Starting phenix.real_space_refine
on Fri Aug 22 18:47:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j18_61071/08_2025/9j18_61071.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j18_61071/08_2025/9j18_61071.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j18_61071/08_2025/9j18_61071.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j18_61071/08_2025/9j18_61071.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j18_61071/08_2025/9j18_61071.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j18_61071/08_2025/9j18_61071.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.046
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      48      5.16       5
     C    4526      2.51       5
     N    1114      2.21       5
     O    1256      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6944
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3456
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 465, 3456
          Classifications: {'peptide': 465}
          Link IDs: {'PTRANS': 12, 'TRANS': 452}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 16
          Unusual residues: {'ZEA': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.94, per 1000 atoms: 0.28
  Number of scatterers: 6944
  At special positions: 0
  Unit cell: (82.5, 102.3, 75.9, 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      48     16.00
     O    1256      8.00
     N    1114      7.00
     C    4526      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  72 " - pdb=" SG  CYS A 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 232 " - pdb=" SG  CYS A 242 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  72 " - pdb=" SG  CYS B 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 232 " - pdb=" SG  CYS B 242 " distance=2.03

  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: 0.62
  Conformation dependent library (CDL) restraints added in 402.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1652

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 4 sheets defined
      67.0% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 23
    Processing helix  chain 'A' and resid 25 through 31
    Processing helix  chain 'A' and resid 39 through 44
    Processing helix  chain 'A' and resid 47 through 55
      removed outlier: 4.103A  pdb=" N   PHE A  51 " --> pdb=" O   ALA A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 69
      removed outlier: 4.009A  pdb=" N   ALA A  62 " --> pdb=" O   ILE A  58 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   SER A  68 " --> pdb=" O   ILE A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 127
      removed outlier: 3.673A  pdb=" N   ARG A 104 " --> pdb=" O   GLN A 100 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL A 111 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   MET A 118 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 145
    Processing helix  chain 'A' and resid 150 through 154
      removed outlier: 3.841A  pdb=" N   GLY A 153 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 161
    Processing helix  chain 'A' and resid 162 through 179
      removed outlier: 3.738A  pdb=" N   VAL A 166 " --> pdb=" O   ALA A 162 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A 179 " --> pdb=" O   ALA A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 189
      removed outlier: 3.588A  pdb=" N   LYS A 184 " --> pdb=" O   GLY A 180 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ARG A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LEU A 188 " --> pdb=" O   LYS A 184 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ILE A 189 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 209
      removed outlier: 3.610A  pdb=" N   ALA A 198 " --> pdb=" O   ARG A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 267
      removed outlier: 5.138A  pdb=" N   VAL A 257 " --> pdb=" O   TRP A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 286
      removed outlier: 3.571A  pdb=" N   PHE A 280 " --> pdb=" O   TYR A 276 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   VAL A 281 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 309
      removed outlier: 3.568A  pdb=" N   ASN A 304 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   ASN A 306 " --> pdb=" O   ASP A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 330
      removed outlier: 4.365A  pdb=" N   ARG A 330 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 327 through 330'
    Processing helix  chain 'A' and resid 331 through 360
      removed outlier: 3.946A  pdb=" N   TRP A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ALA A 337 " --> pdb=" O   GLU A 333 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   LEU A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   TYR A 343 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   VAL A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   LEU A 347 " --> pdb=" O   TYR A 343 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   THR A 350 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   GLY A 351 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   VAL A 352 " --> pdb=" O   GLY A 348 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU A 353 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLY A 360 " --> pdb=" O   MET A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 389
      removed outlier: 3.535A  pdb=" N   ASP A 378 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ALA A 379 " --> pdb=" O   TYR A 375 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   SER A 382 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ALA A 387 " --> pdb=" O   VAL A 383 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LEU A 388 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 405
      removed outlier: 4.271A  pdb=" N   GLY A 402 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLU A 405 " --> pdb=" O   ALA A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 421
    Processing helix  chain 'A' and resid 426 through 430
    Processing helix  chain 'A' and resid 434 through 437
    Processing helix  chain 'A' and resid 438 through 449
      removed outlier: 3.914A  pdb=" N   VAL A 445 " --> pdb=" O   SER A 441 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY A 446 " --> pdb=" O   LEU A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 455
      removed outlier: 3.863A  pdb=" N   LYS A 454 " --> pdb=" O   GLY A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 478
      removed outlier: 3.744A  pdb=" N   VAL A 465 " --> pdb=" O   THR A 461 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   THR A 466 " --> pdb=" O   LYS A 462 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ALA A 467 " --> pdb=" O   GLU A 463 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   MET A 474 " --> pdb=" O   THR A 470 " (cutoff:3.500A)
      Proline residue:  A 475  - end of helix
    Processing helix  chain 'A' and resid 480 through 494
      removed outlier: 3.633A  pdb=" N   ILE A 484 " --> pdb=" O   ILE A 480 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ILE A 485 " --> pdb=" O   ALA A 481 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ALA A 486 " --> pdb=" O   ASN A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 501
      removed outlier: 3.502A  pdb=" N   LEU A 501 " --> pdb=" O   TYR A 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 23
    Processing helix  chain 'B' and resid 25 through 31
    Processing helix  chain 'B' and resid 39 through 44
    Processing helix  chain 'B' and resid 47 through 55
      removed outlier: 4.104A  pdb=" N   PHE B  51 " --> pdb=" O   ALA B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 69
      removed outlier: 4.009A  pdb=" N   ALA B  62 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   SER B  68 " --> pdb=" O   ILE B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 127
      removed outlier: 3.673A  pdb=" N   ARG B 104 " --> pdb=" O   GLN B 100 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL B 111 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   MET B 118 " --> pdb=" O   SER B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 145
    Processing helix  chain 'B' and resid 150 through 154
      removed outlier: 3.840A  pdb=" N   GLY B 153 " --> pdb=" O   GLY B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 161
    Processing helix  chain 'B' and resid 162 through 179
      removed outlier: 3.737A  pdb=" N   VAL B 166 " --> pdb=" O   ALA B 162 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU B 179 " --> pdb=" O   ALA B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 189
      removed outlier: 3.587A  pdb=" N   LYS B 184 " --> pdb=" O   GLY B 180 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ARG B 187 " --> pdb=" O   GLY B 183 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LEU B 188 " --> pdb=" O   LYS B 184 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ILE B 189 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 209
      removed outlier: 3.610A  pdb=" N   ALA B 198 " --> pdb=" O   ARG B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 267
      removed outlier: 5.138A  pdb=" N   VAL B 257 " --> pdb=" O   TRP B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 286
      removed outlier: 3.571A  pdb=" N   PHE B 280 " --> pdb=" O   TYR B 276 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   VAL B 281 " --> pdb=" O   GLY B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 309
      removed outlier: 3.569A  pdb=" N   ASN B 304 " --> pdb=" O   LEU B 300 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   ASN B 306 " --> pdb=" O   ASP B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 330
      removed outlier: 4.365A  pdb=" N   ARG B 330 " --> pdb=" O   THR B 327 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 327 through 330'
    Processing helix  chain 'B' and resid 331 through 360
      removed outlier: 3.945A  pdb=" N   TRP B 335 " --> pdb=" O   LYS B 331 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ALA B 337 " --> pdb=" O   GLU B 333 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   LEU B 341 " --> pdb=" O   ALA B 337 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   TYR B 343 " --> pdb=" O   ALA B 339 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   VAL B 344 " --> pdb=" O   THR B 340 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   LEU B 347 " --> pdb=" O   TYR B 343 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   THR B 350 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   GLY B 351 " --> pdb=" O   LEU B 347 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   VAL B 352 " --> pdb=" O   GLY B 348 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   LEU B 353 " --> pdb=" O   THR B 349 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLY B 360 " --> pdb=" O   MET B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 389
      removed outlier: 3.536A  pdb=" N   ASP B 378 " --> pdb=" O   ALA B 374 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ALA B 379 " --> pdb=" O   TYR B 375 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   SER B 382 " --> pdb=" O   ASP B 378 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ALA B 387 " --> pdb=" O   VAL B 383 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU B 388 " --> pdb=" O   VAL B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 398 through 405
      removed outlier: 4.271A  pdb=" N   GLY B 402 " --> pdb=" O   GLU B 398 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLU B 405 " --> pdb=" O   ALA B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 421
    Processing helix  chain 'B' and resid 426 through 430
    Processing helix  chain 'B' and resid 434 through 437
    Processing helix  chain 'B' and resid 438 through 449
      removed outlier: 3.915A  pdb=" N   VAL B 445 " --> pdb=" O   SER B 441 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY B 446 " --> pdb=" O   LEU B 442 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 455
      removed outlier: 3.863A  pdb=" N   LYS B 454 " --> pdb=" O   GLY B 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 478
      removed outlier: 3.744A  pdb=" N   VAL B 465 " --> pdb=" O   THR B 461 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   THR B 466 " --> pdb=" O   LYS B 462 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ALA B 467 " --> pdb=" O   GLU B 463 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   MET B 474 " --> pdb=" O   THR B 470 " (cutoff:3.500A)
      Proline residue:  B 475  - end of helix
    Processing helix  chain 'B' and resid 480 through 494
      removed outlier: 3.634A  pdb=" N   ILE B 484 " --> pdb=" O   ILE B 480 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ILE B 485 " --> pdb=" O   ALA B 481 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ALA B 486 " --> pdb=" O   ASN B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 501
      removed outlier: 3.502A  pdb=" N   LEU B 501 " --> pdb=" O   TYR B 497 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 221
    Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 235
      removed outlier: 3.756A  pdb=" N   GLY A 244 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 219 through 221
    Processing sheet with id=AA4, first strand: chain 'B' and resid 234 through 235
      removed outlier: 3.756A  pdb=" N   GLY B 244 " --> pdb=" O   GLU B 234 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    915 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: 0.83

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1260
        1.33 -     1.45: 1786
        1.45 -     1.57: 3952
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 7082
  Sorted by residual:
  bond pdb=" N   SER A 386 "
       pdb=" CA  SER A 386 "
    ideal  model  delta    sigma   weight residual
    1.459  1.404  0.055 1.18e-02 7.18e+03 2.21e+01
  bond pdb=" N   SER B 386 "
       pdb=" CA  SER B 386 "
    ideal  model  delta    sigma   weight residual
    1.459  1.404  0.055 1.18e-02 7.18e+03 2.19e+01
  bond pdb=" CA  SER A 386 "
       pdb=" C   SER A 386 "
    ideal  model  delta    sigma   weight residual
    1.524  1.468  0.056 1.24e-02 6.50e+03 2.07e+01
  bond pdb=" CA  SER B 386 "
       pdb=" C   SER B 386 "
    ideal  model  delta    sigma   weight residual
    1.524  1.468  0.056 1.24e-02 6.50e+03 2.02e+01
  bond pdb=" N   VAL A 390 "
       pdb=" CA  VAL A 390 "
    ideal  model  delta    sigma   weight residual
    1.455  1.406  0.049 1.18e-02 7.18e+03 1.73e+01
  ... (remaining 7077 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.66: 9523
        3.66 -     7.32: 67
        7.32 -    10.98: 22
       10.98 -    14.64: 2
       14.64 -    18.29: 2
  Bond angle restraints: 9616
  Sorted by residual:
  angle pdb=" C   VAL A 384 "
        pdb=" CA  VAL A 384 "
        pdb=" CB  VAL A 384 "
      ideal   model   delta    sigma   weight residual
     112.05  122.17  -10.12 1.46e+00 4.69e-01 4.80e+01
  angle pdb=" C   VAL B 384 "
        pdb=" CA  VAL B 384 "
        pdb=" CB  VAL B 384 "
      ideal   model   delta    sigma   weight residual
     112.05  122.15  -10.10 1.46e+00 4.69e-01 4.79e+01
  angle pdb=" N   GLY A 385 "
        pdb=" CA  GLY A 385 "
        pdb=" C   GLY A 385 "
      ideal   model   delta    sigma   weight residual
     113.37  122.41   -9.04 1.34e+00 5.57e-01 4.55e+01
  angle pdb=" N   GLY B 385 "
        pdb=" CA  GLY B 385 "
        pdb=" C   GLY B 385 "
      ideal   model   delta    sigma   weight residual
     113.37  122.41   -9.04 1.34e+00 5.57e-01 4.55e+01
  angle pdb=" N   PHE A 338 "
        pdb=" CA  PHE A 338 "
        pdb=" C   PHE A 338 "
      ideal   model   delta    sigma   weight residual
     113.18  105.66    7.52 1.33e+00 5.65e-01 3.20e+01
  ... (remaining 9611 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.87: 3522
       15.87 -    31.73: 414
       31.73 -    47.60: 120
       47.60 -    63.47: 22
       63.47 -    79.33: 8
  Dihedral angle restraints: 4086
    sinusoidal: 1476
      harmonic: 2610
  Sorted by residual:
  dihedral pdb=" C   VAL B 384 "
           pdb=" N   VAL B 384 "
           pdb=" CA  VAL B 384 "
           pdb=" CB  VAL B 384 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -140.75   18.75     0      2.50e+00 1.60e-01 5.63e+01
  dihedral pdb=" C   VAL A 384 "
           pdb=" N   VAL A 384 "
           pdb=" CA  VAL A 384 "
           pdb=" CB  VAL A 384 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -140.74   18.74     0      2.50e+00 1.60e-01 5.62e+01
  dihedral pdb=" C   ALA B 387 "
           pdb=" N   ALA B 387 "
           pdb=" CA  ALA B 387 "
           pdb=" CB  ALA B 387 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.26   16.66     0      2.50e+00 1.60e-01 4.44e+01
  ... (remaining 4083 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.137: 1150
       0.137 -    0.275: 10
       0.275 -    0.412: 0
       0.412 -    0.549: 0
       0.549 -    0.687: 4
  Chirality restraints: 1164
  Sorted by residual:
  chirality pdb=" CA  ALA B 387 "
            pdb=" N   ALA B 387 "
            pdb=" C   ALA B 387 "
            pdb=" CB  ALA B 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.80    0.69 2.00e-01 2.50e+01 1.18e+01
  chirality pdb=" CA  ALA A 387 "
            pdb=" N   ALA A 387 "
            pdb=" C   ALA A 387 "
            pdb=" CB  ALA A 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.80    0.68 2.00e-01 2.50e+01 1.17e+01
  chirality pdb=" CA  VAL A 384 "
            pdb=" N   VAL A 384 "
            pdb=" C   VAL A 384 "
            pdb=" CB  VAL A 384 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.84    0.60 2.00e-01 2.50e+01 9.12e+00
  ... (remaining 1161 not shown)

  Planarity restraints: 1176
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 382 "    0.010 2.00e-02 2.50e+03   1.90e-02 3.63e+00
        pdb=" C   SER B 382 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   SER B 382 "    0.012 2.00e-02 2.50e+03
        pdb=" N   VAL B 383 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 382 "   -0.010 2.00e-02 2.50e+03   1.90e-02 3.61e+00
        pdb=" C   SER A 382 "    0.033 2.00e-02 2.50e+03
        pdb=" O   SER A 382 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL A 383 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 398 "   -0.008 2.00e-02 2.50e+03   1.59e-02 2.53e+00
        pdb=" CD  GLU B 398 "    0.028 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 398 "   -0.010 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 398 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1173 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 130
        2.66 -     3.22: 6729
        3.22 -     3.78: 10012
        3.78 -     4.34: 13366
        4.34 -     4.90: 22412
  Nonbonded interactions: 52649
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 378 "
            pdb=" OG1 THR B 395 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" OD2 ASP A 378 "
            pdb=" OG1 THR A 395 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" OG1 THR A 192 "
            pdb=" OE1 GLU A 463 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OG1 THR B 192 "
            pdb=" OE1 GLU B 463 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" NH2 ARG B 194 "
            pdb=" OE1 GLU B 358 "
     model   vdw
     2.237 3.120
  ... (remaining 52644 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:             1.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.680
  Find NCS groups from input model:        0.040
  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:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
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      :  0.005   0.068   7086  Z= 0.297
  Angle     :  0.933  18.294   9624  Z= 0.516
  Chirality :  0.058   0.687   1164
  Planarity :  0.003   0.035   1176
  Dihedral  : 15.225  79.334   2422
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.85 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 26.30 %
    Favored  : 73.15 %
  Cbeta Deviations :  0.48 %
  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 aren not related in a simple way.
  whole: -1.88 (0.28), residues: 922
  helix: -0.40 (0.24), residues: 516
  sheet:  None (None), residues: 0
  loop : -2.38 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 152 
 TYR   0.009   0.001   TYR B 343 
 PHE   0.011   0.001   PHE A 425 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.004   0.001   HIS B 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 7082)
  covalent geometry    : angle       0.93283 ( 9616)
  SS BOND              : bond        0.00204 (    4)
  SS BOND              : angle       0.54471 (    8)
  hydrogen bonds       : bond        0.23506 (  321)
  hydrogen bonds       : angle       7.08466 (  915)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 125
  time to evaluate  : 0.163 
Fit side-chains
REVERT: B  313 ASP cc_start: 0.7667 (t70) cc_final: 0.7461 (t70)
  outliers start: 4
  outliers final: 4
  residues processed: 127
  average time/residue: 0.0616
  time to fit residues: 11.5522
Evaluate side-chains
  117 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 113
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  235 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3912 r_free = 0.3912 target = 0.166925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.136301 restraints weight = 8884.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.139567 restraints weight = 5509.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.141931 restraints weight = 4155.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.143321 restraints weight = 3480.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.143687 restraints weight = 3129.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7086  Z= 0.131
  Angle     :  0.676  12.203   9624  Z= 0.339
  Chirality :  0.041   0.139   1164
  Planarity :  0.003   0.041   1176
  Dihedral  :  6.536  49.766    996
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 21.92 %
    Favored  : 72.74 %
  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 aren not related in a simple way.
  whole: -1.54 (0.28), residues: 922
  helix: -0.20 (0.23), residues: 540
  sheet:  None (None), residues: 0
  loop : -2.22 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 194 
 TYR   0.017   0.001   TYR A 159 
 PHE   0.008   0.001   PHE B 425 
 TRP   0.006   0.001   TRP B 335 
 HIS   0.004   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7082)
  covalent geometry    : angle       0.67573 ( 9616)
  SS BOND              : bond        0.00158 (    4)
  SS BOND              : angle       0.46851 (    8)
  hydrogen bonds       : bond        0.04712 (  321)
  hydrogen bonds       : angle       4.55865 (  915)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 134
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  260 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7782 (mp)
REVERT: B  260 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7753 (mp)
  outliers start: 39
  outliers final: 22
  residues processed: 159
  average time/residue: 0.0631
  time to fit residues: 14.6681
Evaluate side-chains
  144 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  496 MET
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  263 SER
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  327 THR
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  496 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0040
   chunk 6 optimal weight:    3.9990
   chunk 52 optimal weight:    0.3980
   chunk 71 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.5592

-------------------------------------------------------------------------------
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 = 0.3678 r_free = 0.3678 target = 0.149912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.116002 restraints weight = 9312.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.119932 restraints weight = 5274.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.122463 restraints weight = 3741.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.124066 restraints weight = 3033.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.124967 restraints weight = 2671.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   7086  Z= 0.112
  Angle     :  0.624   8.741   9624  Z= 0.315
  Chirality :  0.040   0.138   1164
  Planarity :  0.003   0.037   1176
  Dihedral  :  6.123  45.873    994
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.63 %
    Favored  : 89.37 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 23.29 %
    Favored  : 70.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.28), residues: 922
  helix: -0.03 (0.23), residues: 544
  sheet:  None (None), residues: 0
  loop : -2.25 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 435 
 TYR   0.011   0.001   TYR A 343 
 PHE   0.009   0.001   PHE A 425 
 TRP   0.005   0.001   TRP A 436 
 HIS   0.004   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 7082)
  covalent geometry    : angle       0.62403 ( 9616)
  SS BOND              : bond        0.00138 (    4)
  SS BOND              : angle       0.49940 (    8)
  hydrogen bonds       : bond        0.03963 (  321)
  hydrogen bonds       : angle       4.03136 (  915)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 129
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  411 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7005 (tt)
REVERT: A  463 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7389 (mm-30)
REVERT: B  411 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.6892 (tt)
REVERT: B  463 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7385 (mm-30)
  outliers start: 42
  outliers final: 23
  residues processed: 157
  average time/residue: 0.0570
  time to fit residues: 13.4043
Evaluate side-chains
  144 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  263 SER
Chi-restraints excluded: chain B residue  327 THR
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  411 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 72 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0470
   overall best weight:    0.7882

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.148660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.114862 restraints weight = 9315.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.118629 restraints weight = 5390.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.121169 restraints weight = 3883.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.122736 restraints weight = 3190.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.123683 restraints weight = 2823.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7086  Z= 0.123
  Angle     :  0.610   7.199   9624  Z= 0.312
  Chirality :  0.040   0.136   1164
  Planarity :  0.003   0.034   1176
  Dihedral  :  6.061  47.069    994
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.85 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 23.56 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.34 (0.28), residues: 922
  helix:  0.08 (0.23), residues: 542
  sheet: -2.89 (1.01), residues: 20
  loop : -2.27 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 435 
 TYR   0.011   0.001   TYR B 343 
 PHE   0.008   0.001   PHE B  51 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.004   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7082)
  covalent geometry    : angle       0.60988 ( 9616)
  SS BOND              : bond        0.00240 (    4)
  SS BOND              : angle       0.56458 (    8)
  hydrogen bonds       : bond        0.04006 (  321)
  hydrogen bonds       : angle       3.83700 (  915)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 132
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  247 MET cc_start: 0.8648 (mmm) cc_final: 0.7995 (mmm)
REVERT: A  260 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7635 (mp)
REVERT: A  331 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7437 (ptpp)
REVERT: A  411 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7156 (tt)
REVERT: A  463 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7436 (mm-30)
REVERT: B  163 MET cc_start: 0.7122 (tpp) cc_final: 0.6791 (mmp)
REVERT: B  260 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7655 (mp)
REVERT: B  331 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7409 (ptpp)
REVERT: B  411 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7119 (tt)
REVERT: B  463 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7411 (mm-30)
  outliers start: 39
  outliers final: 28
  residues processed: 161
  average time/residue: 0.0625
  time to fit residues: 14.5314
Evaluate side-chains
  159 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 125
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  263 SER
Chi-restraints excluded: chain B residue  327 THR
Chi-restraints excluded: chain B residue  331 LYS
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  461 THR
Chi-restraints excluded: chain B residue  494 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 82 optimal weight:    0.3980
   chunk 68 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0020
   chunk 43 optimal weight:    0.7980
   chunk 71 optimal weight:    0.2980
   chunk 88 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.4188

-------------------------------------------------------------------------------
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 = 0.3706 r_free = 0.3706 target = 0.151605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.117662 restraints weight = 9330.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.121495 restraints weight = 5299.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.124097 restraints weight = 3785.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.125682 restraints weight = 3093.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.126358 restraints weight = 2734.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7086  Z= 0.102
  Angle     :  0.594   6.738   9624  Z= 0.302
  Chirality :  0.040   0.145   1164
  Planarity :  0.003   0.034   1176
  Dihedral  :  5.770  43.252    994
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.63 %
    Favored  : 89.37 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 23.29 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.28), residues: 922
  helix:  0.22 (0.24), residues: 544
  sheet: -2.98 (0.99), residues: 20
  loop : -2.18 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 435 
 TYR   0.016   0.001   TYR B 159 
 PHE   0.007   0.001   PHE B 425 
 TRP   0.003   0.001   TRP B 335 
 HIS   0.004   0.001   HIS B 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 7082)
  covalent geometry    : angle       0.59431 ( 9616)
  SS BOND              : bond        0.00180 (    4)
  SS BOND              : angle       0.43982 (    8)
  hydrogen bonds       : bond        0.03477 (  321)
  hydrogen bonds       : angle       3.71522 (  915)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 124
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  247 MET cc_start: 0.8636 (mmm) cc_final: 0.8061 (mmm)
REVERT: A  260 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7669 (mp)
REVERT: A  329 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7193 (m-80)
REVERT: A  331 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7427 (ptpp)
REVERT: A  463 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7451 (mm-30)
REVERT: B  234 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7810 (mt-10)
REVERT: B  260 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7682 (mp)
REVERT: B  329 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7214 (m-80)
REVERT: B  331 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7406 (ptpp)
REVERT: B  463 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7499 (mm-30)
  outliers start: 38
  outliers final: 25
  residues processed: 151
  average time/residue: 0.0598
  time to fit residues: 13.5823
Evaluate side-chains
  147 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  329 PHE
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  263 SER
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  327 THR
Chi-restraints excluded: chain B residue  329 PHE
Chi-restraints excluded: chain B residue  331 LYS
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain B residue  461 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 25 optimal weight:    0.1980
   chunk 53 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3677 r_free = 0.3677 target = 0.148618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.114997 restraints weight = 9129.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.118711 restraints weight = 5281.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.121168 restraints weight = 3783.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.122600 restraints weight = 3093.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.123258 restraints weight = 2749.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7086  Z= 0.139
  Angle     :  0.630   9.963   9624  Z= 0.319
  Chirality :  0.042   0.174   1164
  Planarity :  0.003   0.033   1176
  Dihedral  :  6.073  50.300    994
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.63 %
    Favored  : 89.37 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 23.84 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.20 (0.28), residues: 922
  helix:  0.23 (0.24), residues: 542
  sheet: -2.97 (0.96), residues: 20
  loop : -2.28 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 435 
 TYR   0.010   0.001   TYR B 343 
 PHE   0.019   0.001   PHE B 338 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.004   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7082)
  covalent geometry    : angle       0.63008 ( 9616)
  SS BOND              : bond        0.00246 (    4)
  SS BOND              : angle       0.52686 (    8)
  hydrogen bonds       : bond        0.04195 (  321)
  hydrogen bonds       : angle       3.83224 (  915)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 127
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6414 (p) cc_final: 0.6004 (t)
REVERT: A  247 MET cc_start: 0.8816 (mmm) cc_final: 0.8215 (mmm)
REVERT: A  260 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7450 (mp)
REVERT: A  329 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7157 (m-80)
REVERT: A  331 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7327 (ptpp)
REVERT: A  463 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7391 (mm-30)
REVERT: B  247 MET cc_start: 0.8797 (mmm) cc_final: 0.8071 (mmm)
REVERT: B  260 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7439 (mp)
REVERT: B  329 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7121 (m-80)
REVERT: B  331 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7273 (ptpp)
REVERT: B  463 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7465 (mm-30)
  outliers start: 37
  outliers final: 26
  residues processed: 156
  average time/residue: 0.0564
  time to fit residues: 13.2735
Evaluate side-chains
  152 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 120
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  329 PHE
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  263 SER
Chi-restraints excluded: chain B residue  327 THR
Chi-restraints excluded: chain B residue  329 PHE
Chi-restraints excluded: chain B residue  331 LYS
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  494 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0980
   chunk 23 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0060
   chunk 59 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.5196

-------------------------------------------------------------------------------
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 = 0.3720 r_free = 0.3720 target = 0.152459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.118980 restraints weight = 9089.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.122759 restraints weight = 5278.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.125160 restraints weight = 3788.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.126772 restraints weight = 3100.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.127568 restraints weight = 2740.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7086  Z= 0.107
  Angle     :  0.612   8.297   9624  Z= 0.307
  Chirality :  0.040   0.133   1164
  Planarity :  0.003   0.033   1176
  Dihedral  :  5.803  48.857    994
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.20 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 24.11 %
    Favored  : 71.64 %
  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 aren not related in a simple way.
  whole: -1.03 (0.28), residues: 922
  helix:  0.34 (0.24), residues: 544
  sheet: -3.03 (0.96), residues: 20
  loop : -2.15 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 435 
 TYR   0.009   0.001   TYR B 343 
 PHE   0.018   0.001   PHE A 338 
 TRP   0.004   0.001   TRP A 335 
 HIS   0.003   0.001   HIS B 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 7082)
  covalent geometry    : angle       0.61235 ( 9616)
  SS BOND              : bond        0.00230 (    4)
  SS BOND              : angle       0.49421 (    8)
  hydrogen bonds       : bond        0.03424 (  321)
  hydrogen bonds       : angle       3.69338 (  915)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6384 (p) cc_final: 0.6015 (t)
REVERT: A  234 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7813 (mt-10)
REVERT: A  247 MET cc_start: 0.8645 (mmm) cc_final: 0.8079 (mmm)
REVERT: A  260 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7650 (mp)
REVERT: A  329 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7252 (m-80)
REVERT: A  435 ARG cc_start: 0.7598 (ptt90) cc_final: 0.6876 (mtm110)
REVERT: A  448 MET cc_start: 0.8177 (ttm) cc_final: 0.7939 (ttm)
REVERT: A  463 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7439 (mm-30)
REVERT: B  156 SER cc_start: 0.6501 (p) cc_final: 0.6079 (t)
REVERT: B  234 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7834 (mt-10)
REVERT: B  247 MET cc_start: 0.8637 (mmm) cc_final: 0.7970 (mmm)
REVERT: B  260 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7649 (mp)
REVERT: B  329 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7280 (m-80)
REVERT: B  435 ARG cc_start: 0.7655 (ptt90) cc_final: 0.6902 (mtm110)
REVERT: B  448 MET cc_start: 0.8172 (ttm) cc_final: 0.7969 (ttm)
REVERT: B  463 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7432 (mm-30)
  outliers start: 31
  outliers final: 23
  residues processed: 158
  average time/residue: 0.0707
  time to fit residues: 16.0493
Evaluate side-chains
  154 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 127
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  329 PHE
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  263 SER
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  327 THR
Chi-restraints excluded: chain B residue  329 PHE
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain B residue  461 THR
Chi-restraints excluded: chain B residue  494 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0050
   chunk 91 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0980
   chunk 75 optimal weight:    0.9980
   chunk 88 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   overall best weight:    0.5394

-------------------------------------------------------------------------------
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 = 0.3681 r_free = 0.3681 target = 0.149449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.115558 restraints weight = 9315.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.119379 restraints weight = 5323.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.121913 restraints weight = 3806.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.123496 restraints weight = 3109.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.124586 restraints weight = 2750.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7086  Z= 0.111
  Angle     :  0.619   7.410   9624  Z= 0.314
  Chirality :  0.040   0.132   1164
  Planarity :  0.003   0.033   1176
  Dihedral  :  5.443  48.439    988
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.52 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 25.07 %
    Favored  : 70.41 %
  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 aren not related in a simple way.
  whole: -0.93 (0.28), residues: 922
  helix:  0.41 (0.24), residues: 544
  sheet:  None (None), residues: 0
  loop : -2.19 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 435 
 TYR   0.009   0.001   TYR B 307 
 PHE   0.018   0.001   PHE B 338 
 TRP   0.004   0.001   TRP A 436 
 HIS   0.003   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 7082)
  covalent geometry    : angle       0.61917 ( 9616)
  SS BOND              : bond        0.00247 (    4)
  SS BOND              : angle       0.45497 (    8)
  hydrogen bonds       : bond        0.03522 (  321)
  hydrogen bonds       : angle       3.68054 (  915)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6398 (p) cc_final: 0.6008 (t)
REVERT: A  234 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7688 (mt-10)
REVERT: A  247 MET cc_start: 0.8595 (mmm) cc_final: 0.7976 (mmm)
REVERT: A  260 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7737 (mp)
REVERT: A  266 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8629 (mt)
REVERT: A  329 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7306 (m-80)
REVERT: A  435 ARG cc_start: 0.7611 (ptt90) cc_final: 0.6940 (mtm110)
REVERT: A  463 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7442 (mm-30)
REVERT: B  156 SER cc_start: 0.6506 (p) cc_final: 0.6076 (t)
REVERT: B  234 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7714 (mt-10)
REVERT: B  247 MET cc_start: 0.8598 (mmm) cc_final: 0.7937 (mmm)
REVERT: B  260 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7748 (mp)
REVERT: B  329 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7291 (m-80)
REVERT: B  435 ARG cc_start: 0.7699 (ptt90) cc_final: 0.6977 (mtm110)
REVERT: B  463 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7433 (mm-30)
  outliers start: 33
  outliers final: 25
  residues processed: 150
  average time/residue: 0.0663
  time to fit residues: 14.6149
Evaluate side-chains
  156 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 126
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  329 PHE
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  263 SER
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  327 THR
Chi-restraints excluded: chain B residue  329 PHE
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain B residue  461 THR
Chi-restraints excluded: chain B residue  494 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 70 optimal weight:    0.5980
   chunk 68 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A  19 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.150293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.116255 restraints weight = 9119.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.120026 restraints weight = 5294.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.122421 restraints weight = 3808.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.123987 restraints weight = 3134.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.124854 restraints weight = 2780.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7086  Z= 0.127
  Angle     :  0.641   7.217   9624  Z= 0.327
  Chirality :  0.041   0.132   1164
  Planarity :  0.003   0.033   1176
  Dihedral  :  5.657  54.066    988
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.30 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 26.16 %
    Favored  : 70.00 %
  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 aren not related in a simple way.
  whole: -0.88 (0.28), residues: 922
  helix:  0.46 (0.24), residues: 544
  sheet:  None (None), residues: 0
  loop : -2.19 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 435 
 TYR   0.010   0.001   TYR A 307 
 PHE   0.017   0.001   PHE A 338 
 TRP   0.005   0.001   TRP A 436 
 HIS   0.004   0.001   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7082)
  covalent geometry    : angle       0.64062 ( 9616)
  SS BOND              : bond        0.00273 (    4)
  SS BOND              : angle       0.54180 (    8)
  hydrogen bonds       : bond        0.03850 (  321)
  hydrogen bonds       : angle       3.77830 (  915)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 125
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6613 (p) cc_final: 0.5968 (t)
REVERT: A  234 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7792 (mt-10)
REVERT: A  247 MET cc_start: 0.8761 (mmm) cc_final: 0.8173 (mmm)
REVERT: A  260 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7524 (mp)
REVERT: A  269 ASN cc_start: 0.7077 (m-40) cc_final: 0.6842 (p0)
REVERT: A  314 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7376 (t80)
REVERT: A  329 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7206 (m-80)
REVERT: A  435 ARG cc_start: 0.7632 (ptt90) cc_final: 0.6805 (mtm110)
REVERT: A  463 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7452 (mm-30)
REVERT: B  156 SER cc_start: 0.6533 (p) cc_final: 0.6140 (t)
REVERT: B  234 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7768 (mt-10)
REVERT: B  247 MET cc_start: 0.8723 (mmm) cc_final: 0.8028 (mmm)
REVERT: B  260 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7535 (mp)
REVERT: B  269 ASN cc_start: 0.7076 (m-40) cc_final: 0.6839 (p0)
REVERT: B  329 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7256 (m-80)
REVERT: B  435 ARG cc_start: 0.7562 (ptt90) cc_final: 0.6822 (mtm110)
REVERT: B  463 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7458 (mm-30)
  outliers start: 28
  outliers final: 22
  residues processed: 146
  average time/residue: 0.0670
  time to fit residues: 14.3204
Evaluate side-chains
  147 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  314 PHE
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  329 PHE
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  263 SER
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  329 PHE
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain B residue  461 THR
Chi-restraints excluded: chain B residue  494 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 84 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 74 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  19 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.149748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.115725 restraints weight = 9128.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.119460 restraints weight = 5312.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.121907 restraints weight = 3835.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.123104 restraints weight = 3153.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.124270 restraints weight = 2831.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7086  Z= 0.130
  Angle     :  0.656   9.106   9624  Z= 0.333
  Chirality :  0.041   0.143   1164
  Planarity :  0.003   0.032   1176
  Dihedral  :  5.668  49.569    988
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 26.58 %
    Favored  : 69.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.28), residues: 922
  helix:  0.51 (0.24), residues: 544
  sheet:  None (None), residues: 0
  loop : -2.19 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 435 
 TYR   0.010   0.001   TYR A 307 
 PHE   0.016   0.001   PHE A 338 
 TRP   0.005   0.001   TRP B 436 
 HIS   0.003   0.001   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7082)
  covalent geometry    : angle       0.65596 ( 9616)
  SS BOND              : bond        0.00266 (    4)
  SS BOND              : angle       0.56382 (    8)
  hydrogen bonds       : bond        0.03882 (  321)
  hydrogen bonds       : angle       3.80798 (  915)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 121
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6441 (p) cc_final: 0.6152 (t)
REVERT: A  234 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7755 (mt-10)
REVERT: A  247 MET cc_start: 0.8744 (mmm) cc_final: 0.8160 (mmm)
REVERT: A  260 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7578 (mp)
REVERT: A  314 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7207 (t80)
REVERT: A  329 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7398 (m-80)
REVERT: A  435 ARG cc_start: 0.7611 (ptt90) cc_final: 0.6775 (mtm110)
REVERT: A  463 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7445 (mm-30)
REVERT: B  156 SER cc_start: 0.6515 (p) cc_final: 0.5935 (t)
REVERT: B  234 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7835 (mt-10)
REVERT: B  247 MET cc_start: 0.8710 (mmm) cc_final: 0.8017 (mmm)
REVERT: B  260 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7582 (mp)
REVERT: B  329 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7391 (m-80)
REVERT: B  435 ARG cc_start: 0.7576 (ptt90) cc_final: 0.6863 (mtm110)
REVERT: B  463 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7452 (mm-30)
  outliers start: 31
  outliers final: 22
  residues processed: 146
  average time/residue: 0.0654
  time to fit residues: 14.0916
Evaluate side-chains
  148 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 121
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  314 PHE
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  329 PHE
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  263 SER
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  329 PHE
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain B residue  452 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 46 optimal weight:   10.0000
   chunk 58 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0570
   chunk 14 optimal weight:    2.9990
   chunk 45 optimal weight:    0.2980
   chunk 87 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 = 0.3654 r_free = 0.3654 target = 0.147864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.115135 restraints weight = 8948.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.118742 restraints weight = 5124.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.120885 restraints weight = 3657.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.122554 restraints weight = 2998.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.123271 restraints weight = 2638.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7086  Z= 0.112
  Angle     :  0.639   8.381   9624  Z= 0.322
  Chirality :  0.041   0.139   1164
  Planarity :  0.003   0.032   1176
  Dihedral  :  5.439  46.968    988
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 27.12 %
    Favored  : 69.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.74 (0.28), residues: 922
  helix:  0.62 (0.24), residues: 538
  sheet:  None (None), residues: 0
  loop : -2.15 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 435 
 TYR   0.009   0.001   TYR B 307 
 PHE   0.016   0.001   PHE B 338 
 TRP   0.003   0.001   TRP B 436 
 HIS   0.004   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7082)
  covalent geometry    : angle       0.63873 ( 9616)
  SS BOND              : bond        0.00208 (    4)
  SS BOND              : angle       0.44030 (    8)
  hydrogen bonds       : bond        0.03449 (  321)
  hydrogen bonds       : angle       3.73199 (  915)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1232.17 seconds
wall clock time: 21 minutes 57.51 seconds (1317.51 seconds total)