Starting phenix.real_space_refine
on Sat May 10 22:17:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j18_61071/05_2025/9j18_61071.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j18_61071/05_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_61071/05_2025/9j18_61071.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j18_61071/05_2025/9j18_61071.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j18_61071/05_2025/9j18_61071.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j18_61071/05_2025/9j18_61071.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.046
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.24, per 1000 atoms: 0.90
  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: 1.79
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.80
  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: 1.90

  Time building geometry restraints manager: 2.04 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: 0.04
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:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.930
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.950
-------------------------------------------------------------------------------
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 : 10.02
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (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
 TRP   0.008   0.001   TRP A 436 
 HIS   0.004   0.001   HIS B 160 
 PHE   0.011   0.001   PHE A 425 
 TYR   0.009   0.001   TYR B 343 
 ARG   0.002   0.000   ARG B 152 

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

*********************** 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  : 0.729 
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: 0.1396
  time to fit residues: 25.8753
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  : 0.739 
-------------------------------------------------------------------------------
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 77 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    0.4980
   chunk 23 optimal weight:    0.0980
   chunk 47 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3926 r_free = 0.3926 target = 0.168133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.137552 restraints weight = 8723.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.140876 restraints weight = 5458.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.142992 restraints weight = 4130.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.1284

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= 0.124
  Angle     :  0.670  12.295   9624  Z= 0.335
  Chirality :  0.041   0.139   1164
  Planarity :  0.003   0.043   1176
  Dihedral  :  6.486  49.086    996
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.87 %
    Favored  : 90.13 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 22.47 %
    Favored  : 72.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.28), residues: 922
  helix: -0.21 (0.23), residues: 540
  sheet:  None (None), residues: 0
  loop : -2.21 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 335 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.009   0.001   PHE B 425 
 TYR   0.018   0.001   TYR A 159 
 ARG   0.002   0.000   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04520 (  321)
  hydrogen bonds       : angle       4.53294 (  915)
  SS BOND              : bond        0.00147 (    4)
  SS BOND              : angle       0.43611 (    8)
  covalent geometry    : bond        0.00259 ( 7082)
  covalent geometry    : angle       0.67035 ( 9616)

*********************** 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  : 0.769 
Fit side-chains
REVERT: A  260 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7797 (mp)
REVERT: B  260 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7782 (mp)
  outliers start: 39
  outliers final: 21
  residues processed: 158
  average time/residue: 0.1379
  time to fit residues: 31.4833
Evaluate side-chains
  142 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
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  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 41 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 82 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0050
   chunk 74 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.7394

-------------------------------------------------------------------------------
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 = 0.3915 r_free = 0.3915 target = 0.167147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.135736 restraints weight = 8900.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.139100 restraints weight = 5650.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.141203 restraints weight = 4305.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   7086  Z= 0.122
  Angle     :  0.630   8.645   9624  Z= 0.320
  Chirality :  0.040   0.139   1164
  Planarity :  0.003   0.036   1176
  Dihedral  :  6.187  46.342    994
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.63 %
    Favored  : 89.37 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 24.52 %
    Favored  : 70.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.28), residues: 922
  helix: -0.02 (0.23), residues: 542
  sheet:  None (None), residues: 0
  loop : -2.37 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 436 
 HIS   0.005   0.001   HIS A 160 
 PHE   0.009   0.001   PHE A 425 
 TYR   0.012   0.001   TYR A 343 
 ARG   0.002   0.000   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04238 (  321)
  hydrogen bonds       : angle       4.03258 (  915)
  SS BOND              : bond        0.00196 (    4)
  SS BOND              : angle       0.56481 (    8)
  covalent geometry    : bond        0.00266 ( 7082)
  covalent geometry    : angle       0.62964 ( 9616)

*********************** 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
  167 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 129
  time to evaluate  : 0.687 
Fit side-chains
REVERT: A  247 MET cc_start: 0.8289 (mmm) cc_final: 0.7737 (mmm)
REVERT: A  260 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7750 (mp)
REVERT: A  411 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7238 (tt)
REVERT: A  463 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7264 (mm-30)
REVERT: B  260 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7750 (mp)
REVERT: B  411 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7194 (tt)
REVERT: B  463 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7248 (mm-30)
  outliers start: 38
  outliers final: 21
  residues processed: 157
  average time/residue: 0.1435
  time to fit residues: 31.8815
Evaluate side-chains
  147 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
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  386 SER
Chi-restraints excluded: chain A residue  411 LEU
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  386 SER
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 62 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0770
   chunk 77 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.7142

-------------------------------------------------------------------------------
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 = 0.148883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.114318 restraints weight = 9411.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.118322 restraints weight = 5154.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.121157 restraints weight = 3611.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.1918

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= 0.117
  Angle     :  0.610   7.201   9624  Z= 0.311
  Chirality :  0.040   0.136   1164
  Planarity :  0.003   0.035   1176
  Dihedral  :  6.041  45.067    994
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.95 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 23.56 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.28), residues: 922
  helix:  0.07 (0.23), residues: 544
  sheet: -2.75 (1.01), residues: 20
  loop : -2.31 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 436 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.008   0.001   PHE B 425 
 TYR   0.013   0.001   TYR B 159 
 ARG   0.006   0.000   ARG B 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03894 (  321)
  hydrogen bonds       : angle       3.80513 (  915)
  SS BOND              : bond        0.00226 (    4)
  SS BOND              : angle       0.54691 (    8)
  covalent geometry    : bond        0.00256 ( 7082)
  covalent geometry    : angle       0.61036 ( 9616)

*********************** 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
  175 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 135
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A  247 MET cc_start: 0.8800 (mmm) cc_final: 0.8238 (mmm)
REVERT: A  260 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7504 (mp)
REVERT: A  331 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7098 (ptpp)
REVERT: A  411 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7041 (tt)
REVERT: A  448 MET cc_start: 0.8191 (ttm) cc_final: 0.7933 (ttm)
REVERT: A  463 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7458 (mm-30)
REVERT: B  260 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7517 (mp)
REVERT: B  331 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7054 (ptpp)
REVERT: B  411 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7055 (tt)
REVERT: B  448 MET cc_start: 0.8188 (ttm) cc_final: 0.7932 (ttm)
REVERT: B  463 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7481 (mm-30)
  outliers start: 40
  outliers final: 26
  residues processed: 164
  average time/residue: 0.1399
  time to fit residues: 33.2910
Evaluate side-chains
  159 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
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  321 LEU
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  461 THR
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  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 23 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 80 optimal weight:    0.5980
   chunk 45 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0980
   chunk 59 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.151050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.117135 restraints weight = 9205.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.120989 restraints weight = 5280.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.123569 restraints weight = 3791.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7086  Z= 0.108
  Angle     :  0.602   6.784   9624  Z= 0.304
  Chirality :  0.040   0.148   1164
  Planarity :  0.003   0.035   1176
  Dihedral  :  5.837  42.133    994
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.85 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 23.70 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.28), residues: 922
  helix:  0.18 (0.24), residues: 546
  sheet: -2.95 (0.98), residues: 20
  loop : -2.27 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 436 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.019   0.001   PHE A 338 
 TYR   0.016   0.001   TYR A 159 
 ARG   0.004   0.000   ARG B 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03637 (  321)
  hydrogen bonds       : angle       3.70921 (  915)
  SS BOND              : bond        0.00201 (    4)
  SS BOND              : angle       0.46812 (    8)
  covalent geometry    : bond        0.00232 ( 7082)
  covalent geometry    : angle       0.60161 ( 9616)

*********************** 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
  166 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 130
  time to evaluate  : 0.698 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6461 (p) cc_final: 0.6180 (t)
REVERT: A  247 MET cc_start: 0.8821 (mmm) cc_final: 0.8247 (mmm)
REVERT: A  260 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7473 (mp)
REVERT: A  331 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7164 (ptpp)
REVERT: A  463 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7476 (mm-30)
REVERT: B  156 SER cc_start: 0.6481 (p) cc_final: 0.6191 (t)
REVERT: B  260 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7456 (mp)
REVERT: B  313 ASP cc_start: 0.7402 (t70) cc_final: 0.7118 (t70)
REVERT: B  331 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7080 (ptpp)
REVERT: B  463 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7418 (mm-30)
  outliers start: 36
  outliers final: 27
  residues processed: 155
  average time/residue: 0.1285
  time to fit residues: 29.0954
Evaluate side-chains
  154 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 123
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
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  331 LYS
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  461 THR
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  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  331 LYS
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain B residue  390 VAL
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 41 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0670
   chunk 59 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.148920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.115205 restraints weight = 9325.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.119072 restraints weight = 5304.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.121579 restraints weight = 3783.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7086  Z= 0.113
  Angle     :  0.610   9.856   9624  Z= 0.305
  Chirality :  0.040   0.132   1164
  Planarity :  0.003   0.034   1176
  Dihedral  :  5.820  42.625    994
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.52 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 24.52 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.28), residues: 922
  helix:  0.27 (0.24), residues: 544
  sheet: -3.01 (0.97), residues: 20
  loop : -2.23 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 436 
 HIS   0.003   0.001   HIS B 160 
 PHE   0.016   0.001   PHE A 338 
 TYR   0.010   0.001   TYR A 497 
 ARG   0.003   0.000   ARG B 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03700 (  321)
  hydrogen bonds       : angle       3.70013 (  915)
  SS BOND              : bond        0.00229 (    4)
  SS BOND              : angle       0.49298 (    8)
  covalent geometry    : bond        0.00246 ( 7082)
  covalent geometry    : angle       0.61019 ( 9616)

*********************** 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
  166 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 129
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6291 (p) cc_final: 0.5961 (t)
REVERT: A  247 MET cc_start: 0.8598 (mmm) cc_final: 0.8061 (mmm)
REVERT: A  260 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7695 (mp)
REVERT: A  329 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7293 (m-80)
REVERT: A  331 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7479 (ptpp)
REVERT: A  463 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7409 (mm-30)
REVERT: B  156 SER cc_start: 0.6252 (p) cc_final: 0.5898 (t)
REVERT: B  163 MET cc_start: 0.7172 (tpp) cc_final: 0.6785 (mmp)
REVERT: B  247 MET cc_start: 0.8573 (mmm) cc_final: 0.7888 (mmm)
REVERT: B  260 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7697 (mp)
REVERT: B  329 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7241 (m-80)
REVERT: B  331 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7411 (ptpp)
REVERT: B  463 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7385 (mm-30)
  outliers start: 37
  outliers final: 28
  residues processed: 159
  average time/residue: 0.1415
  time to fit residues: 32.0628
Evaluate side-chains
  156 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 122
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
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  390 VAL
Chi-restraints excluded: chain A residue  452 VAL
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  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  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  390 VAL
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 69 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9980
   chunk 10 optimal weight:    0.4980
   chunk 73 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 57 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.147983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.114717 restraints weight = 9220.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.118482 restraints weight = 5248.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.120931 restraints weight = 3745.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7086  Z= 0.119
  Angle     :  0.622   8.374   9624  Z= 0.314
  Chirality :  0.040   0.177   1164
  Planarity :  0.003   0.033   1176
  Dihedral  :  5.842  43.529    994
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.52 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 24.79 %
    Favored  : 70.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.28), residues: 922
  helix:  0.31 (0.24), residues: 544
  sheet: -3.09 (0.94), residues: 20
  loop : -2.24 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 436 
 HIS   0.003   0.001   HIS A 160 
 PHE   0.015   0.001   PHE B 338 
 TYR   0.009   0.001   TYR B 343 
 ARG   0.006   0.000   ARG A 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03692 (  321)
  hydrogen bonds       : angle       3.73243 (  915)
  SS BOND              : bond        0.00275 (    4)
  SS BOND              : angle       0.55287 (    8)
  covalent geometry    : bond        0.00263 ( 7082)
  covalent geometry    : angle       0.62163 ( 9616)

*********************** 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
  167 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 131
  time to evaluate  : 0.717 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6337 (p) cc_final: 0.5939 (t)
REVERT: A  163 MET cc_start: 0.7064 (tpp) cc_final: 0.6645 (mmp)
REVERT: A  234 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7848 (mt-10)
REVERT: A  247 MET cc_start: 0.8660 (mmm) cc_final: 0.8111 (mmm)
REVERT: A  260 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7652 (mp)
REVERT: A  307 TYR cc_start: 0.8376 (t80) cc_final: 0.8172 (t80)
REVERT: A  329 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7268 (m-80)
REVERT: A  435 ARG cc_start: 0.7588 (ptt90) cc_final: 0.6881 (mtm110)
REVERT: A  448 MET cc_start: 0.8178 (ttm) cc_final: 0.7977 (ttm)
REVERT: A  463 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7461 (mm-30)
REVERT: B  156 SER cc_start: 0.6318 (p) cc_final: 0.5876 (t)
REVERT: B  163 MET cc_start: 0.7057 (tpp) cc_final: 0.6644 (mmp)
REVERT: B  247 MET cc_start: 0.8624 (mmm) cc_final: 0.7948 (mmm)
REVERT: B  260 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7659 (mp)
REVERT: B  329 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7284 (m-80)
REVERT: B  435 ARG cc_start: 0.7590 (ptt90) cc_final: 0.6873 (mtm110)
REVERT: B  463 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7412 (mm-30)
  outliers start: 36
  outliers final: 29
  residues processed: 158
  average time/residue: 0.1452
  time to fit residues: 32.5048
Evaluate side-chains
  160 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 127
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
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  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  329 PHE
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  390 VAL
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  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  386 SER
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    1.7188

-------------------------------------------------------------------------------
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 = 0.3620 r_free = 0.3620 target = 0.143397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.110280 restraints weight = 9213.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.113756 restraints weight = 5363.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.116066 restraints weight = 3887.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   7086  Z= 0.206
  Angle     :  0.710   8.025   9624  Z= 0.364
  Chirality :  0.044   0.154   1164
  Planarity :  0.004   0.031   1176
  Dihedral  :  6.597  56.065    994
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.63 %
    Favored  : 89.37 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 24.11 %
    Favored  : 69.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.27), residues: 922
  helix:  0.14 (0.23), residues: 540
  sheet:  None (None), residues: 0
  loop : -2.38 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 436 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.016   0.002   PHE A 338 
 TYR   0.015   0.002   TYR B 307 
 ARG   0.006   0.001   ARG A 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05233 (  321)
  hydrogen bonds       : angle       4.16867 (  915)
  SS BOND              : bond        0.00449 (    4)
  SS BOND              : angle       0.82386 (    8)
  covalent geometry    : bond        0.00490 ( 7082)
  covalent geometry    : angle       0.70977 ( 9616)

*********************** 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
  171 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 127
  time to evaluate  : 0.817 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6544 (p) cc_final: 0.6128 (t)
REVERT: A  260 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7363 (mp)
REVERT: A  269 ASN cc_start: 0.7189 (m-40) cc_final: 0.6975 (p0)
REVERT: A  314 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7203 (t80)
REVERT: A  329 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.7060 (m-80)
REVERT: A  448 MET cc_start: 0.8265 (ttm) cc_final: 0.7975 (ttm)
REVERT: A  463 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7427 (mm-30)
REVERT: B  156 SER cc_start: 0.6635 (p) cc_final: 0.6230 (t)
REVERT: B  260 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7369 (mp)
REVERT: B  269 ASN cc_start: 0.7195 (m-40) cc_final: 0.6983 (p0)
REVERT: B  329 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7050 (m-80)
REVERT: B  448 MET cc_start: 0.8262 (ttm) cc_final: 0.7966 (ttm)
REVERT: B  463 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7402 (mm-30)
  outliers start: 44
  outliers final: 28
  residues processed: 164
  average time/residue: 0.1359
  time to fit residues: 32.6580
Evaluate side-chains
  149 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 116
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
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  225 THR
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  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  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  174 LEU
Chi-restraints excluded: chain B residue  225 THR
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 3 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3604 r_free = 0.3604 target = 0.144218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.112594 restraints weight = 9197.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.116176 restraints weight = 5235.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.118572 restraints weight = 3698.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2605

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= 0.125
  Angle     :  0.649   7.632   9624  Z= 0.329
  Chirality :  0.041   0.133   1164
  Planarity :  0.003   0.032   1176
  Dihedral  :  6.187  51.716    994
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.30 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 25.48 %
    Favored  : 70.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.28), residues: 922
  helix:  0.29 (0.24), residues: 544
  sheet:  None (None), residues: 0
  loop : -2.29 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 436 
 HIS   0.004   0.001   HIS B 315 
 PHE   0.014   0.001   PHE B 338 
 TYR   0.015   0.001   TYR A 343 
 ARG   0.006   0.000   ARG B 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03791 (  321)
  hydrogen bonds       : angle       3.88714 (  915)
  SS BOND              : bond        0.00260 (    4)
  SS BOND              : angle       0.59241 (    8)
  covalent geometry    : bond        0.00277 ( 7082)
  covalent geometry    : angle       0.64902 ( 9616)

*********************** 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
  157 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 126
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6495 (p) cc_final: 0.6235 (t)
REVERT: A  247 MET cc_start: 0.8573 (mmm) cc_final: 0.7967 (mmm)
REVERT: A  260 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7701 (mp)
REVERT: A  314 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7127 (t80)
REVERT: A  329 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7290 (m-80)
REVERT: A  435 ARG cc_start: 0.7553 (ptt90) cc_final: 0.6944 (mtm110)
REVERT: A  448 MET cc_start: 0.8166 (ttm) cc_final: 0.7932 (ttm)
REVERT: A  463 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7445 (mm-30)
REVERT: B  156 SER cc_start: 0.6488 (p) cc_final: 0.6185 (t)
REVERT: B  247 MET cc_start: 0.8549 (mmm) cc_final: 0.7909 (mmm)
REVERT: B  260 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7676 (mp)
REVERT: B  329 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7314 (m-80)
REVERT: B  435 ARG cc_start: 0.7554 (ptt90) cc_final: 0.6941 (mtm110)
REVERT: B  448 MET cc_start: 0.8160 (ttm) cc_final: 0.7919 (ttm)
REVERT: B  463 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7446 (mm-30)
  outliers start: 31
  outliers final: 23
  residues processed: 152
  average time/residue: 0.1485
  time to fit residues: 32.3363
Evaluate side-chains
  150 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  225 THR
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  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  102 ILE
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  225 THR
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  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 19 optimal weight:    0.4980
   chunk 89 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B 269 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.146109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.112737 restraints weight = 9517.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.116489 restraints weight = 5440.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.118993 restraints weight = 3891.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.2698

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= 0.120
  Angle     :  0.639   7.149   9624  Z= 0.324
  Chirality :  0.041   0.136   1164
  Planarity :  0.003   0.032   1176
  Dihedral  :  5.714  49.257    988
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.20 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 25.75 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.28), residues: 922
  helix:  0.44 (0.24), residues: 542
  sheet:  None (None), residues: 0
  loop : -2.21 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 436 
 HIS   0.004   0.001   HIS B 315 
 PHE   0.014   0.001   PHE B 338 
 TYR   0.017   0.001   TYR A 343 
 ARG   0.006   0.000   ARG A 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03759 (  321)
  hydrogen bonds       : angle       3.87107 (  915)
  SS BOND              : bond        0.00249 (    4)
  SS BOND              : angle       0.48403 (    8)
  covalent geometry    : bond        0.00262 ( 7082)
  covalent geometry    : angle       0.63933 ( 9616)

********************** 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
  153 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 125
  time to evaluate  : 0.759 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6297 (p) cc_final: 0.6081 (t)
REVERT: A  247 MET cc_start: 0.8603 (mmm) cc_final: 0.7944 (mmm)
REVERT: A  260 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7677 (mp)
REVERT: A  314 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7191 (t80)
REVERT: A  329 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7372 (m-80)
REVERT: A  435 ARG cc_start: 0.7564 (ptt90) cc_final: 0.6974 (mtm110)
REVERT: A  448 MET cc_start: 0.8182 (ttm) cc_final: 0.7969 (ttm)
REVERT: A  463 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7446 (mm-30)
REVERT: B  156 SER cc_start: 0.6377 (p) cc_final: 0.6118 (t)
REVERT: B  247 MET cc_start: 0.8615 (mmm) cc_final: 0.7940 (mmm)
REVERT: B  260 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7657 (mp)
REVERT: B  266 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8604 (mt)
REVERT: B  329 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7358 (m-80)
REVERT: B  435 ARG cc_start: 0.7569 (ptt90) cc_final: 0.6975 (mtm110)
REVERT: B  448 MET cc_start: 0.8187 (ttm) cc_final: 0.7963 (ttm)
REVERT: B  463 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7449 (mm-30)
  outliers start: 28
  outliers final: 20
  residues processed: 149
  average time/residue: 0.1475
  time to fit residues: 31.6056
Evaluate side-chains
  147 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  225 THR
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  266 LEU
Chi-restraints excluded: chain A residue  314 PHE
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  102 ILE
Chi-restraints excluded: chain B residue  127 LEU
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 49 optimal weight:    0.2980
   chunk 16 optimal weight:    0.6980
   chunk 51 optimal weight:    7.9990
   chunk 9 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0170
   chunk 62 optimal weight:    0.6980
   chunk 82 optimal weight:    0.0070
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.3436

-------------------------------------------------------------------------------
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 = 0.3686 r_free = 0.3686 target = 0.149725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.116194 restraints weight = 9276.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.120003 restraints weight = 5248.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.122385 restraints weight = 3743.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.2843

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= 0.106
  Angle     :  0.635   8.824   9624  Z= 0.320
  Chirality :  0.040   0.132   1164
  Planarity :  0.003   0.032   1176
  Dihedral  :  5.400  43.009    988
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.09 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 26.58 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.29), residues: 922
  helix:  0.54 (0.24), residues: 544
  sheet:  None (None), residues: 0
  loop : -2.15 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 286 
 HIS   0.004   0.001   HIS B 315 
 PHE   0.014   0.001   PHE B 338 
 TYR   0.017   0.001   TYR A 343 
 ARG   0.006   0.000   ARG B 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03204 (  321)
  hydrogen bonds       : angle       3.76871 (  915)
  SS BOND              : bond        0.00181 (    4)
  SS BOND              : angle       0.42644 (    8)
  covalent geometry    : bond        0.00217 ( 7082)
  covalent geometry    : angle       0.63538 ( 9616)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2227.91 seconds
wall clock time: 39 minutes 48.86 seconds (2388.86 seconds total)