLU B 264 " (cutoff:3.500A)
      removed outlier: 4.890A  pdb=" N   LEU B 269 " --> pdb=" O   ALA B 265 " (cutoff:3.500A)
      Proline residue:  B 278  - end of helix
      removed outlier: 3.513A  pdb=" N   GLU B 293 " --> pdb=" O   ILE B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 327
      removed outlier: 4.453A  pdb=" N   ALA B 300 " --> pdb=" O   GLY B 296 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   LEU B 321 " --> pdb=" O   GLY B 317 " (cutoff:3.500A)
      Proline residue:  B 322  - end of helix
    Processing helix  chain 'B' and resid 332 through 340
      removed outlier: 3.660A  pdb=" N   PHE B 336 " --> pdb=" O   ASN B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 351
      removed outlier: 3.852A  pdb=" N   LEU B 344 " --> pdb=" O   ILE B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 367
      removed outlier: 3.602A  pdb=" N   GLU B 365 " --> pdb=" O   MET B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 386
      removed outlier: 4.175A  pdb=" N   LEU B 379 " --> pdb=" O   SER B 375 " (cutoff:3.500A)
      Proline residue:  B 380  - end of helix
      removed outlier: 3.630A  pdb=" N   ALA B 383 " --> pdb=" O   LEU B 379 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   THR B 384 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 406
      removed outlier: 3.605A  pdb=" N   VAL B 399 " --> pdb=" O   CYS B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 424
      removed outlier: 3.731A  pdb=" N   THR B 420 " --> pdb=" O   THR B 416 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ALA B 421 " --> pdb=" O   ILE B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 445
      removed outlier: 3.636A  pdb=" N   LEU B 437 " --> pdb=" O   ALA B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 451
      No H-bonds generated for 'chain 'B' and resid 449 through 451'
    Processing helix  chain 'B' and resid 452 through 459
      removed outlier: 3.862A  pdb=" N   ILE B 456 " --> pdb=" O   HIS B 452 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL B 459 " --> pdb=" O   LEU B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 480
      removed outlier: 3.734A  pdb=" N   VAL B 463 " --> pdb=" O   VAL B 459 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   SER B 466 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   VAL B 469 " --> pdb=" O   ARG B 465 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LEU B 470 " --> pdb=" O   SER B 466 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ASN B 471 " --> pdb=" O   ARG B 467 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL B 472 " --> pdb=" O   THR B 468 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ASP B 475 " --> pdb=" O   ASN B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 488
      removed outlier: 3.704A  pdb=" N   ASP B 487 " --> pdb=" O   GLN B 483 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 51
      removed outlier: 3.830A  pdb=" N   CYS C  48 " --> pdb=" O   GLN C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 74
      removed outlier: 3.700A  pdb=" N   ALA C  64 " --> pdb=" O   VAL C  60 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA C  67 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 90
    Processing helix  chain 'C' and resid 90 through 117
      removed outlier: 3.782A  pdb=" N   GLU C  94 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   MET C 102 " --> pdb=" O   ARG C  98 " (cutoff:3.500A)
      Proline residue:  C 106  - end of helix
    Processing helix  chain 'C' and resid 125 through 154
      removed outlier: 4.171A  pdb=" N   ALA C 131 " --> pdb=" O   LEU C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 192
    Processing helix  chain 'C' and resid 197 through 200
    Processing helix  chain 'C' and resid 230 through 249
      removed outlier: 3.934A  pdb=" N   VAL C 236 " --> pdb=" O   LEU C 232 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   PHE C 237 " --> pdb=" O   GLY C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 293
      removed outlier: 3.597A  pdb=" N   SER C 261 " --> pdb=" O   ARG C 257 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU C 264 " --> pdb=" O   ASN C 260 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL C 268 " --> pdb=" O   GLU C 264 " (cutoff:3.500A)
      removed outlier: 4.890A  pdb=" N   LEU C 269 " --> pdb=" O   ALA C 265 " (cutoff:3.500A)
      Proline residue:  C 278  - end of helix
      removed outlier: 3.512A  pdb=" N   GLU C 293 " --> pdb=" O   ILE C 289 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 327
      removed outlier: 4.452A  pdb=" N   ALA C 300 " --> pdb=" O   GLY C 296 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   LEU C 321 " --> pdb=" O   GLY C 317 " (cutoff:3.500A)
      Proline residue:  C 322  - end of helix
    Processing helix  chain 'C' and resid 332 through 340
      removed outlier: 3.660A  pdb=" N   PHE C 336 " --> pdb=" O   ASN C 332 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 351
      removed outlier: 3.853A  pdb=" N   LEU C 344 " --> pdb=" O   ILE C 340 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 356 through 367
      removed outlier: 3.602A  pdb=" N   GLU C 365 " --> pdb=" O   MET C 361 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 373 through 386
      removed outlier: 4.175A  pdb=" N   LEU C 379 " --> pdb=" O   SER C 375 " (cutoff:3.500A)
      Proline residue:  C 380  - end of helix
      removed outlier: 3.631A  pdb=" N   ALA C 383 " --> pdb=" O   LEU C 379 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   THR C 384 " --> pdb=" O   PRO C 380 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 387 through 406
      removed outlier: 3.605A  pdb=" N   VAL C 399 " --> pdb=" O   CYS C 395 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 410 through 424
      removed outlier: 3.731A  pdb=" N   THR C 420 " --> pdb=" O   THR C 416 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ALA C 421 " --> pdb=" O   ILE C 417 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 433 through 445
      removed outlier: 3.636A  pdb=" N   LEU C 437 " --> pdb=" O   ALA C 433 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 449 through 451
      No H-bonds generated for 'chain 'C' and resid 449 through 451'
    Processing helix  chain 'C' and resid 452 through 459
      removed outlier: 3.862A  pdb=" N   ILE C 456 " --> pdb=" O   HIS C 452 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL C 459 " --> pdb=" O   LEU C 455 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 459 through 480
      removed outlier: 3.735A  pdb=" N   VAL C 463 " --> pdb=" O   VAL C 459 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   SER C 466 " --> pdb=" O   LEU C 462 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   VAL C 469 " --> pdb=" O   ARG C 465 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LEU C 470 " --> pdb=" O   SER C 466 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ASN C 471 " --> pdb=" O   ARG C 467 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL C 472 " --> pdb=" O   THR C 468 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ASP C 475 " --> pdb=" O   ASN C 471 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 483 through 488
      removed outlier: 3.704A  pdb=" N   ASP C 487 " --> pdb=" O   GLN C 483 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 210
    Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 210
    Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 210

    651 hydrogen bonds defined for protein.
    1944 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.94

  Time building geometry restraints manager: 2.84 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.320
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   9798  Z= 0.387
  Angle     :  1.030  10.778  13344  Z= 0.538
  Chirality :  0.056   0.252   1668
  Planarity :  0.008   0.066   1656
  Dihedral  : 14.692  75.172   3432
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 13.04 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.00 (0.17), residues: 1278
  helix: -3.03 (0.11), residues: 963
  sheet: -3.60 (0.57), residues: 42
  loop : -3.25 (0.34), residues: 273

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

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

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 200
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 PHE cc_start: 0.8581 (p90) cc_final: 0.8375 (p90)
REVERT: A  279 VAL cc_start: 0.9209 (m) cc_final: 0.8901 (p)
REVERT: A  297 LEU cc_start: 0.8964 (tp) cc_final: 0.8706 (mp)
REVERT: A  325 TYR cc_start: 0.8860 (t80) cc_final: 0.8634 (t80)
REVERT: A  394 GLN cc_start: 0.8426 (mt0) cc_final: 0.8080 (mp10)
REVERT: A  439 LEU cc_start: 0.9410 (tp) cc_final: 0.9070 (tp)
REVERT: A  461 TRP cc_start: 0.8008 (p-90) cc_final: 0.7579 (p-90)
REVERT: A  473 GLU cc_start: 0.8720 (tt0) cc_final: 0.8270 (tt0)
REVERT: B   89 PHE cc_start: 0.7543 (t80) cc_final: 0.7338 (t80)
REVERT: B  178 LYS cc_start: 0.6864 (tptt) cc_final: 0.6525 (mppt)
REVERT: B  201 PHE cc_start: 0.8381 (p90) cc_final: 0.7916 (p90)
REVERT: B  279 VAL cc_start: 0.9119 (m) cc_final: 0.8919 (p)
REVERT: B  297 LEU cc_start: 0.8982 (tp) cc_final: 0.8738 (tp)
REVERT: B  305 TYR cc_start: 0.8954 (t80) cc_final: 0.8681 (t80)
REVERT: B  313 HIS cc_start: 0.8100 (m90) cc_final: 0.7794 (m90)
REVERT: B  325 TYR cc_start: 0.8723 (t80) cc_final: 0.8141 (t80)
REVERT: B  379 LEU cc_start: 0.9227 (tp) cc_final: 0.9017 (tp)
REVERT: B  439 LEU cc_start: 0.9379 (tp) cc_final: 0.9117 (tp)
REVERT: B  461 TRP cc_start: 0.8141 (p-90) cc_final: 0.7075 (p-90)
REVERT: B  473 GLU cc_start: 0.8796 (tt0) cc_final: 0.8408 (tt0)
REVERT: C   89 PHE cc_start: 0.7841 (t80) cc_final: 0.7449 (t80)
REVERT: C  100 LEU cc_start: 0.9130 (mt) cc_final: 0.8926 (mt)
REVERT: C  178 LYS cc_start: 0.6830 (tptt) cc_final: 0.6375 (mppt)
REVERT: C  201 PHE cc_start: 0.8345 (p90) cc_final: 0.7869 (p90)
REVERT: C  297 LEU cc_start: 0.8847 (tp) cc_final: 0.8584 (mp)
REVERT: C  313 HIS cc_start: 0.8158 (m90) cc_final: 0.7843 (m90)
REVERT: C  325 TYR cc_start: 0.8626 (t80) cc_final: 0.8330 (t80)
REVERT: C  395 CYS cc_start: 0.8202 (m) cc_final: 0.7891 (m)
REVERT: C  461 TRP cc_start: 0.8180 (p-90) cc_final: 0.6951 (p-90)
REVERT: C  473 GLU cc_start: 0.8812 (tt0) cc_final: 0.8400 (tt0)
  outliers start: 5
  outliers final: 0
  residues processed: 203
  average time/residue: 0.2082
  time to fit residues: 59.5175
Evaluate side-chains
  141 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 97 optimal weight:   20.0000
   chunk 54 optimal weight:   20.0000
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 101 optimal weight:    7.9990
   chunk 39 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   chunk 75 optimal weight:    0.0770
   chunk 117 optimal weight:    6.9990
   overall best weight:    2.0142

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.073294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.058304 restraints weight = 40986.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.059337 restraints weight = 26221.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.059889 restraints weight = 19657.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9798  Z= 0.195
  Angle     :  0.682   8.130  13344  Z= 0.342
  Chirality :  0.039   0.171   1668
  Planarity :  0.005   0.043   1656
  Dihedral  :  4.971  18.348   1365
  Min Nonbonded Distance : 2.572

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

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.21), residues: 1278
  helix: -1.19 (0.15), residues: 990
  sheet: -2.97 (0.70), residues: 42
  loop : -3.16 (0.37), residues: 246

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

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

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9377 (m) cc_final: 0.9024 (p)
REVERT: A  282 MET cc_start: 0.8888 (tmm) cc_final: 0.8387 (tmm)
REVERT: A  297 LEU cc_start: 0.8962 (tp) cc_final: 0.8656 (mp)
REVERT: A  325 TYR cc_start: 0.8746 (t80) cc_final: 0.8411 (t80)
REVERT: A  394 GLN cc_start: 0.8711 (mt0) cc_final: 0.8272 (mp10)
REVERT: A  410 ASP cc_start: 0.8037 (t0) cc_final: 0.7773 (m-30)
REVERT: A  439 LEU cc_start: 0.9566 (tp) cc_final: 0.9204 (tt)
REVERT: A  461 TRP cc_start: 0.8442 (p-90) cc_final: 0.7706 (p-90)
REVERT: B   89 PHE cc_start: 0.7621 (t80) cc_final: 0.7406 (t80)
REVERT: B   91 PHE cc_start: 0.8419 (t80) cc_final: 0.7968 (t80)
REVERT: B  279 VAL cc_start: 0.9344 (m) cc_final: 0.9114 (p)
REVERT: B  282 MET cc_start: 0.8881 (tmm) cc_final: 0.8481 (tmm)
REVERT: B  297 LEU cc_start: 0.8868 (tp) cc_final: 0.8582 (mp)
REVERT: B  325 TYR cc_start: 0.8666 (t80) cc_final: 0.8093 (t80)
REVERT: B  439 LEU cc_start: 0.9563 (tp) cc_final: 0.9316 (tp)
REVERT: B  461 TRP cc_start: 0.8494 (p-90) cc_final: 0.7492 (p-90)
REVERT: B  473 GLU cc_start: 0.9038 (tt0) cc_final: 0.8577 (tt0)
REVERT: C   89 PHE cc_start: 0.7945 (t80) cc_final: 0.7433 (t80)
REVERT: C  178 LYS cc_start: 0.6720 (tptt) cc_final: 0.6357 (mppt)
REVERT: C  274 MET cc_start: 0.7736 (mtt) cc_final: 0.7504 (mtt)
REVERT: C  282 MET cc_start: 0.8876 (tmm) cc_final: 0.8352 (tmm)
REVERT: C  297 LEU cc_start: 0.8766 (tp) cc_final: 0.8472 (mp)
REVERT: C  313 HIS cc_start: 0.8378 (m90) cc_final: 0.8129 (m90)
REVERT: C  325 TYR cc_start: 0.8687 (t80) cc_final: 0.8405 (t80)
REVERT: C  395 CYS cc_start: 0.8307 (m) cc_final: 0.7986 (m)
REVERT: C  410 ASP cc_start: 0.7987 (t0) cc_final: 0.7748 (m-30)
REVERT: C  439 LEU cc_start: 0.9566 (tp) cc_final: 0.9241 (tp)
REVERT: C  473 GLU cc_start: 0.8983 (tt0) cc_final: 0.8577 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.1873
  time to fit residues: 55.5297
Evaluate side-chains
  143 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 117 optimal weight:    9.9990
   chunk 109 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   chunk 76 optimal weight:    7.9990
   chunk 116 optimal weight:   10.0000
   chunk 115 optimal weight:    0.0060
   chunk 111 optimal weight:   20.0000
   chunk 113 optimal weight:   20.0000
   chunk 93 optimal weight:    4.9990
   chunk 120 optimal weight:    6.9990
   overall best weight:    4.0004

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.071826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.056677 restraints weight = 42400.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.057694 restraints weight = 27146.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.058243 restraints weight = 20310.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9798  Z= 0.266
  Angle     :  0.707   8.008  13344  Z= 0.350
  Chirality :  0.041   0.170   1668
  Planarity :  0.005   0.037   1656
  Dihedral  :  4.716  16.410   1365
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.23), residues: 1278
  helix: -0.53 (0.16), residues: 996
  sheet: -2.65 (0.75), residues: 42
  loop : -2.75 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 461 
 HIS   0.005   0.001   HIS B 316 
 PHE   0.012   0.001   PHE C  91 
 TYR   0.017   0.002   TYR C 305 
 ARG   0.004   0.000   ARG B  85 

*********************** 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
  193 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9412 (m) cc_final: 0.9062 (p)
REVERT: A  282 MET cc_start: 0.8859 (tmm) cc_final: 0.8455 (tmm)
REVERT: A  297 LEU cc_start: 0.8914 (tp) cc_final: 0.8534 (mp)
REVERT: A  325 TYR cc_start: 0.8564 (t80) cc_final: 0.8177 (t80)
REVERT: A  394 GLN cc_start: 0.8615 (mt0) cc_final: 0.8152 (mp10)
REVERT: A  410 ASP cc_start: 0.8121 (t0) cc_final: 0.7802 (m-30)
REVERT: A  461 TRP cc_start: 0.8457 (p-90) cc_final: 0.7660 (p-90)
REVERT: B   91 PHE cc_start: 0.8441 (t80) cc_final: 0.7983 (t80)
REVERT: B  201 PHE cc_start: 0.8450 (p90) cc_final: 0.8179 (p90)
REVERT: B  279 VAL cc_start: 0.9323 (m) cc_final: 0.9106 (p)
REVERT: B  282 MET cc_start: 0.8732 (tmm) cc_final: 0.8464 (tmm)
REVERT: B  297 LEU cc_start: 0.8897 (tp) cc_final: 0.8610 (tp)
REVERT: B  313 HIS cc_start: 0.8497 (m90) cc_final: 0.8224 (m90)
REVERT: B  325 TYR cc_start: 0.8742 (t80) cc_final: 0.8230 (t80)
REVERT: B  461 TRP cc_start: 0.8509 (p-90) cc_final: 0.7489 (p-90)
REVERT: B  473 GLU cc_start: 0.9069 (tt0) cc_final: 0.8549 (tt0)
REVERT: C   89 PHE cc_start: 0.8007 (t80) cc_final: 0.7601 (t80)
REVERT: C  178 LYS cc_start: 0.6824 (tptt) cc_final: 0.6415 (mppt)
REVERT: C  201 PHE cc_start: 0.8333 (p90) cc_final: 0.7971 (p90)
REVERT: C  208 TYR cc_start: 0.7525 (m-80) cc_final: 0.7288 (m-80)
REVERT: C  274 MET cc_start: 0.7706 (mtt) cc_final: 0.7496 (mtt)
REVERT: C  282 MET cc_start: 0.8769 (tmm) cc_final: 0.8347 (tmm)
REVERT: C  313 HIS cc_start: 0.8450 (m90) cc_final: 0.8192 (m90)
REVERT: C  325 TYR cc_start: 0.8657 (t80) cc_final: 0.8307 (t80)
REVERT: C  395 CYS cc_start: 0.8206 (m) cc_final: 0.7947 (m)
REVERT: C  439 LEU cc_start: 0.9473 (tp) cc_final: 0.9178 (tt)
REVERT: C  473 GLU cc_start: 0.8954 (tt0) cc_final: 0.8471 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1795
  time to fit residues: 51.3558
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  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 59 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   chunk 99 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 83 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0570
   chunk 93 optimal weight:    7.9990
   overall best weight:    1.8104

-------------------------------------------------------------------------------
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 = 0.3326 r_free = 0.3326 target = 0.073105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.058169 restraints weight = 40979.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.059202 restraints weight = 25824.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.059834 restraints weight = 19381.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9798  Z= 0.183
  Angle     :  0.658   7.572  13344  Z= 0.321
  Chirality :  0.040   0.169   1668
  Planarity :  0.004   0.035   1656
  Dihedral  :  4.461  15.891   1365
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 9.86
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.24), residues: 1278
  helix: -0.23 (0.17), residues: 996
  sheet: -2.21 (0.82), residues: 42
  loop : -2.58 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 461 
 HIS   0.004   0.001   HIS B 316 
 PHE   0.012   0.001   PHE A 237 
 TYR   0.020   0.002   TYR C 276 
 ARG   0.002   0.000   ARG B  98 

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

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9367 (m) cc_final: 0.9020 (p)
REVERT: A  282 MET cc_start: 0.8826 (tmm) cc_final: 0.8378 (tmm)
REVERT: A  297 LEU cc_start: 0.8951 (tp) cc_final: 0.8541 (mp)
REVERT: A  313 HIS cc_start: 0.8182 (m90) cc_final: 0.7721 (m90)
REVERT: A  316 HIS cc_start: 0.8713 (t-90) cc_final: 0.8483 (t-90)
REVERT: A  325 TYR cc_start: 0.8518 (t80) cc_final: 0.8170 (t80)
REVERT: A  379 LEU cc_start: 0.8998 (tp) cc_final: 0.8457 (tp)
REVERT: A  394 GLN cc_start: 0.8477 (mt0) cc_final: 0.8189 (mp10)
REVERT: A  439 LEU cc_start: 0.9498 (tp) cc_final: 0.9220 (tp)
REVERT: A  461 TRP cc_start: 0.8489 (p-90) cc_final: 0.7680 (p-90)
REVERT: B   91 PHE cc_start: 0.8464 (t80) cc_final: 0.7952 (t80)
REVERT: B  201 PHE cc_start: 0.8537 (p90) cc_final: 0.8031 (p90)
REVERT: B  279 VAL cc_start: 0.9378 (m) cc_final: 0.9119 (p)
REVERT: B  282 MET cc_start: 0.8693 (tmm) cc_final: 0.8369 (tmm)
REVERT: B  297 LEU cc_start: 0.8874 (tp) cc_final: 0.8568 (tp)
REVERT: B  325 TYR cc_start: 0.8644 (t80) cc_final: 0.8159 (t80)
REVERT: B  395 CYS cc_start: 0.8458 (m) cc_final: 0.8138 (m)
REVERT: B  439 LEU cc_start: 0.9569 (tp) cc_final: 0.9290 (tt)
REVERT: B  473 GLU cc_start: 0.9037 (tt0) cc_final: 0.8520 (tt0)
REVERT: C   89 PHE cc_start: 0.8022 (t80) cc_final: 0.7604 (t80)
REVERT: C  178 LYS cc_start: 0.6854 (tptt) cc_final: 0.6412 (mppt)
REVERT: C  282 MET cc_start: 0.8798 (tmm) cc_final: 0.8374 (tmm)
REVERT: C  325 TYR cc_start: 0.8618 (t80) cc_final: 0.8294 (t80)
REVERT: C  395 CYS cc_start: 0.8319 (m) cc_final: 0.8088 (m)
REVERT: C  439 LEU cc_start: 0.9470 (tp) cc_final: 0.9195 (tt)
REVERT: C  473 GLU cc_start: 0.9029 (tt0) cc_final: 0.8540 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.1997
  time to fit residues: 57.8205
Evaluate side-chains
  151 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 51 optimal weight:   30.0000
   chunk 89 optimal weight:    6.9990
   chunk 43 optimal weight:   30.0000
   chunk 18 optimal weight:    6.9990
   chunk 69 optimal weight:    7.9990
   chunk 52 optimal weight:    9.9990
   chunk 108 optimal weight:    0.8980
   chunk 23 optimal weight:    9.9990
   chunk 119 optimal weight:    0.6980
   chunk 7 optimal weight:    4.9990
   chunk 82 optimal weight:    0.0970
   overall best weight:    2.7382

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.072194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.057022 restraints weight = 41453.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.057930 restraints weight = 26678.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.058572 restraints weight = 20504.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.3083

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= 0.215
  Angle     :  0.673   7.534  13344  Z= 0.329
  Chirality :  0.040   0.172   1668
  Planarity :  0.004   0.033   1656
  Dihedral  :  4.393  17.664   1365
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.24), residues: 1278
  helix:  0.05 (0.17), residues: 978
  sheet:  None (None), residues: 0
  loop : -2.71 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 461 
 HIS   0.005   0.001   HIS C 452 
 PHE   0.011   0.001   PHE A 299 
 TYR   0.021   0.002   TYR A 305 
 ARG   0.002   0.000   ARG A 376 

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

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9437 (m) cc_final: 0.9153 (p)
REVERT: A  309 CYS cc_start: 0.8250 (t) cc_final: 0.7675 (t)
REVERT: A  313 HIS cc_start: 0.8245 (m90) cc_final: 0.7770 (m90)
REVERT: A  325 TYR cc_start: 0.8525 (t80) cc_final: 0.8163 (t80)
REVERT: A  394 GLN cc_start: 0.8729 (mt0) cc_final: 0.8272 (mp10)
REVERT: A  439 LEU cc_start: 0.9536 (tp) cc_final: 0.9275 (tp)
REVERT: A  461 TRP cc_start: 0.8505 (p-90) cc_final: 0.7626 (p-90)
REVERT: B   91 PHE cc_start: 0.8448 (t80) cc_final: 0.8000 (t80)
REVERT: B  201 PHE cc_start: 0.8530 (p90) cc_final: 0.8090 (p90)
REVERT: B  279 VAL cc_start: 0.9387 (m) cc_final: 0.9160 (p)
REVERT: B  297 LEU cc_start: 0.8898 (tp) cc_final: 0.8559 (tp)
REVERT: B  313 HIS cc_start: 0.8421 (m90) cc_final: 0.8177 (m90)
REVERT: B  325 TYR cc_start: 0.8652 (t80) cc_final: 0.8190 (t80)
REVERT: B  379 LEU cc_start: 0.9009 (tp) cc_final: 0.8494 (tp)
REVERT: B  473 GLU cc_start: 0.9041 (tt0) cc_final: 0.8452 (tt0)
REVERT: C   89 PHE cc_start: 0.8014 (t80) cc_final: 0.7578 (t80)
REVERT: C  178 LYS cc_start: 0.6706 (tptt) cc_final: 0.6400 (mppt)
REVERT: C  201 PHE cc_start: 0.8441 (p90) cc_final: 0.7911 (p90)
REVERT: C  282 MET cc_start: 0.8819 (tmm) cc_final: 0.8455 (tmm)
REVERT: C  316 HIS cc_start: 0.8803 (t-90) cc_final: 0.8495 (t-90)
REVERT: C  325 TYR cc_start: 0.8607 (t80) cc_final: 0.8261 (t80)
REVERT: C  473 GLU cc_start: 0.9057 (tt0) cc_final: 0.8513 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1776
  time to fit residues: 47.3692
Evaluate side-chains
  143 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 66 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 128 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 108 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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 = 0.3317 r_free = 0.3317 target = 0.072731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.057661 restraints weight = 41554.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.058705 restraints weight = 26578.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.059256 restraints weight = 19999.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9798  Z= 0.218
  Angle     :  0.691   8.687  13344  Z= 0.334
  Chirality :  0.040   0.173   1668
  Planarity :  0.004   0.032   1656
  Dihedral  :  4.368  16.004   1365
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.24), residues: 1278
  helix:  0.10 (0.17), residues: 978
  sheet: -1.94 (0.85), residues: 42
  loop : -2.33 (0.41), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 461 
 HIS   0.005   0.001   HIS B 316 
 PHE   0.011   0.001   PHE C  91 
 TYR   0.022   0.002   TYR A 305 
 ARG   0.004   0.000   ARG B 376 

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

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9445 (m) cc_final: 0.9133 (p)
REVERT: A  282 MET cc_start: 0.8898 (tmm) cc_final: 0.8192 (tmm)
REVERT: A  309 CYS cc_start: 0.8058 (t) cc_final: 0.7417 (t)
REVERT: A  313 HIS cc_start: 0.8215 (m90) cc_final: 0.7761 (m90)
REVERT: A  316 HIS cc_start: 0.8658 (t-90) cc_final: 0.8390 (t-90)
REVERT: A  325 TYR cc_start: 0.8464 (t80) cc_final: 0.8160 (t80)
REVERT: A  394 GLN cc_start: 0.8643 (mt0) cc_final: 0.8164 (mp10)
REVERT: A  439 LEU cc_start: 0.9533 (tp) cc_final: 0.9244 (tp)
REVERT: A  461 TRP cc_start: 0.8502 (p-90) cc_final: 0.7705 (p-90)
REVERT: B   91 PHE cc_start: 0.8501 (t80) cc_final: 0.8079 (t80)
REVERT: B  201 PHE cc_start: 0.8520 (p90) cc_final: 0.8089 (p90)
REVERT: B  279 VAL cc_start: 0.9364 (m) cc_final: 0.9138 (p)
REVERT: B  282 MET cc_start: 0.8881 (tmm) cc_final: 0.8521 (tmm)
REVERT: B  313 HIS cc_start: 0.8377 (m90) cc_final: 0.7812 (m90)
REVERT: B  325 TYR cc_start: 0.8596 (t80) cc_final: 0.8108 (t80)
REVERT: B  473 GLU cc_start: 0.9010 (tt0) cc_final: 0.8427 (tt0)
REVERT: C   91 PHE cc_start: 0.8562 (t80) cc_final: 0.8015 (t80)
REVERT: C  178 LYS cc_start: 0.6713 (tptt) cc_final: 0.6391 (mppt)
REVERT: C  201 PHE cc_start: 0.8494 (p90) cc_final: 0.8021 (p90)
REVERT: C  282 MET cc_start: 0.8784 (tmm) cc_final: 0.8465 (tmm)
REVERT: C  325 TYR cc_start: 0.8564 (t80) cc_final: 0.8249 (t80)
REVERT: C  395 CYS cc_start: 0.8463 (m) cc_final: 0.8205 (m)
REVERT: C  473 GLU cc_start: 0.9041 (tt0) cc_final: 0.8474 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1702
  time to fit residues: 46.4419
Evaluate side-chains
  141 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 120 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 79 optimal weight:    9.9990
   chunk 86 optimal weight:   30.0000
   chunk 118 optimal weight:    8.9990
   chunk 48 optimal weight:    3.9990
   chunk 37 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.3305 r_free = 0.3305 target = 0.073177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.057697 restraints weight = 41569.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.058662 restraints weight = 26748.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.059325 restraints weight = 20355.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9798  Z= 0.236
  Angle     :  0.704   7.920  13344  Z= 0.338
  Chirality :  0.040   0.171   1668
  Planarity :  0.004   0.032   1656
  Dihedral  :  4.368  15.683   1365
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.24), residues: 1278
  helix:  0.19 (0.17), residues: 981
  sheet:  None (None), residues: 0
  loop : -2.78 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C 461 
 HIS   0.004   0.001   HIS C 316 
 PHE   0.022   0.001   PHE C  89 
 TYR   0.021   0.002   TYR B 305 
 ARG   0.003   0.000   ARG B 376 

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

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9462 (m) cc_final: 0.9130 (p)
REVERT: A  282 MET cc_start: 0.8930 (tmm) cc_final: 0.8229 (tmm)
REVERT: A  309 CYS cc_start: 0.8095 (t) cc_final: 0.7419 (t)
REVERT: A  313 HIS cc_start: 0.8252 (m90) cc_final: 0.7760 (m90)
REVERT: A  325 TYR cc_start: 0.8525 (t80) cc_final: 0.8221 (t80)
REVERT: A  379 LEU cc_start: 0.8986 (tp) cc_final: 0.8781 (tp)
REVERT: A  394 GLN cc_start: 0.8650 (mt0) cc_final: 0.8197 (mp10)
REVERT: A  439 LEU cc_start: 0.9543 (tp) cc_final: 0.9262 (tp)
REVERT: A  461 TRP cc_start: 0.8572 (p-90) cc_final: 0.7749 (p-90)
REVERT: B  201 PHE cc_start: 0.8524 (p90) cc_final: 0.8119 (p90)
REVERT: B  279 VAL cc_start: 0.9390 (m) cc_final: 0.9162 (p)
REVERT: B  282 MET cc_start: 0.8915 (tmm) cc_final: 0.8495 (tmm)
REVERT: B  309 CYS cc_start: 0.8363 (t) cc_final: 0.7763 (t)
REVERT: B  313 HIS cc_start: 0.8367 (m90) cc_final: 0.7768 (m90)
REVERT: B  325 TYR cc_start: 0.8696 (t80) cc_final: 0.8189 (t80)
REVERT: B  439 LEU cc_start: 0.9575 (tp) cc_final: 0.9329 (tt)
REVERT: C   89 PHE cc_start: 0.8119 (t80) cc_final: 0.7630 (t80)
REVERT: C   91 PHE cc_start: 0.8574 (t80) cc_final: 0.8132 (t80)
REVERT: C  178 LYS cc_start: 0.6583 (tptt) cc_final: 0.6343 (mmtm)
REVERT: C  201 PHE cc_start: 0.8475 (p90) cc_final: 0.8074 (p90)
REVERT: C  282 MET cc_start: 0.8846 (tmm) cc_final: 0.8542 (tmm)
REVERT: C  325 TYR cc_start: 0.8652 (t80) cc_final: 0.8359 (t80)
REVERT: C  395 CYS cc_start: 0.8465 (m) cc_final: 0.8180 (m)
REVERT: C  439 LEU cc_start: 0.9532 (tp) cc_final: 0.9186 (tt)
REVERT: C  473 GLU cc_start: 0.9049 (tt0) cc_final: 0.8443 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.1855
  time to fit residues: 48.9162
Evaluate side-chains
  142 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 102 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 50 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 12 optimal weight:    9.9990
   chunk 103 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 59 optimal weight:    8.9990
   chunk 54 optimal weight:    6.9990
   chunk 75 optimal weight:    3.9990
   chunk 128 optimal weight:    6.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.074731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.059939 restraints weight = 41537.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.060988 restraints weight = 26188.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.061658 restraints weight = 19471.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.3649

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= 0.166
  Angle     :  0.677   8.187  13344  Z= 0.322
  Chirality :  0.039   0.169   1668
  Planarity :  0.004   0.031   1656
  Dihedral  :  4.210  16.122   1365
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.24), residues: 1278
  helix:  0.40 (0.17), residues: 978
  sheet: -2.18 (0.80), residues: 48
  loop : -2.15 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 461 
 HIS   0.004   0.001   HIS C 452 
 PHE   0.018   0.001   PHE C  89 
 TYR   0.019   0.002   TYR A 305 
 ARG   0.002   0.000   ARG B  98 

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

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9426 (m) cc_final: 0.9081 (p)
REVERT: A  282 MET cc_start: 0.8918 (tmm) cc_final: 0.8266 (tmm)
REVERT: A  309 CYS cc_start: 0.7990 (t) cc_final: 0.7237 (t)
REVERT: A  313 HIS cc_start: 0.7999 (m90) cc_final: 0.7601 (m90)
REVERT: A  325 TYR cc_start: 0.8305 (t80) cc_final: 0.8004 (t80)
REVERT: A  379 LEU cc_start: 0.8897 (tp) cc_final: 0.8621 (tp)
REVERT: A  394 GLN cc_start: 0.8553 (mt0) cc_final: 0.8099 (mp10)
REVERT: A  461 TRP cc_start: 0.8554 (p-90) cc_final: 0.7591 (p-90)
REVERT: B  279 VAL cc_start: 0.9349 (m) cc_final: 0.9138 (p)
REVERT: B  282 MET cc_start: 0.8874 (tmm) cc_final: 0.8483 (tmm)
REVERT: B  309 CYS cc_start: 0.8203 (t) cc_final: 0.7575 (t)
REVERT: B  313 HIS cc_start: 0.8129 (m90) cc_final: 0.7571 (m90)
REVERT: B  325 TYR cc_start: 0.8432 (t80) cc_final: 0.7990 (t80)
REVERT: B  439 LEU cc_start: 0.9527 (tp) cc_final: 0.9293 (tt)
REVERT: B  473 GLU cc_start: 0.8988 (tt0) cc_final: 0.8332 (tt0)
REVERT: C   89 PHE cc_start: 0.8042 (t80) cc_final: 0.7550 (t80)
REVERT: C   91 PHE cc_start: 0.8466 (t80) cc_final: 0.7954 (t80)
REVERT: C  178 LYS cc_start: 0.6700 (tptt) cc_final: 0.6386 (mppt)
REVERT: C  190 ASN cc_start: 0.8750 (m-40) cc_final: 0.7808 (m110)
REVERT: C  282 MET cc_start: 0.8684 (tmm) cc_final: 0.8401 (tmm)
REVERT: C  325 TYR cc_start: 0.8464 (t80) cc_final: 0.8127 (t80)
REVERT: C  395 CYS cc_start: 0.8461 (m) cc_final: 0.8213 (m)
REVERT: C  439 LEU cc_start: 0.9499 (tp) cc_final: 0.9293 (tp)
REVERT: C  473 GLU cc_start: 0.8962 (tt0) cc_final: 0.8376 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 0.1984
  time to fit residues: 58.5963
Evaluate side-chains
  149 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 80 optimal weight:    0.0030
   chunk 63 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 98 optimal weight:    6.9990
   chunk 67 optimal weight:   10.0000
   overall best weight:    0.7592

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.076137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.061234 restraints weight = 41335.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.061932 restraints weight = 26534.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.062125 restraints weight = 20988.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.3963

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= 0.161
  Angle     :  0.689   8.769  13344  Z= 0.324
  Chirality :  0.039   0.168   1668
  Planarity :  0.004   0.031   1656
  Dihedral  :  4.079  15.733   1365
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.24), residues: 1278
  helix:  0.48 (0.17), residues: 981
  sheet: -1.99 (0.80), residues: 48
  loop : -2.41 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 461 
 HIS   0.004   0.001   HIS B 316 
 PHE   0.015   0.001   PHE C  89 
 TYR   0.019   0.002   TYR A 305 
 ARG   0.003   0.000   ARG A  98 

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

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9428 (m) cc_final: 0.9107 (p)
REVERT: A  282 MET cc_start: 0.8887 (tmm) cc_final: 0.8227 (tmm)
REVERT: A  309 CYS cc_start: 0.8092 (t) cc_final: 0.7371 (t)
REVERT: A  313 HIS cc_start: 0.8173 (m90) cc_final: 0.7903 (m-70)
REVERT: A  325 TYR cc_start: 0.8364 (t80) cc_final: 0.8061 (t80)
REVERT: A  394 GLN cc_start: 0.8547 (mt0) cc_final: 0.8090 (mp10)
REVERT: A  461 TRP cc_start: 0.8633 (p-90) cc_final: 0.7651 (p-90)
REVERT: B  190 ASN cc_start: 0.8797 (m-40) cc_final: 0.7840 (m110)
REVERT: B  279 VAL cc_start: 0.9350 (m) cc_final: 0.9148 (p)
REVERT: B  282 MET cc_start: 0.8877 (tmm) cc_final: 0.8483 (tmm)
REVERT: B  309 CYS cc_start: 0.8308 (t) cc_final: 0.7599 (t)
REVERT: B  313 HIS cc_start: 0.8156 (m90) cc_final: 0.7616 (m90)
REVERT: B  325 TYR cc_start: 0.8069 (t80) cc_final: 0.7729 (t80)
REVERT: B  361 MET cc_start: 0.7224 (mmm) cc_final: 0.7010 (tpt)
REVERT: B  376 ARG cc_start: 0.8535 (mpt180) cc_final: 0.8031 (mpt180)
REVERT: B  394 GLN cc_start: 0.8503 (mt0) cc_final: 0.8186 (mt0)
REVERT: B  439 LEU cc_start: 0.9478 (tp) cc_final: 0.9233 (tt)
REVERT: B  473 GLU cc_start: 0.9063 (tt0) cc_final: 0.8384 (tt0)
REVERT: C   91 PHE cc_start: 0.8402 (t80) cc_final: 0.7864 (t80)
REVERT: C  178 LYS cc_start: 0.6571 (tptt) cc_final: 0.6282 (mmtm)
REVERT: C  190 ASN cc_start: 0.8720 (m-40) cc_final: 0.7881 (m110)
REVERT: C  282 MET cc_start: 0.8708 (tmm) cc_final: 0.8437 (tmm)
REVERT: C  325 TYR cc_start: 0.8496 (t80) cc_final: 0.8090 (t80)
REVERT: C  395 CYS cc_start: 0.8382 (m) cc_final: 0.8167 (m)
REVERT: C  439 LEU cc_start: 0.9447 (tp) cc_final: 0.9230 (tp)
REVERT: C  473 GLU cc_start: 0.9062 (tt0) cc_final: 0.8447 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.1696
  time to fit residues: 48.4198
Evaluate side-chains
  141 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 123 optimal weight:    0.4980
   chunk 5 optimal weight:    3.9990
   chunk 121 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9980
   chunk 70 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0020
   chunk 65 optimal weight:    0.8980
   chunk 102 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.0790

-------------------------------------------------------------------------------
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 = 0.3378 r_free = 0.3378 target = 0.076761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.061473 restraints weight = 41805.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.062445 restraints weight = 27364.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.062967 restraints weight = 21009.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.4091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9798  Z= 0.166
  Angle     :  0.688   8.396  13344  Z= 0.326
  Chirality :  0.040   0.175   1668
  Planarity :  0.004   0.031   1656
  Dihedral  :  4.140  19.708   1365
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.24), residues: 1278
  helix:  0.50 (0.17), residues: 981
  sheet:  None (None), residues: 0
  loop : -2.67 (0.32), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 461 
 HIS   0.004   0.001   HIS A 316 
 PHE   0.015   0.001   PHE C  89 
 TYR   0.020   0.001   TYR A 305 
 ARG   0.003   0.000   ARG B 376 

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

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 1.169 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 VAL cc_start: 0.9407 (m) cc_final: 0.9096 (p)
REVERT: A  282 MET cc_start: 0.8786 (tmm) cc_final: 0.8149 (tmm)
REVERT: A  309 CYS cc_start: 0.7926 (t) cc_final: 0.7064 (t)
REVERT: A  313 HIS cc_start: 0.8113 (m90) cc_final: 0.7767 (m90)
REVERT: A  325 TYR cc_start: 0.8225 (t80) cc_final: 0.7914 (t80)
REVERT: A  394 GLN cc_start: 0.8518 (mt0) cc_final: 0.8057 (mp10)
REVERT: A  461 TRP cc_start: 0.8555 (p-90) cc_final: 0.7553 (p-90)
REVERT: B  190 ASN cc_start: 0.8716 (m-40) cc_final: 0.7826 (m110)
REVERT: B  279 VAL cc_start: 0.9351 (m) cc_final: 0.9140 (p)
REVERT: B  282 MET cc_start: 0.8875 (tmm) cc_final: 0.8484 (tmm)
REVERT: B  309 CYS cc_start: 0.8192 (t) cc_final: 0.7410 (t)
REVERT: B  313 HIS cc_start: 0.8267 (m90) cc_final: 0.7718 (m90)
REVERT: B  376 ARG cc_start: 0.8475 (mpt180) cc_final: 0.8251 (mmt-90)
REVERT: B  379 LEU cc_start: 0.8888 (tp) cc_final: 0.8608 (tp)
REVERT: B  394 GLN cc_start: 0.8526 (mt0) cc_final: 0.8177 (mt0)
REVERT: B  439 LEU cc_start: 0.9488 (tp) cc_final: 0.9277 (tp)
REVERT: C   91 PHE cc_start: 0.8350 (t80) cc_final: 0.7865 (t80)
REVERT: C  178 LYS cc_start: 0.6664 (tptt) cc_final: 0.6343 (mmtm)
REVERT: C  190 ASN cc_start: 0.8802 (m-40) cc_final: 0.7965 (m110)
REVERT: C  282 MET cc_start: 0.8769 (tmm) cc_final: 0.8492 (tmm)
REVERT: C  325 TYR cc_start: 0.8410 (t80) cc_final: 0.8051 (t80)
REVERT: C  361 MET cc_start: 0.7920 (mtp) cc_final: 0.7681 (ttt)
REVERT: C  395 CYS cc_start: 0.8400 (m) cc_final: 0.8151 (m)
REVERT: C  439 LEU cc_start: 0.9452 (tp) cc_final: 0.9238 (tp)
REVERT: C  473 GLU cc_start: 0.9006 (tt0) cc_final: 0.8415 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1732
  time to fit residues: 46.0804
Evaluate side-chains
  143 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 122 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 72 optimal weight:   20.0000
   chunk 110 optimal weight:    9.9990
   chunk 62 optimal weight:    7.9990
   chunk 68 optimal weight:    0.1980
   chunk 93 optimal weight:    0.9980
   chunk 77 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 126 optimal weight:    6.9990
   overall best weight:    1.8184

-------------------------------------------------------------------------------
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 = 0.3359 r_free = 0.3359 target = 0.075486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.060123 restraints weight = 41742.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.061074 restraints weight = 27416.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.061700 restraints weight = 21125.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.4109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9798  Z= 0.182
  Angle     :  0.684   8.222  13344  Z= 0.324
  Chirality :  0.040   0.168   1668
  Planarity :  0.004   0.031   1656
  Dihedral  :  4.116  17.874   1365
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.24), residues: 1278
  helix:  0.55 (0.17), residues: 981
  sheet:  None (None), residues: 0
  loop : -2.63 (0.32), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 461 
 HIS   0.005   0.001   HIS A 452 
 PHE   0.021   0.001   PHE B  89 
 TYR   0.020   0.002   TYR B 305 
 ARG   0.002   0.000   ARG B 376 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2532.80 seconds
wall clock time: 46 minutes 25.57 seconds (2785.57 seconds total)