Starting phenix.real_space_refine
on Wed Jun  3 18:21:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9h8o_51938/06_2026/9h8o_51938.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9h8o_51938/06_2026/9h8o_51938.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9h8o_51938/06_2026/9h8o_51938.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9h8o_51938/06_2026/9h8o_51938.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9h8o_51938/06_2026/9h8o_51938.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9h8o_51938/06_2026/9h8o_51938.map"
  }
  resolution = 4.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
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      32      5.16       5
     C    5034      2.51       5
     N    1286      2.21       5
     O    1468      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7820
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 510, 3910
          Classifications: {'peptide': 510}
          Link IDs: {'PTRANS': 16, 'TRANS': 493}
          Chain breaks: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.94, per 1000 atoms: 0.38
  Number of scatterers: 7820
  At special positions: 0
  Unit cell: (116.63, 65.27, 125.19, 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      32     16.00
     O    1468      8.00
     N    1286      7.00
     C    5034      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 123 " - pdb=" SG  CYS A 428 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 123 " - pdb=" SG  CYS B 428 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 310.6 milliseconds
  

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1876

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 4 sheets defined
      57.3% alpha, 8.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 22
      removed outlier: 4.620A  pdb=" N   ARG A  21 " --> pdb=" O   ALA A  17 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   THR A  22 " --> pdb=" O   LEU A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 55
      removed outlier: 3.647A  pdb=" N   THR A  40 " --> pdb=" O   SER A  36 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU A  41 " --> pdb=" O   VAL A  37 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A  45 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      Proline residue:  A  47  - end of helix
      removed outlier: 3.771A  pdb=" N   GLN A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   ASP A  55 " --> pdb=" O   LYS A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 108
    Processing helix  chain 'A' and resid 113 through 118
    Processing helix  chain 'A' and resid 129 through 161
      removed outlier: 3.732A  pdb=" N   VAL A 133 " --> pdb=" O   ASN A 129 " (cutoff:3.500A)
      removed outlier: 5.358A  pdb=" N   VAL A 134 " --> pdb=" O   ASP A 130 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LYS A 135 " --> pdb=" O   THR A 131 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   ILE A 142 " --> pdb=" O   ILE A 138 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   SER A 143 " --> pdb=" O   THR A 139 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE A 160 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ILE A 161 " --> pdb=" O   THR A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 182
      removed outlier: 3.867A  pdb=" N   LEU A 168 " --> pdb=" O   TRP A 164 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL A 174 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      Proline residue:  A 175  - end of helix
      removed outlier: 4.356A  pdb=" N   VAL A 182 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 275
      removed outlier: 3.563A  pdb=" N   GLY A 251 " --> pdb=" O   GLN A 247 " (cutoff:3.500A)
      Proline residue:  A 252  - end of helix
      removed outlier: 4.767A  pdb=" N   LEU A 256 " --> pdb=" O   PRO A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 322
      removed outlier: 3.617A  pdb=" N   TYR A 289 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A 290 " --> pdb=" O   PHE A 286 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE A 291 " --> pdb=" O   ILE A 287 " (cutoff:3.500A)
      Proline residue:  A 296  - end of helix
      removed outlier: 4.246A  pdb=" N   GLN A 299 " --> pdb=" O   MET A 295 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   THR A 302 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
      removed outlier: 5.068A  pdb=" N   GLN A 308 " --> pdb=" O   PHE A 304 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LYS A 309 " --> pdb=" O   THR A 305 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 5.585A  pdb=" N   GLY A 312 " --> pdb=" O   GLN A 308 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   ALA A 313 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ILE A 318 " --> pdb=" O   THR A 314 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE A 320 " --> pdb=" O   ARG A 316 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   LEU A 321 " --> pdb=" O   MET A 317 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   ALA A 322 " --> pdb=" O   ILE A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 388
    Processing helix  chain 'A' and resid 410 through 416
    Processing helix  chain 'A' and resid 431 through 436
    Processing helix  chain 'A' and resid 445 through 455
    Processing helix  chain 'A' and resid 458 through 462
    Processing helix  chain 'A' and resid 481 through 495
      removed outlier: 3.837A  pdb=" N   ALA A 488 " --> pdb=" O   ARG A 484 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ARG A 495 " --> pdb=" O   ARG A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 525
      removed outlier: 4.434A  pdb=" N   GLN A 519 " --> pdb=" O   LYS A 515 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   ALA A 520 " --> pdb=" O   SER A 516 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   GLU A 522 " --> pdb=" O   GLN A 518 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL A 523 " --> pdb=" O   GLN A 519 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU A 524 " --> pdb=" O   ALA A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 566
    Processing helix  chain 'A' and resid 571 through 575
    Processing helix  chain 'B' and resid 11 through 22
      removed outlier: 4.621A  pdb=" N   ARG B  21 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   THR B  22 " --> pdb=" O   LEU B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 55
      removed outlier: 3.647A  pdb=" N   THR B  40 " --> pdb=" O   SER B  36 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU B  41 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU B  45 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      Proline residue:  B  47  - end of helix
      removed outlier: 3.771A  pdb=" N   GLN B  52 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   ASP B  55 " --> pdb=" O   LYS B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 108
    Processing helix  chain 'B' and resid 113 through 118
    Processing helix  chain 'B' and resid 129 through 161
      removed outlier: 3.733A  pdb=" N   VAL B 133 " --> pdb=" O   ASN B 129 " (cutoff:3.500A)
      removed outlier: 5.358A  pdb=" N   VAL B 134 " --> pdb=" O   ASP B 130 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LYS B 135 " --> pdb=" O   THR B 131 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   ILE B 142 " --> pdb=" O   ILE B 138 " (cutoff:3.500A)
      removed outlier: 5.941A  pdb=" N   SER B 143 " --> pdb=" O   THR B 139 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE B 160 " --> pdb=" O   LEU B 156 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE B 161 " --> pdb=" O   THR B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 182
      removed outlier: 3.867A  pdb=" N   LEU B 168 " --> pdb=" O   TRP B 164 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL B 174 " --> pdb=" O   VAL B 170 " (cutoff:3.500A)
      Proline residue:  B 175  - end of helix
      removed outlier: 4.357A  pdb=" N   VAL B 182 " --> pdb=" O   ALA B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 275
      removed outlier: 3.563A  pdb=" N   GLY B 251 " --> pdb=" O   GLN B 247 " (cutoff:3.500A)
      Proline residue:  B 252  - end of helix
      removed outlier: 4.767A  pdb=" N   LEU B 256 " --> pdb=" O   PRO B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 322
      removed outlier: 3.617A  pdb=" N   TYR B 289 " --> pdb=" O   ALA B 285 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU B 290 " --> pdb=" O   PHE B 286 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE B 291 " --> pdb=" O   ILE B 287 " (cutoff:3.500A)
      Proline residue:  B 296  - end of helix
      removed outlier: 4.247A  pdb=" N   GLN B 299 " --> pdb=" O   MET B 295 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   THR B 302 " --> pdb=" O   GLY B 298 " (cutoff:3.500A)
      removed outlier: 5.068A  pdb=" N   GLN B 308 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   LYS B 309 " --> pdb=" O   THR B 305 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE B 311 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   GLY B 312 " --> pdb=" O   GLN B 308 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   ALA B 313 " --> pdb=" O   LYS B 309 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ILE B 318 " --> pdb=" O   THR B 314 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE B 320 " --> pdb=" O   ARG B 316 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   LEU B 321 " --> pdb=" O   MET B 317 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   ALA B 322 " --> pdb=" O   ILE B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 388
    Processing helix  chain 'B' and resid 410 through 416
    Processing helix  chain 'B' and resid 431 through 436
    Processing helix  chain 'B' and resid 445 through 455
    Processing helix  chain 'B' and resid 458 through 462
    Processing helix  chain 'B' and resid 481 through 495
      removed outlier: 3.837A  pdb=" N   ALA B 488 " --> pdb=" O   ARG B 484 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ARG B 495 " --> pdb=" O   ARG B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 514 through 525
      removed outlier: 4.434A  pdb=" N   GLN B 519 " --> pdb=" O   LYS B 515 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   ALA B 520 " --> pdb=" O   SER B 516 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   GLU B 522 " --> pdb=" O   GLN B 518 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL B 523 " --> pdb=" O   GLN B 519 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU B 524 " --> pdb=" O   ALA B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 566
    Processing helix  chain 'B' and resid 571 through 575
    Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 364
      removed outlier: 7.079A  pdb=" N   LYS A 358 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   SER A 347 " --> pdb=" O   LYS A 358 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   VAL A 360 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   ARG A 345 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   ALA A 362 " --> pdb=" O   LEU A 343 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 421
      removed outlier: 4.056A  pdb=" N   GLY A 418 " --> pdb=" O   ILE A 499 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   THR A 530 " --> pdb=" O   LYS A 368 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLN A 545 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ALA A 371 " --> pdb=" O   GLN A 545 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL A 373 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   LEU A 546 " --> pdb=" O   ARG A 557 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ARG A 557 " --> pdb=" O   LEU A 546 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   PHE A 548 " --> pdb=" O   THR A 555 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   THR A 555 " --> pdb=" O   PHE A 548 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 357 through 364
      removed outlier: 7.079A  pdb=" N   LYS B 358 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
      removed outlier: 5.410A  pdb=" N   SER B 347 " --> pdb=" O   LYS B 358 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   VAL B 360 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   ARG B 345 " --> pdb=" O   VAL B 360 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   ALA B 362 " --> pdb=" O   LEU B 343 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 417 through 421
      removed outlier: 4.056A  pdb=" N   GLY B 418 " --> pdb=" O   ILE B 499 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   THR B 530 " --> pdb=" O   LYS B 368 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLN B 545 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ALA B 371 " --> pdb=" O   GLN B 545 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL B 373 " --> pdb=" O   LEU B 547 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   LEU B 546 " --> pdb=" O   ARG B 557 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ARG B 557 " --> pdb=" O   LEU B 546 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   PHE B 548 " --> pdb=" O   THR B 555 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   THR B 555 " --> pdb=" O   PHE B 548 " (cutoff:3.500A)

    388 hydrogen bonds defined for protein.
    1140 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.01

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1978
        1.34 -     1.46: 1311
        1.46 -     1.58: 4593
        1.58 -     1.70: 0
        1.70 -     1.82: 60
  Bond restraints: 7942
  Sorted by residual:
  bond pdb=" CZ  ARG A 399 "
       pdb=" NH1 ARG A 399 "
    ideal  model  delta    sigma   weight residual
    1.323  1.273  0.050 1.40e-02 5.10e+03 1.26e+01
  bond pdb=" CZ  ARG B 399 "
       pdb=" NH1 ARG B 399 "
    ideal  model  delta    sigma   weight residual
    1.323  1.274  0.049 1.40e-02 5.10e+03 1.25e+01
  bond pdb=" N   PRO B 252 "
       pdb=" CA  PRO B 252 "
    ideal  model  delta    sigma   weight residual
    1.469  1.444  0.024 7.40e-03 1.83e+04 1.08e+01
  bond pdb=" N   PRO A 252 "
       pdb=" CA  PRO A 252 "
    ideal  model  delta    sigma   weight residual
    1.469  1.445  0.024 7.40e-03 1.83e+04 1.06e+01
  bond pdb=" CZ  ARG A 399 "
       pdb=" NH2 ARG A 399 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.04e+01
  ... (remaining 7937 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 6523
        1.55 -     3.09: 3085
        3.09 -     4.64: 987
        4.64 -     6.19: 157
        6.19 -     7.74: 12
  Bond angle restraints: 10764
  Sorted by residual:
  angle pdb=" CA  PHE A 286 "
        pdb=" CB  PHE A 286 "
        pdb=" CG  PHE A 286 "
      ideal   model   delta    sigma   weight residual
     113.80  107.97    5.83 1.00e+00 1.00e+00 3.39e+01
  angle pdb=" CA  PHE B 286 "
        pdb=" CB  PHE B 286 "
        pdb=" CG  PHE B 286 "
      ideal   model   delta    sigma   weight residual
     113.80  108.01    5.79 1.00e+00 1.00e+00 3.35e+01
  angle pdb=" C   ILE A 417 "
        pdb=" N   GLY A 418 "
        pdb=" CA  GLY A 418 "
      ideal   model   delta    sigma   weight residual
     121.65  125.42   -3.77 6.80e-01 2.16e+00 3.08e+01
  angle pdb=" C   ILE B 417 "
        pdb=" N   GLY B 418 "
        pdb=" CA  GLY B 418 "
      ideal   model   delta    sigma   weight residual
     121.65  125.41   -3.76 6.80e-01 2.16e+00 3.06e+01
  angle pdb=" CA  PHE B 115 "
        pdb=" CB  PHE B 115 "
        pdb=" CG  PHE B 115 "
      ideal   model   delta    sigma   weight residual
     113.80  119.21   -5.41 1.00e+00 1.00e+00 2.93e+01
  ... (remaining 10759 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 4337
       17.53 -    35.06: 347
       35.06 -    52.59: 78
       52.59 -    70.12: 18
       70.12 -    87.65: 10
  Dihedral angle restraints: 4790
    sinusoidal: 1870
      harmonic: 2920
  Sorted by residual:
  dihedral pdb=" CA  ASN B 336 "
           pdb=" C   ASN B 336 "
           pdb=" N   ALA B 337 "
           pdb=" CA  ALA B 337 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.27  -28.73     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" CA  ASN A 336 "
           pdb=" C   ASN A 336 "
           pdb=" N   ALA A 337 "
           pdb=" CA  ALA A 337 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.28  -28.72     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" CA  THR B 397 "
           pdb=" C   THR B 397 "
           pdb=" N   ILE B 398 "
           pdb=" CA  ILE B 398 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.03   27.97     0      5.00e+00 4.00e-02 3.13e+01
  ... (remaining 4787 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 825
       0.092 -    0.183: 414
       0.183 -    0.274: 63
       0.274 -    0.366: 10
       0.366 -    0.457: 2
  Chirality restraints: 1314
  Sorted by residual:
  chirality pdb=" CA  ARG A 484 "
            pdb=" N   ARG A 484 "
            pdb=" C   ARG A 484 "
            pdb=" CB  ARG A 484 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.23e+00
  chirality pdb=" CA  ARG B 484 "
            pdb=" N   ARG B 484 "
            pdb=" C   ARG B 484 "
            pdb=" CB  ARG B 484 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.22e+00
  chirality pdb=" CA  PRO B 175 "
            pdb=" N   PRO B 175 "
            pdb=" C   PRO B 175 "
            pdb=" CB  PRO B 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.40    0.31 2.00e-01 2.50e+01 2.47e+00
  ... (remaining 1311 not shown)

  Planarity restraints: 1346
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  90 "    0.079 2.00e-02 2.50e+03   4.13e-02 3.42e+01
        pdb=" CG  TYR B  90 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  90 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  90 "   -0.037 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  90 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  90 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  90 "    0.012 2.00e-02 2.50e+03
        pdb=" OH  TYR B  90 "    0.050 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  90 "   -0.079 2.00e-02 2.50e+03   4.12e-02 3.40e+01
        pdb=" CG  TYR A  90 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  90 "    0.046 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  90 "    0.036 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  90 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  90 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  90 "   -0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR A  90 "   -0.051 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 286 "   -0.059 2.00e-02 2.50e+03   3.64e-02 2.32e+01
        pdb=" CG  PHE B 286 "    0.050 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 286 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 286 "    0.036 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 286 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 286 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 286 "   -0.035 2.00e-02 2.50e+03
  ... (remaining 1343 not shown)

  Histogram of nonbonded interaction distances:
        2.53 -     3.01: 3865
        3.01 -     3.48: 8536
        3.48 -     3.95: 11793
        3.95 -     4.43: 12912
        4.43 -     4.90: 20632
  Nonbonded interactions: 57738
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 275 "
            pdb=" OE1 GLU B 277 "
     model   vdw
     2.531 3.040
  nonbonded pdb=" OG  SER A 275 "
            pdb=" OE1 GLU A 277 "
     model   vdw
     2.532 3.040
  nonbonded pdb=" OE2 GLU B 122 "
            pdb=" OG  SER B 125 "
     model   vdw
     2.574 3.040
  nonbonded pdb=" OE2 GLU A 122 "
            pdb=" OG  SER A 125 "
     model   vdw
     2.574 3.040
  nonbonded pdb=" OH  TYR B 419 "
            pdb=" OD2 ASP B 503 "
     model   vdw
     2.577 3.040
  ... (remaining 57733 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.140
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6141
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      :  0.013   0.050   7944  Z= 0.799
  Angle     :  1.875   7.737  10768  Z= 1.249
  Chirality :  0.099   0.457   1314
  Planarity :  0.013   0.110   1346
  Dihedral  : 14.488  87.645   2908
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 0.38
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.10 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  7.69 %
    Favored  : 90.91 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.70 (0.23), residues: 1012
  helix: -1.88 (0.19), residues: 532
  sheet: -0.90 (0.64), residues: 50
  loop : -1.58 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 536 
 TYR   0.079   0.015   TYR B  90 
 PHE   0.059   0.017   PHE B 286 
 TRP   0.049   0.018   TRP A 164 
 HIS   0.011   0.003   HIS A 416 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01288 /  0.80 ( 7942)
  covalent geometry    : angle       1.87432 /  1.25 (10764)
  SS BOND              : bond        0.00657 /  0.33 (    2)
  SS BOND              : angle       3.17278 /  1.59 (    4)
  hydrogen bonds       : bond        0.19461 / 12.79 (  388)
  hydrogen bonds       : angle       9.13979 /  6.39 ( 1140)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 160
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LEU cc_start: 0.7290 (tp) cc_final: 0.7056 (tp)
REVERT: A  114 TYR cc_start: -0.5036 (OUTLIER) cc_final: -0.5514 (t80)
REVERT: B  114 TYR cc_start: -0.5053 (OUTLIER) cc_final: -0.5534 (t80)
  outliers start: 12
  outliers final: 4
  residues processed: 170
  average time/residue: 0.0938
  time to fit residues: 21.2007
Evaluate side-chains
  112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:   50.0000
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 560 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.085273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.069175 restraints weight = 67896.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.070912 restraints weight = 41454.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.072164 restraints weight = 29422.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.072996 restraints weight = 22954.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.073539 restraints weight = 19112.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7944  Z= 0.169
  Angle     :  0.734   6.559  10768  Z= 0.390
  Chirality :  0.044   0.157   1314
  Planarity :  0.004   0.031   1346
  Dihedral  :  6.426  20.911   1084
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.95 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.03 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.26), residues: 1012
  helix: -0.25 (0.22), residues: 528
  sheet: -0.51 (0.59), residues: 66
  loop : -0.89 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 557 
 TYR   0.022   0.002   TYR B  86 
 PHE   0.015   0.002   PHE A 303 
 TRP   0.008   0.002   TRP A 104 
 HIS   0.005   0.001   HIS B 416 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.17 ( 7942)
  covalent geometry    : angle       0.73338 /  0.39 (10764)
  SS BOND              : bond        0.00233 /  0.12 (    2)
  SS BOND              : angle       1.74785 /  0.87 (    4)
  hydrogen bonds       : bond        0.05598 /  3.65 (  388)
  hydrogen bonds       : angle       5.85148 /  3.96 ( 1140)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 131
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LEU cc_start: 0.9506 (tp) cc_final: 0.9178 (tp)
REVERT: A   80 LEU cc_start: 0.9379 (tp) cc_final: 0.9030 (tp)
REVERT: A  132 MET cc_start: 0.9214 (mmp) cc_final: 0.8649 (mmm)
REVERT: A  297 MET cc_start: 0.9682 (mmp) cc_final: 0.9452 (mmm)
REVERT: A  561 HIS cc_start: 0.9163 (t-90) cc_final: 0.8956 (t-90)
REVERT: B   80 LEU cc_start: 0.9534 (mp) cc_final: 0.9080 (tp)
REVERT: B  132 MET cc_start: 0.9196 (mmp) cc_final: 0.8604 (mmm)
REVERT: B  297 MET cc_start: 0.9654 (mmp) cc_final: 0.9439 (mmm)
REVERT: B  408 TYR cc_start: 0.8459 (m-80) cc_final: 0.8128 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1002
  time to fit residues: 17.4213
Evaluate side-chains
  84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 13 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 518 GLN
A 560 HIS
B 518 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.081329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.065444 restraints weight = 69519.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.067015 restraints weight = 41996.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.068192 restraints weight = 30209.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.068954 restraints weight = 23740.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.069404 restraints weight = 20003.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.4189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7944  Z= 0.154
  Angle     :  0.664   6.556  10768  Z= 0.345
  Chirality :  0.042   0.151   1314
  Planarity :  0.004   0.039   1346
  Dihedral  :  5.797  20.159   1084
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.34 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.85 %
    Favored  : 95.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.26), residues: 1012
  helix:  0.36 (0.22), residues: 530
  sheet: -0.21 (0.58), residues: 56
  loop : -0.92 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 414 
 TYR   0.014   0.001   TYR B 408 
 PHE   0.018   0.002   PHE B 384 
 TRP   0.009   0.002   TRP A 413 
 HIS   0.006   0.001   HIS A 416 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.15 ( 7942)
  covalent geometry    : angle       0.66260 /  0.34 (10764)
  SS BOND              : bond        0.00800 /  0.40 (    2)
  SS BOND              : angle       2.27663 /  1.14 (    4)
  hydrogen bonds       : bond        0.04704 /  3.10 (  388)
  hydrogen bonds       : angle       5.28651 /  3.54 ( 1140)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 LEU cc_start: 0.9405 (tp) cc_final: 0.9158 (tp)
REVERT: A  132 MET cc_start: 0.9254 (mmp) cc_final: 0.8685 (mmm)
REVERT: A  171 LEU cc_start: 0.9534 (tp) cc_final: 0.9185 (pp)
REVERT: A  408 TYR cc_start: 0.8661 (m-80) cc_final: 0.8176 (m-80)
REVERT: A  413 TRP cc_start: 0.9077 (t-100) cc_final: 0.8844 (t-100)
REVERT: A  561 HIS cc_start: 0.9151 (t-90) cc_final: 0.8928 (t-90)
REVERT: B   80 LEU cc_start: 0.9625 (mp) cc_final: 0.9107 (tp)
REVERT: B  132 MET cc_start: 0.9228 (mmp) cc_final: 0.8671 (mmm)
REVERT: B  171 LEU cc_start: 0.9539 (tp) cc_final: 0.9231 (pp)
REVERT: B  408 TYR cc_start: 0.8599 (m-80) cc_final: 0.8225 (m-80)
REVERT: B  413 TRP cc_start: 0.9056 (t-100) cc_final: 0.8828 (t-100)
REVERT: B  427 MET cc_start: 0.9439 (tpt) cc_final: 0.9223 (tpt)
  outliers start: 2
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0996
  time to fit residues: 14.2106
Evaluate side-chains
  87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 100 optimal weight:    0.0030
   chunk 51 optimal weight:   20.0000
   chunk 61 optimal weight:    6.9990
   chunk 71 optimal weight:    0.7980
   chunk 1 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 57 optimal weight:    0.6980
   chunk 29 optimal weight:   10.0000
   overall best weight:    0.6190

-------------------------------------------------------------------------------
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 = 0.3874 r_free = 0.3874 target = 0.082579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.066500 restraints weight = 69696.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.068046 restraints weight = 42363.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.069310 restraints weight = 30845.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.070146 restraints weight = 23897.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.070698 restraints weight = 19873.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.4604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7944  Z= 0.117
  Angle     :  0.616   6.580  10768  Z= 0.313
  Chirality :  0.040   0.142   1314
  Planarity :  0.004   0.038   1346
  Dihedral  :  5.315  20.191   1084
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.85 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.26 %
    Favored  : 96.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.26), residues: 1012
  helix:  0.73 (0.22), residues: 530
  sheet:  0.10 (0.60), residues: 56
  loop : -0.90 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 484 
 TYR   0.010   0.001   TYR B  86 
 PHE   0.011   0.001   PHE B  31 
 TRP   0.006   0.001   TRP A 104 
 HIS   0.002   0.001   HIS A 416 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.12 ( 7942)
  covalent geometry    : angle       0.61434 /  0.31 (10764)
  SS BOND              : bond        0.00748 /  0.38 (    2)
  SS BOND              : angle       2.56786 /  1.30 (    4)
  hydrogen bonds       : bond        0.04074 /  2.67 (  388)
  hydrogen bonds       : angle       4.85720 /  3.27 ( 1140)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 LEU cc_start: 0.9452 (tp) cc_final: 0.9113 (tp)
REVERT: A  132 MET cc_start: 0.9291 (mmp) cc_final: 0.8682 (mmm)
REVERT: A  171 LEU cc_start: 0.9502 (tp) cc_final: 0.9161 (pp)
REVERT: A  297 MET cc_start: 0.9640 (mmp) cc_final: 0.9421 (mmm)
REVERT: A  408 TYR cc_start: 0.8272 (m-80) cc_final: 0.7811 (m-80)
REVERT: A  413 TRP cc_start: 0.8934 (t-100) cc_final: 0.8733 (t-100)
REVERT: A  478 MET cc_start: 0.8179 (mmp) cc_final: 0.7504 (tpp)
REVERT: B   80 LEU cc_start: 0.9628 (mp) cc_final: 0.9116 (tp)
REVERT: B  132 MET cc_start: 0.9271 (mmp) cc_final: 0.8659 (mmm)
REVERT: B  171 LEU cc_start: 0.9503 (tp) cc_final: 0.9166 (pp)
REVERT: B  295 MET cc_start: 0.9113 (ttm) cc_final: 0.8713 (tmm)
REVERT: B  408 TYR cc_start: 0.8394 (m-80) cc_final: 0.8008 (m-80)
REVERT: B  413 TRP cc_start: 0.8926 (t-100) cc_final: 0.8699 (t-100)
REVERT: B  453 GLU cc_start: 0.9733 (mt-10) cc_final: 0.9446 (pt0)
REVERT: B  454 MET cc_start: 0.8996 (mmp) cc_final: 0.8776 (mmt)
REVERT: B  478 MET cc_start: 0.8198 (mmp) cc_final: 0.7508 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0899
  time to fit residues: 13.2101
Evaluate side-chains
  83 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 80 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 32 optimal weight:    0.2980
   chunk 34 optimal weight:    0.6980
   chunk 76 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.7986

-------------------------------------------------------------------------------
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 = 0.3827 r_free = 0.3827 target = 0.079637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.063837 restraints weight = 70094.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.065413 restraints weight = 43020.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.066589 restraints weight = 30873.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.067364 restraints weight = 24217.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.067822 restraints weight = 20398.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.5026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7944  Z= 0.147
  Angle     :  0.623   6.595  10768  Z= 0.323
  Chirality :  0.041   0.180   1314
  Planarity :  0.004   0.037   1346
  Dihedral  :  5.228  19.977   1084
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.94 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.27), residues: 1012
  helix:  0.70 (0.23), residues: 540
  sheet:  0.09 (0.61), residues: 56
  loop : -0.91 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 571 
 TYR   0.013   0.001   TYR B 408 
 PHE   0.019   0.001   PHE B 286 
 TRP   0.008   0.001   TRP A 413 
 HIS   0.004   0.001   HIS B 416 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.15 ( 7942)
  covalent geometry    : angle       0.62123 /  0.32 (10764)
  SS BOND              : bond        0.00276 /  0.14 (    2)
  SS BOND              : angle       2.68896 /  1.35 (    4)
  hydrogen bonds       : bond        0.03921 /  2.57 (  388)
  hydrogen bonds       : angle       4.98537 /  3.37 ( 1140)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 LEU cc_start: 0.9447 (tp) cc_final: 0.9109 (tp)
REVERT: A  132 MET cc_start: 0.9357 (mmp) cc_final: 0.8752 (mmm)
REVERT: A  171 LEU cc_start: 0.9516 (tp) cc_final: 0.9249 (pp)
REVERT: A  259 MET cc_start: 0.9505 (mmp) cc_final: 0.9139 (mmp)
REVERT: A  295 MET cc_start: 0.8988 (ttm) cc_final: 0.8676 (tmm)
REVERT: A  408 TYR cc_start: 0.8531 (m-80) cc_final: 0.8064 (m-80)
REVERT: A  413 TRP cc_start: 0.9025 (t-100) cc_final: 0.8823 (t-100)
REVERT: A  427 MET cc_start: 0.9404 (tpt) cc_final: 0.9158 (tpt)
REVERT: A  478 MET cc_start: 0.8250 (mmp) cc_final: 0.7597 (tpp)
REVERT: B   80 LEU cc_start: 0.9581 (mp) cc_final: 0.9110 (tp)
REVERT: B  132 MET cc_start: 0.9348 (mmp) cc_final: 0.8720 (mmm)
REVERT: B  171 LEU cc_start: 0.9522 (tp) cc_final: 0.9257 (pp)
REVERT: B  259 MET cc_start: 0.9517 (mmp) cc_final: 0.9182 (mmp)
REVERT: B  295 MET cc_start: 0.9075 (ttm) cc_final: 0.8704 (tmm)
REVERT: B  408 TYR cc_start: 0.8582 (m-80) cc_final: 0.8198 (m-80)
REVERT: B  413 TRP cc_start: 0.9014 (t-100) cc_final: 0.8793 (t-100)
REVERT: B  427 MET cc_start: 0.9395 (tpt) cc_final: 0.9152 (tpt)
REVERT: B  478 MET cc_start: 0.8246 (mmp) cc_final: 0.7619 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0854
  time to fit residues: 12.5214
Evaluate side-chains
  79 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 91 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 60 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 1 optimal weight:    0.4980
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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 = 0.3807 r_free = 0.3807 target = 0.078126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.062503 restraints weight = 70856.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.064088 restraints weight = 43296.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.065266 restraints weight = 30863.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.066051 restraints weight = 24262.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.066499 restraints weight = 20441.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.5575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7944  Z= 0.141
  Angle     :  0.641   6.842  10768  Z= 0.325
  Chirality :  0.042   0.151   1314
  Planarity :  0.004   0.039   1346
  Dihedral  :  5.053  19.683   1084
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.74 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.27), residues: 1012
  helix:  0.85 (0.23), residues: 542
  sheet: -0.50 (0.57), residues: 56
  loop : -0.93 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 528 
 TYR   0.010   0.001   TYR B 408 
 PHE   0.012   0.001   PHE B 286 
 TRP   0.006   0.001   TRP B 413 
 HIS   0.003   0.001   HIS B 560 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.14 ( 7942)
  covalent geometry    : angle       0.63990 /  0.32 (10764)
  SS BOND              : bond        0.00323 /  0.16 (    2)
  SS BOND              : angle       2.08329 /  1.05 (    4)
  hydrogen bonds       : bond        0.03849 /  2.52 (  388)
  hydrogen bonds       : angle       4.83955 /  3.28 ( 1140)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 LEU cc_start: 0.9461 (tp) cc_final: 0.9125 (tp)
REVERT: A  132 MET cc_start: 0.9509 (mmp) cc_final: 0.8948 (mmm)
REVERT: A  171 LEU cc_start: 0.9561 (tp) cc_final: 0.9296 (pp)
REVERT: A  295 MET cc_start: 0.8999 (ttm) cc_final: 0.8640 (tmm)
REVERT: A  408 TYR cc_start: 0.8457 (m-80) cc_final: 0.7997 (m-80)
REVERT: A  413 TRP cc_start: 0.9071 (t-100) cc_final: 0.8862 (t-100)
REVERT: A  454 MET cc_start: 0.8855 (tpp) cc_final: 0.8396 (mmm)
REVERT: A  478 MET cc_start: 0.8317 (mmp) cc_final: 0.8077 (tpp)
REVERT: A  501 MET cc_start: 0.9509 (tpt) cc_final: 0.9278 (tpt)
REVERT: A  561 HIS cc_start: 0.9010 (t-90) cc_final: 0.8695 (t-90)
REVERT: A  564 MET cc_start: 0.8382 (mmm) cc_final: 0.7751 (mmp)
REVERT: B   80 LEU cc_start: 0.9645 (mp) cc_final: 0.9142 (tp)
REVERT: B  132 MET cc_start: 0.9497 (mmp) cc_final: 0.8897 (mmm)
REVERT: B  171 LEU cc_start: 0.9565 (tp) cc_final: 0.9301 (pp)
REVERT: B  297 MET cc_start: 0.9602 (mmp) cc_final: 0.9394 (mmp)
REVERT: B  408 TYR cc_start: 0.8559 (m-80) cc_final: 0.8177 (m-80)
REVERT: B  413 TRP cc_start: 0.9113 (t-100) cc_final: 0.8910 (t-100)
REVERT: B  478 MET cc_start: 0.8339 (mmp) cc_final: 0.8052 (tpp)
REVERT: B  501 MET cc_start: 0.9491 (tpt) cc_final: 0.9278 (tpt)
REVERT: B  561 HIS cc_start: 0.9016 (t-90) cc_final: 0.8718 (t-90)
REVERT: B  564 MET cc_start: 0.8413 (mmm) cc_final: 0.7787 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0871
  time to fit residues: 12.4508
Evaluate side-chains
  77 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 94 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 60 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 75 optimal weight:    9.9990
   chunk 39 optimal weight:    0.0970
   chunk 51 optimal weight:    9.9990
   chunk 74 optimal weight:    2.9990
   chunk 81 optimal weight:    9.9990
   overall best weight:    1.9784

-------------------------------------------------------------------------------
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 = 0.3787 r_free = 0.3787 target = 0.076577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.060996 restraints weight = 71693.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.062574 restraints weight = 43061.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.063721 restraints weight = 30853.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.064496 restraints weight = 24269.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.064979 restraints weight = 20524.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.6006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7944  Z= 0.155
  Angle     :  0.661   9.113  10768  Z= 0.333
  Chirality :  0.041   0.171   1314
  Planarity :  0.004   0.043   1346
  Dihedral  :  5.010  18.834   1084
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.84 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.27), residues: 1012
  helix:  0.79 (0.22), residues: 552
  sheet: -1.05 (0.54), residues: 62
  loop : -0.91 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 557 
 TYR   0.014   0.001   TYR B 408 
 PHE   0.010   0.002   PHE B 384 
 TRP   0.007   0.001   TRP A 413 
 HIS   0.004   0.001   HIS B 416 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.15 ( 7942)
  covalent geometry    : angle       0.65998 /  0.33 (10764)
  SS BOND              : bond        0.00506 /  0.25 (    2)
  SS BOND              : angle       1.91220 /  0.96 (    4)
  hydrogen bonds       : bond        0.03723 /  2.42 (  388)
  hydrogen bonds       : angle       4.87359 /  3.31 ( 1140)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 LEU cc_start: 0.9409 (tp) cc_final: 0.9075 (tp)
REVERT: A  132 MET cc_start: 0.9486 (mmp) cc_final: 0.8865 (mmm)
REVERT: A  171 LEU cc_start: 0.9535 (tp) cc_final: 0.9287 (pp)
REVERT: A  408 TYR cc_start: 0.8544 (m-80) cc_final: 0.8082 (m-80)
REVERT: A  413 TRP cc_start: 0.9048 (t-100) cc_final: 0.8838 (t-100)
REVERT: A  454 MET cc_start: 0.8824 (tpp) cc_final: 0.8339 (tpp)
REVERT: A  478 MET cc_start: 0.8235 (mmp) cc_final: 0.7961 (tpp)
REVERT: A  501 MET cc_start: 0.9528 (tpt) cc_final: 0.9172 (tpt)
REVERT: A  561 HIS cc_start: 0.8981 (t-90) cc_final: 0.8779 (t-90)
REVERT: B   80 LEU cc_start: 0.9590 (mp) cc_final: 0.9165 (tp)
REVERT: B  132 MET cc_start: 0.9481 (mmp) cc_final: 0.8922 (mmm)
REVERT: B  171 LEU cc_start: 0.9551 (tp) cc_final: 0.9295 (pp)
REVERT: B  408 TYR cc_start: 0.8518 (m-80) cc_final: 0.8119 (m-80)
REVERT: B  478 MET cc_start: 0.8174 (mmp) cc_final: 0.7903 (tpp)
REVERT: B  501 MET cc_start: 0.9481 (tpt) cc_final: 0.9149 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0941
  time to fit residues: 13.0435
Evaluate side-chains
  70 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 47 optimal weight:    8.9990
   chunk 10 optimal weight:    0.1980
   chunk 36 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 17 optimal weight:    8.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.076772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.061070 restraints weight = 72078.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.062738 restraints weight = 43408.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.063916 restraints weight = 30808.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.064676 restraints weight = 24269.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.065215 restraints weight = 20556.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.6242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7944  Z= 0.139
  Angle     :  0.653   7.344  10768  Z= 0.327
  Chirality :  0.041   0.148   1314
  Planarity :  0.004   0.047   1346
  Dihedral  :  4.920  18.994   1084
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.15 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.27), residues: 1012
  helix:  0.78 (0.22), residues: 566
  sheet: -1.04 (0.55), residues: 62
  loop : -0.90 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 484 
 TYR   0.011   0.001   TYR B 408 
 PHE   0.011   0.001   PHE B  31 
 TRP   0.007   0.001   TRP A 164 
 HIS   0.003   0.001   HIS B 416 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.14 ( 7942)
  covalent geometry    : angle       0.65201 /  0.33 (10764)
  SS BOND              : bond        0.00383 /  0.19 (    2)
  SS BOND              : angle       1.72495 /  0.86 (    4)
  hydrogen bonds       : bond        0.03656 /  2.40 (  388)
  hydrogen bonds       : angle       4.81851 /  3.25 ( 1140)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 LEU cc_start: 0.9452 (tp) cc_final: 0.9111 (tp)
REVERT: A  132 MET cc_start: 0.9545 (mmp) cc_final: 0.8989 (mmm)
REVERT: A  171 LEU cc_start: 0.9543 (tp) cc_final: 0.9279 (pp)
REVERT: A  408 TYR cc_start: 0.8505 (m-80) cc_final: 0.8064 (m-80)
REVERT: A  413 TRP cc_start: 0.9155 (t-100) cc_final: 0.8939 (t-100)
REVERT: A  427 MET cc_start: 0.9204 (tpt) cc_final: 0.8997 (tpt)
REVERT: A  454 MET cc_start: 0.8940 (tpp) cc_final: 0.8512 (tpp)
REVERT: A  478 MET cc_start: 0.8235 (mmp) cc_final: 0.8013 (tpp)
REVERT: A  501 MET cc_start: 0.9593 (tpt) cc_final: 0.9107 (tpt)
REVERT: B   80 LEU cc_start: 0.9631 (mp) cc_final: 0.9189 (tp)
REVERT: B  132 MET cc_start: 0.9541 (mmp) cc_final: 0.8948 (mmm)
REVERT: B  171 LEU cc_start: 0.9548 (tp) cc_final: 0.9297 (pp)
REVERT: B  408 TYR cc_start: 0.8578 (m-80) cc_final: 0.8183 (m-80)
REVERT: B  413 TRP cc_start: 0.9260 (t-100) cc_final: 0.8996 (t-100)
REVERT: B  478 MET cc_start: 0.8232 (mmp) cc_final: 0.7976 (tpp)
REVERT: B  501 MET cc_start: 0.9566 (tpt) cc_final: 0.9100 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0907
  time to fit residues: 12.0570
Evaluate side-chains
  69 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 56 optimal weight:    0.0980
   chunk 79 optimal weight:    8.9990
   chunk 45 optimal weight:    7.9990
   chunk 35 optimal weight:    0.5980
   chunk 76 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 416 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.078750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.063212 restraints weight = 70516.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.064916 restraints weight = 42688.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.066106 restraints weight = 30184.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.066906 restraints weight = 23643.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.067403 restraints weight = 19862.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.6412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055   7944  Z= 0.110
  Angle     :  0.636   7.429  10768  Z= 0.313
  Chirality :  0.041   0.149   1314
  Planarity :  0.004   0.048   1346
  Dihedral  :  4.696  18.744   1084
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.05 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.27), residues: 1012
  helix:  1.02 (0.23), residues: 542
  sheet: -0.26 (0.57), residues: 56
  loop : -0.80 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 316 
 TYR   0.008   0.001   TYR B 408 
 PHE   0.006   0.001   PHE A 286 
 TRP   0.007   0.001   TRP B 164 
 HIS   0.002   0.001   HIS A 416 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.11 ( 7942)
  covalent geometry    : angle       0.63525 /  0.31 (10764)
  SS BOND              : bond        0.00273 /  0.14 (    2)
  SS BOND              : angle       1.27044 /  0.63 (    4)
  hydrogen bonds       : bond        0.03467 /  2.26 (  388)
  hydrogen bonds       : angle       4.58447 /  3.12 ( 1140)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 LEU cc_start: 0.9420 (tp) cc_final: 0.9056 (tp)
REVERT: A  132 MET cc_start: 0.9564 (mmp) cc_final: 0.8999 (mmm)
REVERT: A  171 LEU cc_start: 0.9536 (tp) cc_final: 0.9271 (pp)
REVERT: A  297 MET cc_start: 0.9617 (mmp) cc_final: 0.9408 (mmp)
REVERT: A  408 TYR cc_start: 0.8275 (m-80) cc_final: 0.8071 (m-80)
REVERT: A  427 MET cc_start: 0.9239 (tpt) cc_final: 0.9021 (tpt)
REVERT: A  454 MET cc_start: 0.8947 (tpp) cc_final: 0.8384 (mmm)
REVERT: A  478 MET cc_start: 0.8412 (mmp) cc_final: 0.7901 (tpp)
REVERT: A  501 MET cc_start: 0.9592 (tpt) cc_final: 0.9214 (tpt)
REVERT: B   35 LEU cc_start: 0.9630 (mt) cc_final: 0.9423 (mt)
REVERT: B   80 LEU cc_start: 0.9622 (mp) cc_final: 0.9120 (tp)
REVERT: B  132 MET cc_start: 0.9551 (mmp) cc_final: 0.8952 (mmm)
REVERT: B  171 LEU cc_start: 0.9548 (tp) cc_final: 0.9279 (pp)
REVERT: B  297 MET cc_start: 0.9623 (mmp) cc_final: 0.9413 (mmp)
REVERT: B  408 TYR cc_start: 0.8291 (m-80) cc_final: 0.7906 (m-80)
REVERT: B  413 TRP cc_start: 0.9165 (t-100) cc_final: 0.8878 (t-100)
REVERT: B  427 MET cc_start: 0.9249 (tpt) cc_final: 0.9032 (tpt)
REVERT: B  478 MET cc_start: 0.8321 (mmp) cc_final: 0.7783 (tpp)
REVERT: B  501 MET cc_start: 0.9602 (tpt) cc_final: 0.9255 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0876
  time to fit residues: 11.4166
Evaluate side-chains
  74 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 56 optimal weight:    0.0050
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    0.6980
   chunk 97 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0970
   chunk 89 optimal weight:    0.6980
   chunk 50 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9980
   chunk 69 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0670
   overall best weight:    0.3130

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

Flipped N/Q/H residues before XYZ refinement:
A 416 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.079935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.064425 restraints weight = 70191.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.066120 restraints weight = 42354.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.067201 restraints weight = 30106.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.068075 restraints weight = 23889.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.068612 restraints weight = 19895.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.6595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   7944  Z= 0.107
  Angle     :  0.631   8.291  10768  Z= 0.306
  Chirality :  0.041   0.147   1314
  Planarity :  0.004   0.049   1346
  Dihedral  :  4.473  17.589   1084
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.46 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.27), residues: 1012
  helix:  1.16 (0.23), residues: 542
  sheet:  0.15 (0.61), residues: 56
  loop : -0.82 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 528 
 TYR   0.008   0.001   TYR B 268 
 PHE   0.005   0.001   PHE A 460 
 TRP   0.004   0.001   TRP B 164 
 HIS   0.004   0.001   HIS A 416 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.11 ( 7942)
  covalent geometry    : angle       0.63112 /  0.31 (10764)
  SS BOND              : bond        0.00149 /  0.07 (    2)
  SS BOND              : angle       1.24111 /  0.62 (    4)
  hydrogen bonds       : bond        0.03278 /  2.15 (  388)
  hydrogen bonds       : angle       4.42408 /  3.04 ( 1140)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 LEU cc_start: 0.9375 (tp) cc_final: 0.9020 (tp)
REVERT: A  132 MET cc_start: 0.9565 (mmp) cc_final: 0.8971 (mmm)
REVERT: A  166 LEU cc_start: 0.9695 (tp) cc_final: 0.9440 (tp)
REVERT: A  171 LEU cc_start: 0.9552 (tp) cc_final: 0.9265 (pp)
REVERT: A  408 TYR cc_start: 0.8055 (m-80) cc_final: 0.7814 (m-80)
REVERT: A  427 MET cc_start: 0.9264 (tpt) cc_final: 0.9048 (tpt)
REVERT: A  454 MET cc_start: 0.9059 (tpp) cc_final: 0.8712 (tpp)
REVERT: A  478 MET cc_start: 0.8282 (mmp) cc_final: 0.7771 (tpp)
REVERT: A  562 GLU cc_start: 0.9216 (tp30) cc_final: 0.8852 (tm-30)
REVERT: A  564 MET cc_start: 0.8046 (mmm) cc_final: 0.7502 (mmm)
REVERT: B   35 LEU cc_start: 0.9585 (mt) cc_final: 0.9361 (mt)
REVERT: B   80 LEU cc_start: 0.9599 (mp) cc_final: 0.9099 (tp)
REVERT: B  132 MET cc_start: 0.9528 (mmp) cc_final: 0.8926 (mmm)
REVERT: B  166 LEU cc_start: 0.9677 (tp) cc_final: 0.9453 (tp)
REVERT: B  171 LEU cc_start: 0.9554 (tp) cc_final: 0.9280 (pp)
REVERT: B  408 TYR cc_start: 0.8041 (m-80) cc_final: 0.7659 (m-80)
REVERT: B  413 TRP cc_start: 0.9116 (t-100) cc_final: 0.8894 (t-100)
REVERT: B  427 MET cc_start: 0.9289 (tpt) cc_final: 0.9080 (tpt)
REVERT: B  478 MET cc_start: 0.8332 (mmp) cc_final: 0.7826 (tpp)
REVERT: B  501 MET cc_start: 0.9565 (tpt) cc_final: 0.9254 (tpt)
REVERT: B  562 GLU cc_start: 0.9188 (tp30) cc_final: 0.8820 (tm-30)
REVERT: B  564 MET cc_start: 0.8032 (mmm) cc_final: 0.7506 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0913
  time to fit residues: 12.8295
Evaluate side-chains
  78 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 77 optimal weight:   20.0000
   chunk 74 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 90 optimal weight:    3.9990
   chunk 87 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 26 optimal weight:   20.0000
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    8.9990
   chunk 3 optimal weight:    0.2980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 535 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.077345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.061819 restraints weight = 71227.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.063401 restraints weight = 43415.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.064527 restraints weight = 31242.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.065313 restraints weight = 24764.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.065775 restraints weight = 20923.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.6833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7944  Z= 0.120
  Angle     :  0.639   7.823  10768  Z= 0.312
  Chirality :  0.041   0.141   1314
  Planarity :  0.004   0.049   1346
  Dihedral  :  4.481  17.490   1084
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.74 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.28), residues: 1012
  helix:  1.05 (0.23), residues: 562
  sheet:  0.14 (0.63), residues: 56
  loop : -0.79 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 528 
 TYR   0.011   0.001   TYR A 408 
 PHE   0.010   0.001   PHE A 384 
 TRP   0.008   0.001   TRP A 413 
 HIS   0.004   0.001   HIS A 416 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 ( 7942)
  covalent geometry    : angle       0.63801 /  0.31 (10764)
  SS BOND              : bond        0.00300 /  0.15 (    2)
  SS BOND              : angle       1.49950 /  0.75 (    4)
  hydrogen bonds       : bond        0.03272 /  2.12 (  388)
  hydrogen bonds       : angle       4.51827 /  3.11 ( 1140)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1492.01 seconds
wall clock time: 26 minutes 28.35 seconds (1588.35 seconds total)