Starting phenix.real_space_refine
on Fri Jun  6 01:27:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j18_61071/06_2025/9j18_61071.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j18_61071/06_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_61071/06_2025/9j18_61071.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j18_61071/06_2025/9j18_61071.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j18_61071/06_2025/9j18_61071.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j18_61071/06_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.95, per 1000 atoms: 0.86
  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: 1.67
  Conformation dependent library (CDL) restraints added in 985.8 milliseconds
  

  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: 0.68
  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: 1.64

  Time building geometry restraints manager: 1.95 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 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: 0.03
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:             98.060
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.520
  Find NCS groups from input model:        0.110
  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:2.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  121.610
-------------------------------------------------------------------------------
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  : 0.706 
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: 0.1403
  time to fit residues: 25.9858
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  : 0.764 
-------------------------------------------------------------------------------
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 = 41)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.140833 restraints weight = 5459.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.143121 restraints weight = 4133.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
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  : 0.842 
Fit side-chains
REVERT: A  260 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7796 (mp)
REVERT: B  260 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7781 (mp)
  outliers start: 39
  outliers final: 21
  residues processed: 158
  average time/residue: 0.1396
  time to fit residues: 32.1113
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  : 0.688 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 40 optimal weight:    0.5980
   chunk 82 optimal weight:    0.6980
   chunk 56 optimal weight:    0.2980
   chunk 32 optimal weight:    0.7980
   chunk 74 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3919 r_free = 0.3919 target = 0.167444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.136131 restraints weight = 8836.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.139440 restraints weight = 5496.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.141733 restraints weight = 4161.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   7086  Z= 0.116
  Angle     :  0.625   8.468   9624  Z= 0.316
  Chirality :  0.040   0.138   1164
  Planarity :  0.003   0.037   1176
  Dihedral  :  6.156  45.419    994
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.63 %
    Favored  : 89.37 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 24.11 %
    Favored  : 70.55 %
  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: -1.44 (0.28), residues: 922
  helix: -0.04 (0.23), residues: 544
  sheet:  None (None), residues: 0
  loop : -2.34 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 436 
 HIS   0.005   0.001   HIS A 160 
 PHE   0.009   0.001   PHE A 425 
 TYR   0.011   0.001   TYR A 343 
 ARG   0.001   0.000   ARG A 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04145 (  321)
  hydrogen bonds       : angle       4.02667 (  915)
  SS BOND              : bond        0.00183 (    4)
  SS BOND              : angle       0.57371 (    8)
  covalent geometry    : bond        0.00248 ( 7082)
  covalent geometry    : angle       0.62455 ( 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
  169 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 130
  time to evaluate  : 1.255 
Fit side-chains
REVERT: A  247 MET cc_start: 0.8426 (mmm) cc_final: 0.7856 (mmm)
REVERT: A  260 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7725 (mp)
REVERT: A  411 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7108 (tt)
REVERT: A  463 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7330 (mm-30)
REVERT: B  260 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7738 (mp)
REVERT: B  411 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7105 (tt)
REVERT: B  463 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7312 (mm-30)
  outliers start: 39
  outliers final: 22
  residues processed: 159
  average time/residue: 0.2106
  time to fit residues: 48.5318
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  : 0.911 
-------------------------------------------------------------------------------
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  386 SER
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  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  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:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3649 r_free = 0.3649 target = 0.146085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.112310 restraints weight = 9460.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.115995 restraints weight = 5528.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.118524 restraints weight = 4009.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   7086  Z= 0.163
  Angle     :  0.651   7.427   9624  Z= 0.334
  Chirality :  0.042   0.139   1164
  Planarity :  0.003   0.033   1176
  Dihedral  :  6.409  51.945    994
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.74 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 23.56 %
    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: -1.46 (0.28), residues: 922
  helix: -0.02 (0.23), residues: 542
  sheet: -2.72 (0.99), residues: 20
  loop : -2.33 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 436 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.010   0.001   PHE B 259 
 TYR   0.013   0.001   TYR B 159 
 ARG   0.005   0.000   ARG B 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04624 (  321)
  hydrogen bonds       : angle       3.99248 (  915)
  SS BOND              : bond        0.00308 (    4)
  SS BOND              : angle       0.61650 (    8)
  covalent geometry    : bond        0.00379 ( 7082)
  covalent geometry    : angle       0.65070 ( 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
  165 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 128
  time to evaluate  : 0.852 
Fit side-chains
REVERT: A  260 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7527 (mp)
REVERT: A  463 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7462 (mm-30)
REVERT: B  260 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7533 (mp)
REVERT: B  411 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7234 (tt)
REVERT: B  463 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7486 (mm-30)
  outliers start: 37
  outliers final: 27
  residues processed: 155
  average time/residue: 0.1796
  time to fit residues: 42.8809
Evaluate side-chains
  154 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
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  386 SER
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  263 SER
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  327 THR
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  461 THR
Chi-restraints excluded: chain B residue  494 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   chunk 80 optimal weight:    3.9990
   chunk 45 optimal weight:    0.4980
   chunk 16 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0270
   chunk 59 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.6038

-------------------------------------------------------------------------------
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 = 0.3675 r_free = 0.3675 target = 0.148712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.115289 restraints weight = 9269.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.119077 restraints weight = 5292.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.121601 restraints weight = 3781.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7086  Z= 0.111
  Angle     :  0.603   7.061   9624  Z= 0.306
  Chirality :  0.040   0.141   1164
  Planarity :  0.003   0.033   1176
  Dihedral  :  6.077  50.701    994
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.95 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 23.97 %
    Favored  : 71.23 %
  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: -1.28 (0.28), residues: 922
  helix:  0.14 (0.23), residues: 544
  sheet: -2.87 (0.98), residues: 20
  loop : -2.27 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 436 
 HIS   0.003   0.001   HIS B 160 
 PHE   0.009   0.001   PHE B 425 
 TYR   0.011   0.001   TYR B 159 
 ARG   0.005   0.000   ARG B 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03746 (  321)
  hydrogen bonds       : angle       3.81858 (  915)
  SS BOND              : bond        0.00192 (    4)
  SS BOND              : angle       0.49424 (    8)
  covalent geometry    : bond        0.00240 ( 7082)
  covalent geometry    : angle       0.60262 ( 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
  164 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 129
  time to evaluate  : 1.261 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6477 (p) cc_final: 0.6181 (t)
REVERT: A  247 MET cc_start: 0.8615 (mmm) cc_final: 0.7983 (mmm)
REVERT: A  331 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7319 (ptpp)
REVERT: A  411 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7170 (tt)
REVERT: A  463 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7451 (mm-30)
REVERT: B  156 SER cc_start: 0.6427 (p) cc_final: 0.6106 (t)
REVERT: B  247 MET cc_start: 0.8677 (mmm) cc_final: 0.8030 (mmm)
REVERT: B  331 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7260 (ptpp)
REVERT: B  411 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7224 (tt)
REVERT: B  463 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7396 (mm-30)
  outliers start: 35
  outliers final: 27
  residues processed: 154
  average time/residue: 0.2663
  time to fit residues: 59.1639
Evaluate side-chains
  155 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 124
  time to evaluate  : 2.315 
-------------------------------------------------------------------------------
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  263 SER
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  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  263 SER
Chi-restraints excluded: chain B residue  321 LEU
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0980
   chunk 69 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.147955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.114443 restraints weight = 9364.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.118251 restraints weight = 5341.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.120782 restraints weight = 3811.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7086  Z= 0.115
  Angle     :  0.609   6.902   9624  Z= 0.311
  Chirality :  0.040   0.168   1164
  Planarity :  0.003   0.033   1176
  Dihedral  :  5.995  51.249    994
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.52 %
    Favored  : 89.48 %
  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: -1.20 (0.28), residues: 922
  helix:  0.22 (0.24), residues: 544
  sheet: -2.98 (0.94), residues: 20
  loop : -2.26 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 436 
 HIS   0.003   0.001   HIS A 160 
 PHE   0.007   0.001   PHE B  51 
 TYR   0.010   0.001   TYR B 343 
 ARG   0.006   0.000   ARG A 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03752 (  321)
  hydrogen bonds       : angle       3.76433 (  915)
  SS BOND              : bond        0.00235 (    4)
  SS BOND              : angle       0.47952 (    8)
  covalent geometry    : bond        0.00251 ( 7082)
  covalent geometry    : angle       0.60953 ( 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
  168 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 128
  time to evaluate  : 0.720 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6301 (p) cc_final: 0.5995 (t)
REVERT: A  247 MET cc_start: 0.8781 (mmm) cc_final: 0.8114 (mmm)
REVERT: A  260 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7477 (mp)
REVERT: A  269 ASN cc_start: 0.7090 (m-40) cc_final: 0.6771 (p0)
REVERT: A  329 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7085 (m-80)
REVERT: A  331 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7197 (ptpp)
REVERT: A  463 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7455 (mm-30)
REVERT: B  156 SER cc_start: 0.6318 (p) cc_final: 0.5993 (t)
REVERT: B  247 MET cc_start: 0.8775 (mmm) cc_final: 0.8075 (mmm)
REVERT: B  260 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7488 (mp)
REVERT: B  329 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7035 (m-80)
REVERT: B  331 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7145 (ptpp)
REVERT: B  463 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7460 (mm-30)
  outliers start: 40
  outliers final: 29
  residues processed: 161
  average time/residue: 0.1301
  time to fit residues: 30.8544
Evaluate side-chains
  157 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 122
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
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  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  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  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  461 THR
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:    0.9980
   chunk 82 optimal weight:    0.0870
   chunk 10 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 57 optimal weight:    0.4980
   chunk 54 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.6158

-------------------------------------------------------------------------------
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 = 0.3678 r_free = 0.3678 target = 0.148850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.115353 restraints weight = 9236.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.119160 restraints weight = 5295.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.121688 restraints weight = 3784.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7086  Z= 0.110
  Angle     :  0.626  11.033   9624  Z= 0.309
  Chirality :  0.040   0.141   1164
  Planarity :  0.003   0.033   1176
  Dihedral  :  5.895  51.959    994
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.41 %
    Favored  : 89.59 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 24.11 %
    Favored  : 70.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.08 (0.28), residues: 922
  helix:  0.31 (0.24), residues: 544
  sheet: -2.96 (0.98), residues: 20
  loop : -2.21 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 436 
 HIS   0.003   0.001   HIS B 160 
 PHE   0.007   0.001   PHE A 425 
 TYR   0.009   0.001   TYR A 343 
 ARG   0.006   0.000   ARG A 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03611 (  321)
  hydrogen bonds       : angle       3.71770 (  915)
  SS BOND              : bond        0.00271 (    4)
  SS BOND              : angle       0.51275 (    8)
  covalent geometry    : bond        0.00239 ( 7082)
  covalent geometry    : angle       0.62578 ( 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: 37
    poor density    : 130
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6256 (p) cc_final: 0.5944 (t)
REVERT: A  247 MET cc_start: 0.8655 (mmm) cc_final: 0.8025 (mmm)
REVERT: A  260 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7669 (mp)
REVERT: A  314 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7590 (t80)
REVERT: A  329 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7272 (m-80)
REVERT: A  463 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7471 (mm-30)
REVERT: B  156 SER cc_start: 0.6313 (p) cc_final: 0.5979 (t)
REVERT: B  247 MET cc_start: 0.8629 (mmm) cc_final: 0.8040 (mmm)
REVERT: B  260 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7673 (mp)
REVERT: B  329 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7271 (m-80)
REVERT: B  435 ARG cc_start: 0.7727 (ptt90) cc_final: 0.6929 (mtm110)
REVERT: B  448 MET cc_start: 0.8165 (ttm) cc_final: 0.7957 (ttm)
REVERT: B  463 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7474 (mm-30)
  outliers start: 37
  outliers final: 26
  residues processed: 156
  average time/residue: 0.2413
  time to fit residues: 54.6271
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  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  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  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  461 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  263 SER
Chi-restraints excluded: chain B residue  327 THR
Chi-restraints excluded: chain B residue  329 PHE
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain B residue  390 VAL
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:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 73 optimal weight:    0.0070
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.6998

-------------------------------------------------------------------------------
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 = 0.3660 r_free = 0.3660 target = 0.147335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.113937 restraints weight = 9252.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.117776 restraints weight = 5243.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.120338 restraints weight = 3727.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7086  Z= 0.118
  Angle     :  0.642   9.796   9624  Z= 0.320
  Chirality :  0.041   0.132   1164
  Planarity :  0.003   0.032   1176
  Dihedral  :  5.650  50.822    988
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.20 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 24.11 %
    Favored  : 70.14 %
  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: -1.00 (0.28), residues: 922
  helix:  0.36 (0.24), residues: 544
  sheet: -2.81 (0.98), residues: 20
  loop : -2.14 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 436 
 HIS   0.004   0.001   HIS B 160 
 PHE   0.007   0.001   PHE B 425 
 TYR   0.009   0.001   TYR A 343 
 ARG   0.005   0.000   ARG A 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03713 (  321)
  hydrogen bonds       : angle       3.75324 (  915)
  SS BOND              : bond        0.00256 (    4)
  SS BOND              : angle       0.49775 (    8)
  covalent geometry    : bond        0.00259 ( 7082)
  covalent geometry    : angle       0.64238 ( 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: 42
    poor density    : 129
  time to evaluate  : 0.650 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6355 (p) cc_final: 0.6034 (t)
REVERT: A  247 MET cc_start: 0.8665 (mmm) cc_final: 0.8025 (mmm)
REVERT: A  260 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7694 (mp)
REVERT: A  314 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7425 (t80)
REVERT: A  329 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7198 (m-80)
REVERT: A  463 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7459 (mm-30)
REVERT: B  156 SER cc_start: 0.6511 (p) cc_final: 0.6026 (t)
REVERT: B  247 MET cc_start: 0.8669 (mmm) cc_final: 0.8024 (mmm)
REVERT: B  260 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7701 (mp)
REVERT: B  314 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7515 (t80)
REVERT: B  328 GLU cc_start: 0.8556 (tp30) cc_final: 0.8356 (tp30)
REVERT: B  329 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7175 (m-80)
REVERT: B  435 ARG cc_start: 0.7712 (ptt90) cc_final: 0.6924 (mtm110)
REVERT: B  448 MET cc_start: 0.8199 (ttm) cc_final: 0.7978 (ttm)
REVERT: B  463 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7483 (mm-30)
  outliers start: 42
  outliers final: 30
  residues processed: 160
  average time/residue: 0.1507
  time to fit residues: 34.8322
Evaluate side-chains
  158 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 122
  time to evaluate  : 1.752 
-------------------------------------------------------------------------------
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  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  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 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  314 PHE
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.4980
   chunk 57 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 62 optimal weight:    0.1980
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3666 r_free = 0.3666 target = 0.147335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.113452 restraints weight = 9224.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.117135 restraints weight = 5370.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.119500 restraints weight = 3872.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7086  Z= 0.151
  Angle     :  0.679   9.346   9624  Z= 0.344
  Chirality :  0.042   0.134   1164
  Planarity :  0.003   0.033   1176
  Dihedral  :  5.953  54.412    988
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.52 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 25.21 %
    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: -1.01 (0.28), residues: 922
  helix:  0.39 (0.24), residues: 540
  sheet:  None (None), residues: 0
  loop : -2.26 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 436 
 HIS   0.005   0.001   HIS A 315 
 PHE   0.009   0.001   PHE A 259 
 TYR   0.011   0.001   TYR A 307 
 ARG   0.005   0.000   ARG A 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04240 (  321)
  hydrogen bonds       : angle       3.92399 (  915)
  SS BOND              : bond        0.00305 (    4)
  SS BOND              : angle       0.60309 (    8)
  covalent geometry    : bond        0.00348 ( 7082)
  covalent geometry    : angle       0.67891 ( 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
  156 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 124
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A  156 SER cc_start: 0.6394 (p) cc_final: 0.6025 (t)
REVERT: A  163 MET cc_start: 0.7317 (tpp) cc_final: 0.6889 (mmp)
REVERT: A  247 MET cc_start: 0.8620 (mmm) cc_final: 0.8022 (mmm)
REVERT: A  260 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7701 (mp)
REVERT: A  314 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7202 (t80)
REVERT: A  329 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7377 (m-80)
REVERT: A  463 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7382 (mm-30)
REVERT: B  156 SER cc_start: 0.6447 (p) cc_final: 0.6107 (t)
REVERT: B  163 MET cc_start: 0.7321 (tpp) cc_final: 0.6892 (mmp)
REVERT: B  247 MET cc_start: 0.8600 (mmm) cc_final: 0.8038 (mmm)
REVERT: B  260 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7694 (mp)
REVERT: B  314 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7325 (t80)
REVERT: B  329 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7372 (m-80)
REVERT: B  448 MET cc_start: 0.8186 (ttm) cc_final: 0.7947 (ttm)
REVERT: B  463 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7433 (mm-30)
  outliers start: 32
  outliers final: 25
  residues processed: 147
  average time/residue: 0.1387
  time to fit residues: 30.3465
Evaluate side-chains
  152 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 121
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  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 A residue  461 THR
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  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  314 PHE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 19 optimal weight:    0.0670
   chunk 89 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 88 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   chunk 86 optimal weight:    0.0010
   chunk 55 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.4724

-------------------------------------------------------------------------------
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 = 0.3708 r_free = 0.3708 target = 0.151459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.117011 restraints weight = 9282.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.120803 restraints weight = 5366.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.123252 restraints weight = 3863.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7086  Z= 0.112
  Angle     :  0.651   8.935   9624  Z= 0.327
  Chirality :  0.041   0.132   1164
  Planarity :  0.003   0.032   1176
  Dihedral  :  5.531  47.339    988
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.41 %
    Favored  : 89.59 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 25.62 %
    Favored  : 70.68 %
  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: -0.86 (0.29), residues: 922
  helix:  0.50 (0.24), residues: 540
  sheet:  None (None), residues: 0
  loop : -2.20 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 286 
 HIS   0.003   0.001   HIS A 315 
 PHE   0.010   0.001   PHE A 425 
 TYR   0.012   0.001   TYR A 343 
 ARG   0.005   0.000   ARG A 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03271 (  321)
  hydrogen bonds       : angle       3.71064 (  915)
  SS BOND              : bond        0.00198 (    4)
  SS BOND              : angle       0.42552 (    8)
  covalent geometry    : bond        0.00235 ( 7082)
  covalent geometry    : angle       0.65150 ( 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
  149 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 0.761 
Fit side-chains
REVERT: A  234 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7772 (mt-10)
REVERT: A  247 MET cc_start: 0.8579 (mmm) cc_final: 0.8017 (mmm)
REVERT: A  260 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7732 (mp)
REVERT: A  329 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7499 (m-80)
REVERT: A  463 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7475 (mm-30)
REVERT: B  234 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7769 (mt-10)
REVERT: B  247 MET cc_start: 0.8571 (mmm) cc_final: 0.7965 (mmm)
REVERT: B  260 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7733 (mp)
REVERT: B  314 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7485 (t80)
REVERT: B  329 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7418 (m-80)
REVERT: B  435 ARG cc_start: 0.7672 (ptt90) cc_final: 0.6988 (mtm110)
REVERT: B  450 MET cc_start: 0.8271 (ttt) cc_final: 0.8045 (mtt)
REVERT: B  463 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7461 (mm-30)
  outliers start: 27
  outliers final: 20
  residues processed: 142
  average time/residue: 0.1570
  time to fit residues: 32.8609
Evaluate side-chains
  142 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  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  321 LEU
Chi-restraints excluded: chain A residue  329 PHE
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  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  314 PHE
Chi-restraints excluded: chain B residue  329 PHE
Chi-restraints excluded: chain B residue  461 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 72 optimal weight:    0.0170
   chunk 62 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   overall best weight:    0.5618

-------------------------------------------------------------------------------
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 = 0.3672 r_free = 0.3672 target = 0.148356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.114519 restraints weight = 9245.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.118350 restraints weight = 5266.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.120820 restraints weight = 3768.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   7086  Z= 0.116
  Angle     :  0.648   8.404   9624  Z= 0.327
  Chirality :  0.041   0.132   1164
  Planarity :  0.003   0.035   1176
  Dihedral  :  5.522  47.033    988
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.09 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 25.34 %
    Favored  : 70.68 %
  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: -0.77 (0.29), residues: 922
  helix:  0.59 (0.24), residues: 538
  sheet:  None (None), residues: 0
  loop : -2.17 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 436 
 HIS   0.004   0.001   HIS A 315 
 PHE   0.007   0.001   PHE A 425 
 TYR   0.012   0.001   TYR A 343 
 ARG   0.005   0.000   ARG A 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03532 (  321)
  hydrogen bonds       : angle       3.74837 (  915)
  SS BOND              : bond        0.00223 (    4)
  SS BOND              : angle       0.46731 (    8)
  covalent geometry    : bond        0.00249 ( 7082)
  covalent geometry    : angle       0.64778 ( 9616)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2872.74 seconds
wall clock time: 52 minutes 17.18 seconds (3137.18 seconds total)