Starting phenix.real_space_refine
on Fri Dec 27 16:49:22 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bp3_30143/12_2024/7bp3_30143.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bp3_30143/12_2024/7bp3_30143.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bp3_30143/12_2024/7bp3_30143.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bp3_30143/12_2024/7bp3_30143.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bp3_30143/12_2024/7bp3_30143.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bp3_30143/12_2024/7bp3_30143.cif"
  }
  resolution = 3.8
  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=   0.021 sd=   0.104
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      42      5.16       5
     C    4054      2.51       5
     N     960      2.21       5
     O    1024      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 6080
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3040
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3040
          Classifications: {'peptide': 394}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 376}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.14, per 1000 atoms: 0.85
  Number of scatterers: 6080
  At special positions: 0
  Unit cell: (101.905, 77.0505, 86.164, 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      42     16.00
     O    1024      8.00
     N     960      7.00
     C    4054      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.42
  Conformation dependent library (CDL) restraints added in 913.9 milliseconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 0 sheets defined
      89.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 52
      removed outlier: 4.110A  pdb=" N   TYR A  34 " --> pdb=" O   ILE A  30 " (cutoff:3.500A)
      Proline residue:  A  37  - end of helix
      removed outlier: 5.117A  pdb=" N   VAL A  42 " --> pdb=" O   LYS A  38 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   PHE A  43 " --> pdb=" O   ALA A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 81
      removed outlier: 3.879A  pdb=" N   ILE A  58 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   GLY A  73 " --> pdb=" O   MET A  69 " (cutoff:3.500A)
      Proline residue:  A  74  - end of helix
    Processing helix  chain 'A' and resid 84 through 106
      removed outlier: 3.918A  pdb=" N   VAL A  88 " --> pdb=" O   GLY A  84 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   SER A 106 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 139
      Proline residue:  A 130  - end of helix
    Processing helix  chain 'A' and resid 143 through 154
      removed outlier: 3.748A  pdb=" N   ASN A 147 " --> pdb=" O   ARG A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 160
    Processing helix  chain 'A' and resid 161 through 170
    Processing helix  chain 'A' and resid 173 through 193
    Processing helix  chain 'A' and resid 234 through 238
    Processing helix  chain 'A' and resid 246 through 258
      removed outlier: 3.556A  pdb=" N   GLY A 253 " --> pdb=" O   ILE A 249 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   ILE A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 267
      removed outlier: 4.443A  pdb=" N   ILE A 265 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 276
      removed outlier: 3.511A  pdb=" N   ALA A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LYS A 273 " --> pdb=" O   ALA A 269 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ASP A 274 " --> pdb=" O   PRO A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 283
      removed outlier: 4.577A  pdb=" N   ALA A 283 " --> pdb=" O   GLU A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 295
      removed outlier: 4.055A  pdb=" N   ALA A 290 " --> pdb=" O   LEU A 286 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   PHE A 291 " --> pdb=" O   SER A 287 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL A 292 " --> pdb=" O   VAL A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 307
      removed outlier: 4.211A  pdb=" N   ALA A 304 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   ASN A 305 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   SER A 306 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LYS A 307 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 311
      No H-bonds generated for 'chain 'A' and resid 309 through 311'
    Processing helix  chain 'A' and resid 312 through 328
      removed outlier: 3.945A  pdb=" N   PHE A 316 " --> pdb=" O   ARG A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 358
      removed outlier: 3.776A  pdb=" N   LEU A 340 " --> pdb=" O   ASP A 336 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   PHE A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   SER A 356 " --> pdb=" O   GLY A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 367
    Processing helix  chain 'A' and resid 370 through 383
      removed outlier: 3.503A  pdb=" N   VAL A 375 " --> pdb=" O   PHE A 371 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   GLY A 376 " --> pdb=" O   SER A 372 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU A 377 " --> pdb=" O   SER A 373 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE A 380 " --> pdb=" O   GLY A 376 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   CYS A 383 " --> pdb=" O   THR A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 389
      removed outlier: 3.641A  pdb=" N   LEU A 388 " --> pdb=" O   GLY A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 401
      removed outlier: 3.779A  pdb=" N   LYS A 395 " --> pdb=" O   PRO A 391 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   LEU A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   VAL A 397 " --> pdb=" O   ALA A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 440
      removed outlier: 3.574A  pdb=" N   MET A 408 " --> pdb=" O   LYS A 404 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   SER A 409 " --> pdb=" O   TYR A 405 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   VAL A 414 " --> pdb=" O   CYS A 410 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LEU A 421 " --> pdb=" O   ALA A 417 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLY A 424 " --> pdb=" O   TRP A 420 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ARG A 430 " --> pdb=" O   ALA A 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 52
      removed outlier: 4.110A  pdb=" N   TYR B  34 " --> pdb=" O   ILE B  30 " (cutoff:3.500A)
      Proline residue:  B  37  - end of helix
      removed outlier: 5.118A  pdb=" N   VAL B  42 " --> pdb=" O   LYS B  38 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   PHE B  43 " --> pdb=" O   ALA B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 81
      removed outlier: 3.878A  pdb=" N   ILE B  58 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   GLY B  73 " --> pdb=" O   MET B  69 " (cutoff:3.500A)
      Proline residue:  B  74  - end of helix
    Processing helix  chain 'B' and resid 84 through 106
      removed outlier: 3.917A  pdb=" N   VAL B  88 " --> pdb=" O   GLY B  84 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   SER B 106 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 139
      Proline residue:  B 130  - end of helix
    Processing helix  chain 'B' and resid 143 through 154
      removed outlier: 3.746A  pdb=" N   ASN B 147 " --> pdb=" O   ARG B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 160
    Processing helix  chain 'B' and resid 161 through 170
    Processing helix  chain 'B' and resid 173 through 193
    Processing helix  chain 'B' and resid 234 through 238
    Processing helix  chain 'B' and resid 246 through 258
      removed outlier: 3.555A  pdb=" N   GLY B 253 " --> pdb=" O   ILE B 249 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   ILE B 256 " --> pdb=" O   SER B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 267
      removed outlier: 4.442A  pdb=" N   ILE B 265 " --> pdb=" O   PHE B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 276
      removed outlier: 3.510A  pdb=" N   ALA B 272 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LYS B 273 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ASP B 274 " --> pdb=" O   PRO B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 283
      removed outlier: 4.578A  pdb=" N   ALA B 283 " --> pdb=" O   GLU B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 295
      removed outlier: 4.057A  pdb=" N   ALA B 290 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   PHE B 291 " --> pdb=" O   SER B 287 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL B 292 " --> pdb=" O   VAL B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 307
      removed outlier: 4.210A  pdb=" N   ALA B 304 " --> pdb=" O   VAL B 300 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ASN B 305 " --> pdb=" O   GLY B 301 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   SER B 306 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   LYS B 307 " --> pdb=" O   ILE B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 311
      No H-bonds generated for 'chain 'B' and resid 309 through 311'
    Processing helix  chain 'B' and resid 312 through 328
      removed outlier: 3.946A  pdb=" N   PHE B 316 " --> pdb=" O   ARG B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 358
      removed outlier: 3.777A  pdb=" N   LEU B 340 " --> pdb=" O   ASP B 336 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   PHE B 346 " --> pdb=" O   LEU B 342 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   SER B 356 " --> pdb=" O   GLY B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 367
    Processing helix  chain 'B' and resid 370 through 383
      removed outlier: 3.503A  pdb=" N   VAL B 375 " --> pdb=" O   PHE B 371 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   GLY B 376 " --> pdb=" O   SER B 372 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU B 377 " --> pdb=" O   SER B 373 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE B 380 " --> pdb=" O   GLY B 376 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   CYS B 383 " --> pdb=" O   THR B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 389
      removed outlier: 3.641A  pdb=" N   LEU B 388 " --> pdb=" O   GLY B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 401
      removed outlier: 3.778A  pdb=" N   LYS B 395 " --> pdb=" O   PRO B 391 " (cutoff:3.500A)
      removed outlier: 5.668A  pdb=" N   LEU B 396 " --> pdb=" O   LEU B 392 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   VAL B 397 " --> pdb=" O   ALA B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 440
      removed outlier: 3.575A  pdb=" N   MET B 408 " --> pdb=" O   LYS B 404 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   SER B 409 " --> pdb=" O   TYR B 405 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   VAL B 414 " --> pdb=" O   CYS B 410 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LEU B 421 " --> pdb=" O   ALA B 417 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLY B 424 " --> pdb=" O   TRP B 420 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ARG B 430 " --> pdb=" O   ALA B 426 " (cutoff:3.500A)

    422 hydrogen bonds defined for protein.
    1266 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: 1.61

  Time building geometry restraints manager: 1.65 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1783
        1.34 -     1.47: 1722
        1.47 -     1.59: 2669
        1.59 -     1.71: 0
        1.71 -     1.84: 70
  Bond restraints: 6244
  Sorted by residual:
  bond pdb=" CB  TYR B 167 "
       pdb=" CG  TYR B 167 "
    ideal  model  delta    sigma   weight residual
    1.512  1.460  0.052 2.20e-02 2.07e+03 5.49e+00
  bond pdb=" CB  TYR A 167 "
       pdb=" CG  TYR A 167 "
    ideal  model  delta    sigma   weight residual
    1.512  1.461  0.051 2.20e-02 2.07e+03 5.44e+00
  bond pdb=" C   SER A 154 "
       pdb=" N   PRO A 155 "
    ideal  model  delta    sigma   weight residual
    1.339  1.415 -0.076 3.40e-02 8.65e+02 5.01e+00
  bond pdb=" C   SER B 154 "
       pdb=" N   PRO B 155 "
    ideal  model  delta    sigma   weight residual
    1.339  1.415 -0.076 3.40e-02 8.65e+02 4.99e+00
  bond pdb=" CB  TRP A 174 "
       pdb=" CG  TRP A 174 "
    ideal  model  delta    sigma   weight residual
    1.498  1.430  0.068 3.10e-02 1.04e+03 4.88e+00
  ... (remaining 6239 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 8136
        2.28 -     4.55: 264
        4.55 -     6.83: 45
        6.83 -     9.10: 19
        9.10 -    11.38: 6
  Bond angle restraints: 8470
  Sorted by residual:
  angle pdb=" CA  PHE A 284 "
        pdb=" CB  PHE A 284 "
        pdb=" CG  PHE A 284 "
      ideal   model   delta    sigma   weight residual
     113.80  117.73   -3.93 1.00e+00 1.00e+00 1.55e+01
  angle pdb=" CA  PHE B 284 "
        pdb=" CB  PHE B 284 "
        pdb=" CG  PHE B 284 "
      ideal   model   delta    sigma   weight residual
     113.80  117.69   -3.89 1.00e+00 1.00e+00 1.51e+01
  angle pdb=" N   PHE B  36 "
        pdb=" CA  PHE B  36 "
        pdb=" C   PHE B  36 "
      ideal   model   delta    sigma   weight residual
     112.55  117.72   -5.17 1.35e+00 5.49e-01 1.47e+01
  angle pdb=" N   PHE A  36 "
        pdb=" CA  PHE A  36 "
        pdb=" C   PHE A  36 "
      ideal   model   delta    sigma   weight residual
     112.55  117.72   -5.17 1.35e+00 5.49e-01 1.47e+01
  angle pdb=" CB  LEU A 168 "
        pdb=" CG  LEU A 168 "
        pdb=" CD2 LEU A 168 "
      ideal   model   delta    sigma   weight residual
     110.70   99.32   11.38 3.00e+00 1.11e-01 1.44e+01
  ... (remaining 8465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.48: 3003
       15.48 -    30.96: 447
       30.96 -    46.45: 122
       46.45 -    61.93: 18
       61.93 -    77.41: 8
  Dihedral angle restraints: 3598
    sinusoidal: 1342
      harmonic: 2256
  Sorted by residual:
  dihedral pdb=" CA  ASN B 170 "
           pdb=" C   ASN B 170 "
           pdb=" N   THR B 171 "
           pdb=" CA  THR B 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.32   29.68     0      5.00e+00 4.00e-02 3.52e+01
  dihedral pdb=" CA  ASN A 170 "
           pdb=" C   ASN A 170 "
           pdb=" N   THR A 171 "
           pdb=" CA  THR A 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.33   29.67     0      5.00e+00 4.00e-02 3.52e+01
  dihedral pdb=" CA  PRO B 155 "
           pdb=" C   PRO B 155 "
           pdb=" N   VAL B 156 "
           pdb=" CA  VAL B 156 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.27   23.73     0      5.00e+00 4.00e-02 2.25e+01
  ... (remaining 3595 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 515
       0.038 -    0.076: 292
       0.076 -    0.114: 90
       0.114 -    0.152: 53
       0.152 -    0.190: 10
  Chirality restraints: 960
  Sorted by residual:
  chirality pdb=" CA  CYS A 331 "
            pdb=" N   CYS A 331 "
            pdb=" C   CYS A 331 "
            pdb=" CB  CYS A 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.99e-01
  chirality pdb=" CA  CYS B 331 "
            pdb=" N   CYS B 331 "
            pdb=" C   CYS B 331 "
            pdb=" CB  CYS B 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.96e-01
  chirality pdb=" CA  PHE B  36 "
            pdb=" N   PHE B  36 "
            pdb=" C   PHE B  36 "
            pdb=" CB  PHE B  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.68e-01
  ... (remaining 957 not shown)

  Planarity restraints: 1042
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 284 "    0.036 2.00e-02 2.50e+03   2.70e-02 1.28e+01
        pdb=" CG  PHE B 284 "   -0.060 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 284 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 284 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 284 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 284 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 284 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 284 "   -0.036 2.00e-02 2.50e+03   2.68e-02 1.26e+01
        pdb=" CG  PHE A 284 "    0.060 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 284 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 284 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 284 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 284 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 284 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 331 "    0.052 5.00e-02 4.00e+02   7.72e-02 9.53e+00
        pdb=" N   PRO A 332 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "    0.043 5.00e-02 4.00e+02
  ... (remaining 1039 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1444
        2.77 -     3.30: 5739
        3.30 -     3.83: 10425
        3.83 -     4.37: 11498
        4.37 -     4.90: 18879
  Nonbonded interactions: 47985
  Sorted by model distance:
  nonbonded pdb=" O   SER A 281 "
            pdb=" OH  TYR A 337 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   SER B 281 "
            pdb=" OH  TYR B 337 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   ASP B 336 "
            pdb=" OG  SER B 339 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   ASP A 336 "
            pdb=" OG  SER A 339 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OG  SER B 160 "
            pdb=" OG  SER B 287 "
     model   vdw
     2.279 3.040
  ... (remaining 47980 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.290
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.400
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
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      :  0.007   0.076   6244  Z= 0.462
  Angle     :  1.051  11.380   8470  Z= 0.557
  Chirality :  0.057   0.190    960
  Planarity :  0.008   0.077   1042
  Dihedral  : 16.157  77.409   2166
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.81 %
    Favored  : 87.19 %
  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: -4.77 (0.22), residues: 780
  helix: -2.93 (0.15), residues: 600
  sheet:  None (None), residues: 0
  loop : -3.11 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 174 
 HIS   0.006   0.002   HIS A 328 
 PHE   0.060   0.002   PHE B 284 
 TYR   0.017   0.002   TYR A 271 
 ARG   0.005   0.001   ARG B 446 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 HIS cc_start: 0.6772 (p-80) cc_final: 0.5737 (m-70)
REVERT: A  127 ASN cc_start: 0.9268 (t0) cc_final: 0.8963 (t0)
REVERT: A  129 GLN cc_start: 0.8367 (tp-100) cc_final: 0.8159 (tp40)
REVERT: A  143 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7612 (mtt180)
REVERT: A  147 ASN cc_start: 0.7600 (m-40) cc_final: 0.7151 (m110)
REVERT: A  151 MET cc_start: 0.7229 (mmp) cc_final: 0.6387 (mmt)
REVERT: A  166 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8172 (mm-40)
REVERT: A  169 PHE cc_start: 0.8186 (m-10) cc_final: 0.7759 (m-80)
REVERT: A  175 LYS cc_start: 0.5891 (mptt) cc_final: 0.5529 (pttt)
REVERT: A  274 ASP cc_start: 0.8702 (t0) cc_final: 0.8440 (t0)
REVERT: A  284 PHE cc_start: 0.5441 (p90) cc_final: 0.5181 (p90)
REVERT: A  289 MET cc_start: 0.8593 (ppp) cc_final: 0.7752 (ppp)
REVERT: A  404 LYS cc_start: 0.7735 (mptt) cc_final: 0.7457 (mtpt)
REVERT: A  430 ARG cc_start: 0.7978 (mtt-85) cc_final: 0.7224 (ptm160)
REVERT: B   20 TRP cc_start: 0.8799 (p-90) cc_final: 0.8184 (p-90)
REVERT: B   52 HIS cc_start: 0.7031 (p-80) cc_final: 0.6149 (m-70)
REVERT: B   57 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7512 (mp0)
REVERT: B   68 VAL cc_start: 0.9114 (t) cc_final: 0.8899 (p)
REVERT: B   79 LEU cc_start: 0.8824 (tp) cc_final: 0.8562 (tp)
REVERT: B  127 ASN cc_start: 0.9383 (t0) cc_final: 0.8684 (t0)
REVERT: B  166 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8183 (mm-40)
REVERT: B  184 LEU cc_start: 0.8655 (mp) cc_final: 0.8372 (mt)
REVERT: B  241 LEU cc_start: 0.8100 (tp) cc_final: 0.7892 (tp)
REVERT: B  242 PHE cc_start: 0.7886 (m-10) cc_final: 0.7040 (p90)
REVERT: B  248 LEU cc_start: 0.8777 (tp) cc_final: 0.8558 (tp)
REVERT: B  330 LEU cc_start: 0.7730 (mt) cc_final: 0.7455 (tt)
REVERT: B  331 CYS cc_start: 0.7744 (p) cc_final: 0.7331 (p)
REVERT: B  359 PHE cc_start: 0.8639 (m-80) cc_final: 0.8355 (m-10)
REVERT: B  365 LEU cc_start: 0.8983 (mt) cc_final: 0.8542 (tt)
REVERT: B  408 MET cc_start: 0.5932 (ttp) cc_final: 0.5422 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.1892
  time to fit residues: 64.0758
Evaluate side-chains
  169 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 70 optimal weight:    7.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN
A 166 GLN
A 187 ASN
A 234 ASN
A 254 ASN
A 305 ASN
B 166 GLN
B 234 ASN
B 244 HIS
B 275 GLN
B 305 ASN
** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6244  Z= 0.278
  Angle     :  0.779  10.841   8470  Z= 0.401
  Chirality :  0.046   0.206    960
  Planarity :  0.006   0.059   1042
  Dihedral  :  5.801  24.214    850
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 20.31 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.27), residues: 780
  helix: -0.94 (0.19), residues: 628
  sheet:  None (None), residues: 0
  loop : -3.62 (0.46), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 420 
 HIS   0.006   0.003   HIS A  52 
 PHE   0.055   0.002   PHE B 284 
 TYR   0.019   0.002   TYR B 140 
 ARG   0.004   0.001   ARG B 143 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 192
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 SER cc_start: 0.8923 (t) cc_final: 0.8380 (t)
REVERT: A   34 TYR cc_start: 0.8376 (t80) cc_final: 0.7994 (t80)
REVERT: A   52 HIS cc_start: 0.6976 (p-80) cc_final: 0.5693 (m170)
REVERT: A   65 MET cc_start: 0.8619 (ttm) cc_final: 0.8268 (ttm)
REVERT: A  124 LEU cc_start: 0.8590 (mt) cc_final: 0.8378 (mt)
REVERT: A  127 ASN cc_start: 0.9352 (t0) cc_final: 0.9076 (t0)
REVERT: A  129 GLN cc_start: 0.8534 (tp40) cc_final: 0.8139 (tp40)
REVERT: A  151 MET cc_start: 0.7341 (mmp) cc_final: 0.6320 (mmt)
REVERT: A  166 GLN cc_start: 0.8446 (mm110) cc_final: 0.7923 (mm110)
REVERT: A  169 PHE cc_start: 0.8153 (m-10) cc_final: 0.7854 (m-80)
REVERT: A  175 LYS cc_start: 0.5893 (mptt) cc_final: 0.5356 (pttt)
REVERT: A  244 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.7275 (t70)
REVERT: A  274 ASP cc_start: 0.8699 (t0) cc_final: 0.8436 (t0)
REVERT: A  289 MET cc_start: 0.8401 (ppp) cc_final: 0.7795 (tmm)
REVERT: A  294 MET cc_start: 0.8989 (tmm) cc_final: 0.8658 (tmm)
REVERT: A  404 LYS cc_start: 0.8048 (mptt) cc_final: 0.7439 (mtpt)
REVERT: A  430 ARG cc_start: 0.7938 (mtt-85) cc_final: 0.7366 (tmt170)
REVERT: B   52 HIS cc_start: 0.7099 (p-80) cc_final: 0.6123 (m-70)
REVERT: B   96 CYS cc_start: 0.8384 (p) cc_final: 0.8133 (p)
REVERT: B  120 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8389 (t)
REVERT: B  127 ASN cc_start: 0.9442 (t0) cc_final: 0.8836 (t0)
REVERT: B  134 ILE cc_start: 0.9092 (mm) cc_final: 0.8871 (tp)
REVERT: B  184 LEU cc_start: 0.8581 (mp) cc_final: 0.8374 (mt)
REVERT: B  196 ARG cc_start: 0.5949 (ttt180) cc_final: 0.5052 (tpt170)
REVERT: B  242 PHE cc_start: 0.7993 (m-10) cc_final: 0.7020 (p90)
REVERT: B  248 LEU cc_start: 0.8659 (tp) cc_final: 0.8454 (tp)
REVERT: B  315 TYR cc_start: 0.8295 (m-10) cc_final: 0.8031 (m-10)
REVERT: B  365 LEU cc_start: 0.8980 (mt) cc_final: 0.8753 (tt)
REVERT: B  408 MET cc_start: 0.5944 (ttp) cc_final: 0.5351 (tmm)
  outliers start: 34
  outliers final: 15
  residues processed: 208
  average time/residue: 0.1494
  time to fit residues: 42.3026
Evaluate side-chains
  180 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 163
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   60 TRP
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  189 CYS
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 70 optimal weight:    7.9990
   chunk 76 optimal weight:    8.9990
   chunk 63 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN
A 166 GLN
** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 ASN
** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 425 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6244  Z= 0.252
  Angle     :  0.727   9.867   8470  Z= 0.369
  Chirality :  0.044   0.165    960
  Planarity :  0.005   0.053   1042
  Dihedral  :  5.542  26.284    850
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 23.59 %
    Favored  : 71.41 %
  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: -1.40 (0.29), residues: 780
  helix: -0.20 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -3.91 (0.43), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  20 
 HIS   0.006   0.002   HIS A  52 
 PHE   0.054   0.002   PHE B 284 
 TYR   0.016   0.002   TYR B 167 
 ARG   0.005   0.000   ARG B 297 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 173
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8375 (t80) cc_final: 0.7955 (t80)
REVERT: A   52 HIS cc_start: 0.6755 (p-80) cc_final: 0.5110 (m-70)
REVERT: A   57 GLU cc_start: 0.8469 (mp0) cc_final: 0.8244 (mp0)
REVERT: A   65 MET cc_start: 0.8710 (ttm) cc_final: 0.8378 (ttp)
REVERT: A   69 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7911 (tpt)
REVERT: A  127 ASN cc_start: 0.9327 (t0) cc_final: 0.9094 (t0)
REVERT: A  129 GLN cc_start: 0.8621 (tp40) cc_final: 0.8216 (tp40)
REVERT: A  151 MET cc_start: 0.7271 (mmp) cc_final: 0.6148 (mmt)
REVERT: A  166 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8012 (mm-40)
REVERT: A  169 PHE cc_start: 0.8185 (m-10) cc_final: 0.7911 (m-80)
REVERT: A  175 LYS cc_start: 0.5601 (mptt) cc_final: 0.5084 (pttt)
REVERT: A  244 HIS cc_start: 0.7791 (OUTLIER) cc_final: 0.7354 (t-90)
REVERT: A  274 ASP cc_start: 0.8740 (t0) cc_final: 0.8468 (t0)
REVERT: A  289 MET cc_start: 0.8347 (ppp) cc_final: 0.7968 (tmm)
REVERT: A  294 MET cc_start: 0.8894 (tmm) cc_final: 0.8689 (tmm)
REVERT: A  312 ARG cc_start: 0.7752 (mmt180) cc_final: 0.7131 (mtt180)
REVERT: A  404 LYS cc_start: 0.8046 (mptt) cc_final: 0.7457 (mtpt)
REVERT: A  413 ILE cc_start: 0.8917 (tt) cc_final: 0.8698 (tt)
REVERT: A  430 ARG cc_start: 0.7928 (mtt-85) cc_final: 0.7486 (tmt170)
REVERT: B   20 TRP cc_start: 0.8711 (p-90) cc_final: 0.8189 (p-90)
REVERT: B   40 VAL cc_start: 0.8402 (m) cc_final: 0.8181 (p)
REVERT: B   52 HIS cc_start: 0.7169 (p-80) cc_final: 0.6011 (m-70)
REVERT: B   96 CYS cc_start: 0.8336 (p) cc_final: 0.8006 (p)
REVERT: B  126 PHE cc_start: 0.8370 (m-80) cc_final: 0.8153 (t80)
REVERT: B  127 ASN cc_start: 0.9462 (t0) cc_final: 0.8876 (t0)
REVERT: B  196 ARG cc_start: 0.5904 (ttt180) cc_final: 0.5174 (tpt170)
REVERT: B  242 PHE cc_start: 0.8076 (m-10) cc_final: 0.7012 (p90)
REVERT: B  279 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8137 (tm-30)
REVERT: B  315 TYR cc_start: 0.8304 (m-10) cc_final: 0.8045 (m-10)
REVERT: B  408 MET cc_start: 0.5940 (ttp) cc_final: 0.5309 (tmm)
  outliers start: 32
  outliers final: 17
  residues processed: 189
  average time/residue: 0.1553
  time to fit residues: 39.5103
Evaluate side-chains
  174 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 155
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  167 TYR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 67 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 ASN
** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.4426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6244  Z= 0.224
  Angle     :  0.709   9.204   8470  Z= 0.353
  Chirality :  0.043   0.155    960
  Planarity :  0.005   0.048   1042
  Dihedral  :  5.319  26.648    850
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 27.50 %
    Favored  : 67.66 %
  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: -0.88 (0.30), residues: 780
  helix:  0.19 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -3.69 (0.45), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  60 
 HIS   0.007   0.002   HIS A  52 
 PHE   0.040   0.002   PHE B 139 
 TYR   0.014   0.001   TYR A 343 
 ARG   0.003   0.000   ARG B 196 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 174
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8440 (t80) cc_final: 0.7922 (t80)
REVERT: A   52 HIS cc_start: 0.6731 (p-80) cc_final: 0.4933 (m170)
REVERT: A   65 MET cc_start: 0.8613 (ttm) cc_final: 0.8322 (ttp)
REVERT: A   69 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7921 (tpt)
REVERT: A  127 ASN cc_start: 0.9329 (t0) cc_final: 0.9111 (t0)
REVERT: A  129 GLN cc_start: 0.8613 (tp40) cc_final: 0.8225 (tp40)
REVERT: A  151 MET cc_start: 0.7042 (mmp) cc_final: 0.5847 (mmt)
REVERT: A  166 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8090 (mm-40)
REVERT: A  169 PHE cc_start: 0.8138 (m-10) cc_final: 0.7833 (m-80)
REVERT: A  175 LYS cc_start: 0.5568 (mptt) cc_final: 0.5057 (pttt)
REVERT: A  244 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.7484 (t-90)
REVERT: A  274 ASP cc_start: 0.8724 (t0) cc_final: 0.8468 (t0)
REVERT: A  289 MET cc_start: 0.8227 (ppp) cc_final: 0.7964 (tmm)
REVERT: A  312 ARG cc_start: 0.7574 (mmt180) cc_final: 0.7213 (mtt180)
REVERT: A  404 LYS cc_start: 0.8071 (mptt) cc_final: 0.7517 (mtpt)
REVERT: A  430 ARG cc_start: 0.7894 (mtt-85) cc_final: 0.7461 (tmt170)
REVERT: B   20 TRP cc_start: 0.8616 (p-90) cc_final: 0.8020 (p-90)
REVERT: B   52 HIS cc_start: 0.7226 (p-80) cc_final: 0.5969 (m-70)
REVERT: B  127 ASN cc_start: 0.9426 (t0) cc_final: 0.8925 (t0)
REVERT: B  157 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7467 (t80)
REVERT: B  196 ARG cc_start: 0.5910 (ttt180) cc_final: 0.5308 (tpt170)
REVERT: B  242 PHE cc_start: 0.8087 (m-10) cc_final: 0.7096 (p90)
REVERT: B  279 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7637 (tm-30)
REVERT: B  315 TYR cc_start: 0.8268 (m-10) cc_final: 0.7984 (m-10)
REVERT: B  408 MET cc_start: 0.5991 (ttp) cc_final: 0.5313 (tmm)
  outliers start: 31
  outliers final: 21
  residues processed: 189
  average time/residue: 0.1636
  time to fit residues: 42.1566
Evaluate side-chains
  178 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 154
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  167 TYR
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  331 CYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 TYR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  319 PHE
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  418 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 56 optimal weight:   10.0000
   chunk 31 optimal weight:    0.0770
   chunk 64 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 0 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0670
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.4876

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.4781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6244  Z= 0.197
  Angle     :  0.713   9.027   8470  Z= 0.349
  Chirality :  0.044   0.178    960
  Planarity :  0.005   0.049   1042
  Dihedral  :  5.147  30.220    850
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 29.38 %
    Favored  : 65.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -0.70 (0.30), residues: 780
  helix:  0.30 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -3.66 (0.45), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  60 
 HIS   0.007   0.002   HIS A  52 
 PHE   0.039   0.002   PHE B 139 
 TYR   0.013   0.001   TYR A 343 
 ARG   0.003   0.000   ARG B 297 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 181
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8472 (t80) cc_final: 0.7982 (t80)
REVERT: A   52 HIS cc_start: 0.6674 (p-80) cc_final: 0.4841 (m170)
REVERT: A   57 GLU cc_start: 0.8404 (mp0) cc_final: 0.8143 (mp0)
REVERT: A   65 MET cc_start: 0.8539 (ttm) cc_final: 0.8333 (ttp)
REVERT: A   69 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7929 (tpt)
REVERT: A  129 GLN cc_start: 0.8588 (tp40) cc_final: 0.8220 (tp40)
REVERT: A  166 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7866 (mm-40)
REVERT: A  169 PHE cc_start: 0.7998 (m-10) cc_final: 0.7649 (m-80)
REVERT: A  175 LYS cc_start: 0.5742 (mptt) cc_final: 0.5181 (pttt)
REVERT: A  274 ASP cc_start: 0.8708 (t0) cc_final: 0.8444 (t0)
REVERT: A  299 SER cc_start: 0.8745 (m) cc_final: 0.8370 (p)
REVERT: A  312 ARG cc_start: 0.7634 (mmt180) cc_final: 0.7280 (mtt180)
REVERT: A  404 LYS cc_start: 0.8006 (mptt) cc_final: 0.7489 (mtpt)
REVERT: A  430 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.7556 (tmt170)
REVERT: B   52 HIS cc_start: 0.7191 (p-80) cc_final: 0.5841 (m-70)
REVERT: B  127 ASN cc_start: 0.9431 (t0) cc_final: 0.9095 (t0)
REVERT: B  129 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8245 (tm-30)
REVERT: B  196 ARG cc_start: 0.5831 (ttt180) cc_final: 0.5399 (tpp80)
REVERT: B  266 ILE cc_start: 0.9549 (OUTLIER) cc_final: 0.9254 (mp)
REVERT: B  279 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8301 (tm-30)
REVERT: B  289 MET cc_start: 0.8632 (ppp) cc_final: 0.8215 (ppp)
REVERT: B  315 TYR cc_start: 0.8165 (m-10) cc_final: 0.7918 (m-10)
REVERT: B  408 MET cc_start: 0.5964 (ttp) cc_final: 0.5287 (tmm)
  outliers start: 33
  outliers final: 16
  residues processed: 197
  average time/residue: 0.1514
  time to fit residues: 40.5357
Evaluate side-chains
  165 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  167 TYR
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  331 CYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  167 TYR
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 75 optimal weight:    0.8980
   chunk 62 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 72 optimal weight:    0.0970
   chunk 8 optimal weight:   20.0000
   chunk 42 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.5256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6244  Z= 0.205
  Angle     :  0.737   9.222   8470  Z= 0.357
  Chirality :  0.043   0.165    960
  Planarity :  0.005   0.049   1042
  Dihedral  :  5.106  31.973    850
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 30.31 %
    Favored  : 64.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -0.56 (0.31), residues: 780
  helix:  0.40 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -3.59 (0.44), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B  60 
 HIS   0.008   0.002   HIS A  52 
 PHE   0.036   0.002   PHE B 284 
 TYR   0.012   0.001   TYR B 337 
 ARG   0.002   0.000   ARG B 297 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 159
  time to evaluate  : 0.680 
Fit side-chains
REVERT: A   34 TYR cc_start: 0.8486 (t80) cc_final: 0.7907 (t80)
REVERT: A   43 PHE cc_start: 0.5971 (m-80) cc_final: 0.5575 (m-80)
REVERT: A   52 HIS cc_start: 0.6667 (p-80) cc_final: 0.4818 (m170)
REVERT: A   57 GLU cc_start: 0.8353 (mp0) cc_final: 0.8093 (mp0)
REVERT: A   69 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7870 (tpp)
REVERT: A  129 GLN cc_start: 0.8581 (tp40) cc_final: 0.8266 (tp40)
REVERT: A  166 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7359 (mm-40)
REVERT: A  169 PHE cc_start: 0.8039 (m-10) cc_final: 0.7683 (m-80)
REVERT: A  175 LYS cc_start: 0.5967 (mptt) cc_final: 0.5416 (pttt)
REVERT: A  274 ASP cc_start: 0.8715 (t0) cc_final: 0.8441 (t0)
REVERT: A  299 SER cc_start: 0.8755 (m) cc_final: 0.8368 (p)
REVERT: A  312 ARG cc_start: 0.7671 (mmt180) cc_final: 0.7296 (mtt180)
REVERT: A  322 MET cc_start: 0.8211 (ppp) cc_final: 0.7819 (ppp)
REVERT: A  404 LYS cc_start: 0.8021 (mptt) cc_final: 0.7483 (mtpt)
REVERT: A  430 ARG cc_start: 0.7881 (mtt-85) cc_final: 0.7508 (tmt170)
REVERT: B   52 HIS cc_start: 0.7204 (p-80) cc_final: 0.5761 (m-70)
REVERT: B  127 ASN cc_start: 0.9424 (t0) cc_final: 0.9185 (t0)
REVERT: B  196 ARG cc_start: 0.5808 (ttt180) cc_final: 0.5488 (tpp80)
REVERT: B  274 ASP cc_start: 0.8181 (t0) cc_final: 0.7981 (t0)
REVERT: B  279 GLU cc_start: 0.8582 (tm-30) cc_final: 0.7879 (tm-30)
REVERT: B  289 MET cc_start: 0.8635 (ppp) cc_final: 0.8207 (ppp)
REVERT: B  363 MET cc_start: 0.8656 (tpt) cc_final: 0.8070 (tpp)
REVERT: B  406 MET cc_start: 0.7808 (tmm) cc_final: 0.7583 (tmm)
REVERT: B  408 MET cc_start: 0.5954 (ttp) cc_final: 0.5259 (tmm)
REVERT: B  428 ASN cc_start: 0.8537 (t0) cc_final: 0.8270 (t0)
REVERT: B  443 GLN cc_start: 0.6078 (OUTLIER) cc_final: 0.5489 (mm110)
  outliers start: 31
  outliers final: 19
  residues processed: 175
  average time/residue: 0.1544
  time to fit residues: 36.4351
Evaluate side-chains
  175 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue  167 TYR
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  331 CYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  167 TYR
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  443 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.2980
   chunk 42 optimal weight:    0.9980
   chunk 63 optimal weight:    7.9990
   chunk 75 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.5435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6244  Z= 0.215
  Angle     :  0.757  14.690   8470  Z= 0.362
  Chirality :  0.044   0.172    960
  Planarity :  0.005   0.049   1042
  Dihedral  :  5.119  34.415    850
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 32.50 %
    Favored  : 63.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -0.44 (0.31), residues: 780
  helix:  0.48 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -3.54 (0.45), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B  60 
 HIS   0.008   0.002   HIS A  52 
 PHE   0.038   0.002   PHE B 284 
 TYR   0.012   0.001   TYR B 167 
 ARG   0.003   0.000   ARG A 196 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 164
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8441 (t80) cc_final: 0.7810 (t80)
REVERT: A   43 PHE cc_start: 0.5865 (m-80) cc_final: 0.5426 (m-80)
REVERT: A   52 HIS cc_start: 0.6716 (p-80) cc_final: 0.4845 (m170)
REVERT: A   69 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7865 (tpp)
REVERT: A  129 GLN cc_start: 0.8587 (tp40) cc_final: 0.8314 (tp40)
REVERT: A  166 GLN cc_start: 0.8319 (mm-40) cc_final: 0.7373 (mm-40)
REVERT: A  169 PHE cc_start: 0.8120 (m-10) cc_final: 0.7804 (m-80)
REVERT: A  175 LYS cc_start: 0.5998 (mptt) cc_final: 0.5420 (pttt)
REVERT: A  274 ASP cc_start: 0.8713 (t0) cc_final: 0.8435 (t0)
REVERT: A  299 SER cc_start: 0.8786 (m) cc_final: 0.8393 (p)
REVERT: A  312 ARG cc_start: 0.7682 (mmt180) cc_final: 0.7325 (mtt180)
REVERT: A  322 MET cc_start: 0.8239 (ppp) cc_final: 0.7846 (ppp)
REVERT: A  404 LYS cc_start: 0.8024 (mptt) cc_final: 0.7492 (mttt)
REVERT: A  430 ARG cc_start: 0.7882 (mtt-85) cc_final: 0.7529 (tmt170)
REVERT: B   52 HIS cc_start: 0.7400 (p-80) cc_final: 0.5847 (m170)
REVERT: B  126 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.8101 (t80)
REVERT: B  151 MET cc_start: 0.7038 (mmp) cc_final: 0.6801 (tpp)
REVERT: B  196 ARG cc_start: 0.5846 (ttt180) cc_final: 0.5558 (tpp80)
REVERT: B  274 ASP cc_start: 0.8188 (t0) cc_final: 0.7988 (t0)
REVERT: B  289 MET cc_start: 0.8667 (ppp) cc_final: 0.8222 (ppp)
REVERT: B  363 MET cc_start: 0.8722 (tpt) cc_final: 0.8144 (tpp)
REVERT: B  406 MET cc_start: 0.7849 (tmm) cc_final: 0.7609 (tmm)
REVERT: B  408 MET cc_start: 0.5953 (ttp) cc_final: 0.5274 (tmm)
REVERT: B  428 ASN cc_start: 0.8644 (t0) cc_final: 0.8330 (t0)
REVERT: B  443 GLN cc_start: 0.6156 (OUTLIER) cc_final: 0.5551 (mm110)
  outliers start: 27
  outliers final: 20
  residues processed: 178
  average time/residue: 0.1506
  time to fit residues: 36.6343
Evaluate side-chains
  176 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  167 TYR
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  331 CYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain B residue  126 PHE
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  167 TYR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  443 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    0.4980
   chunk 47 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 68 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.5461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6244  Z= 0.240
  Angle     :  0.759  12.483   8470  Z= 0.371
  Chirality :  0.044   0.159    960
  Planarity :  0.005   0.049   1042
  Dihedral  :  5.125  33.324    850
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 32.81 %
    Favored  : 62.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -0.41 (0.31), residues: 780
  helix:  0.54 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -3.59 (0.45), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  60 
 HIS   0.008   0.002   HIS A  52 
 PHE   0.043   0.002   PHE B 284 
 TYR   0.016   0.001   TYR B 167 
 ARG   0.004   0.000   ARG A 196 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8437 (t80) cc_final: 0.8219 (t80)
REVERT: A   57 GLU cc_start: 0.8420 (mp0) cc_final: 0.8086 (mp0)
REVERT: A   69 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7887 (tpp)
REVERT: A  129 GLN cc_start: 0.8591 (tp40) cc_final: 0.8275 (tp40)
REVERT: A  168 LEU cc_start: 0.6275 (tp) cc_final: 0.5449 (tt)
REVERT: A  169 PHE cc_start: 0.8288 (m-10) cc_final: 0.7993 (m-80)
REVERT: A  175 LYS cc_start: 0.5854 (mptt) cc_final: 0.5284 (pttt)
REVERT: A  274 ASP cc_start: 0.8741 (t0) cc_final: 0.8461 (t0)
REVERT: A  299 SER cc_start: 0.8822 (m) cc_final: 0.8419 (p)
REVERT: A  312 ARG cc_start: 0.7716 (mmt180) cc_final: 0.7379 (mtt180)
REVERT: A  322 MET cc_start: 0.8263 (ppp) cc_final: 0.7903 (ppp)
REVERT: A  404 LYS cc_start: 0.7988 (mptt) cc_final: 0.7447 (mttt)
REVERT: A  430 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7575 (tmt170)
REVERT: B   65 MET cc_start: 0.8187 (tpp) cc_final: 0.7979 (tpp)
REVERT: B  124 LEU cc_start: 0.9027 (tp) cc_final: 0.8701 (tt)
REVERT: B  126 PHE cc_start: 0.8404 (t80) cc_final: 0.8068 (t80)
REVERT: B  151 MET cc_start: 0.7429 (mmp) cc_final: 0.7180 (tpp)
REVERT: B  166 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8161 (mm-40)
REVERT: B  168 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.5890 (tt)
REVERT: B  196 ARG cc_start: 0.5940 (ttt180) cc_final: 0.5586 (tpt170)
REVERT: B  257 MET cc_start: 0.8791 (ppp) cc_final: 0.8578 (ppp)
REVERT: B  279 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8360 (tm-30)
REVERT: B  289 MET cc_start: 0.8713 (ppp) cc_final: 0.8357 (ppp)
REVERT: B  363 MET cc_start: 0.8792 (tpt) cc_final: 0.8194 (tpp)
REVERT: B  406 MET cc_start: 0.7881 (tmm) cc_final: 0.7643 (tmm)
REVERT: B  408 MET cc_start: 0.5941 (ttp) cc_final: 0.5296 (tmm)
REVERT: B  428 ASN cc_start: 0.8719 (t0) cc_final: 0.8402 (t0)
REVERT: B  443 GLN cc_start: 0.6299 (OUTLIER) cc_final: 0.5652 (mm110)
  outliers start: 30
  outliers final: 20
  residues processed: 170
  average time/residue: 0.1652
  time to fit residues: 37.8735
Evaluate side-chains
  172 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  167 TYR
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  331 CYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain B residue   60 TRP
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  167 TYR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  319 PHE
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  443 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 66 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 46 optimal weight:    9.9990
   chunk 74 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.5518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6244  Z= 0.245
  Angle     :  0.779  12.145   8470  Z= 0.381
  Chirality :  0.045   0.180    960
  Planarity :  0.005   0.049   1042
  Dihedral  :  5.162  31.585    850
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 33.44 %
    Favored  : 62.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.31), residues: 780
  helix:  0.56 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -3.58 (0.46), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  20 
 HIS   0.008   0.002   HIS A  52 
 PHE   0.043   0.002   PHE B 284 
 TYR   0.015   0.001   TYR B 167 
 ARG   0.004   0.000   ARG A 196 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 0.852 
Fit side-chains
REVERT: A   34 TYR cc_start: 0.8422 (t80) cc_final: 0.8219 (t80)
REVERT: A   43 PHE cc_start: 0.6193 (m-80) cc_final: 0.5963 (m-80)
REVERT: A   52 HIS cc_start: 0.6760 (p-80) cc_final: 0.4640 (m170)
REVERT: A   57 GLU cc_start: 0.8442 (mp0) cc_final: 0.8105 (mp0)
REVERT: A   69 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7853 (tpp)
REVERT: A  129 GLN cc_start: 0.8609 (tp40) cc_final: 0.8298 (tp40)
REVERT: A  166 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7189 (mm-40)
REVERT: A  168 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5474 (tt)
REVERT: A  169 PHE cc_start: 0.8339 (m-10) cc_final: 0.8069 (m-80)
REVERT: A  175 LYS cc_start: 0.5897 (mptt) cc_final: 0.5279 (pttt)
REVERT: A  274 ASP cc_start: 0.8736 (t0) cc_final: 0.8460 (t0)
REVERT: A  299 SER cc_start: 0.8824 (m) cc_final: 0.8424 (p)
REVERT: A  312 ARG cc_start: 0.7733 (mmt180) cc_final: 0.7348 (mtt180)
REVERT: A  322 MET cc_start: 0.8337 (ppp) cc_final: 0.7959 (ppp)
REVERT: A  404 LYS cc_start: 0.7964 (mptt) cc_final: 0.7425 (mttt)
REVERT: A  430 ARG cc_start: 0.7944 (mtt-85) cc_final: 0.7656 (tmt170)
REVERT: B   65 MET cc_start: 0.8095 (tpp) cc_final: 0.7441 (mmt)
REVERT: B  124 LEU cc_start: 0.9099 (tp) cc_final: 0.8837 (tt)
REVERT: B  126 PHE cc_start: 0.8421 (t80) cc_final: 0.8071 (t80)
REVERT: B  196 ARG cc_start: 0.5973 (ttt180) cc_final: 0.5549 (tpt170)
REVERT: B  279 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8255 (tm-30)
REVERT: B  289 MET cc_start: 0.8742 (ppp) cc_final: 0.8405 (ppp)
REVERT: B  363 MET cc_start: 0.8792 (tpt) cc_final: 0.8204 (tpp)
REVERT: B  408 MET cc_start: 0.5932 (ttp) cc_final: 0.5271 (tmm)
REVERT: B  428 ASN cc_start: 0.8739 (t0) cc_final: 0.8421 (t0)
REVERT: B  443 GLN cc_start: 0.6300 (OUTLIER) cc_final: 0.5671 (mm110)
  outliers start: 29
  outliers final: 20
  residues processed: 166
  average time/residue: 0.1620
  time to fit residues: 36.8688
Evaluate side-chains
  170 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  167 TYR
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  331 CYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  167 TYR
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  319 PHE
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  443 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 71 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 275 GLN
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.5708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6244  Z= 0.218
  Angle     :  0.797  12.183   8470  Z= 0.377
  Chirality :  0.044   0.172    960
  Planarity :  0.005   0.050   1042
  Dihedral  :  5.123  32.412    850
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 34.69 %
    Favored  : 61.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -0.36 (0.31), residues: 780
  helix:  0.59 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -3.70 (0.44), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B  60 
 HIS   0.008   0.002   HIS A  52 
 PHE   0.035   0.001   PHE B 284 
 TYR   0.015   0.001   TYR B 167 
 ARG   0.003   0.000   ARG A 196 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7891 (tpp)
REVERT: A  129 GLN cc_start: 0.8583 (tp40) cc_final: 0.8255 (tp40)
REVERT: A  169 PHE cc_start: 0.8267 (m-10) cc_final: 0.7914 (m-80)
REVERT: A  175 LYS cc_start: 0.5755 (mptt) cc_final: 0.5198 (pttt)
REVERT: A  274 ASP cc_start: 0.8715 (t0) cc_final: 0.8435 (t0)
REVERT: A  299 SER cc_start: 0.8819 (m) cc_final: 0.8425 (p)
REVERT: A  312 ARG cc_start: 0.7708 (mmt180) cc_final: 0.7368 (mtt180)
REVERT: A  322 MET cc_start: 0.8285 (ppp) cc_final: 0.7884 (ppp)
REVERT: A  404 LYS cc_start: 0.7963 (mptt) cc_final: 0.7410 (mttt)
REVERT: A  430 ARG cc_start: 0.7880 (mtt-85) cc_final: 0.7615 (tmt170)
REVERT: B  124 LEU cc_start: 0.9112 (tp) cc_final: 0.8851 (tt)
REVERT: B  126 PHE cc_start: 0.8405 (t80) cc_final: 0.8053 (t80)
REVERT: B  168 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.5477 (tt)
REVERT: B  196 ARG cc_start: 0.5985 (ttt180) cc_final: 0.5650 (tpt170)
REVERT: B  279 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8378 (tm-30)
REVERT: B  289 MET cc_start: 0.8711 (ppp) cc_final: 0.8428 (ppp)
REVERT: B  363 MET cc_start: 0.8725 (tpt) cc_final: 0.8179 (tpp)
REVERT: B  408 MET cc_start: 0.5918 (ttp) cc_final: 0.5302 (tmm)
REVERT: B  428 ASN cc_start: 0.8676 (t0) cc_final: 0.8350 (t0)
REVERT: B  443 GLN cc_start: 0.6223 (OUTLIER) cc_final: 0.5626 (mm110)
  outliers start: 24
  outliers final: 20
  residues processed: 170
  average time/residue: 0.1663
  time to fit residues: 38.5401
Evaluate side-chains
  173 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue  126 PHE
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  167 TYR
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  331 CYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  167 TYR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  319 PHE
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  443 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 44 optimal weight:    3.9990
   chunk 70 optimal weight:    0.5980
   chunk 41 optimal weight:    5.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.140591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.128291 restraints weight = 14620.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.131561 restraints weight = 8181.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.133800 restraints weight = 5139.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.5903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6244  Z= 0.212
  Angle     :  0.791  12.162   8470  Z= 0.377
  Chirality :  0.044   0.172    960
  Planarity :  0.005   0.050   1042
  Dihedral  :  5.071  31.272    850
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 35.62 %
    Favored  : 60.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -0.33 (0.31), residues: 780
  helix:  0.64 (0.21), residues: 626
  sheet:  None (None), residues: 0
  loop : -3.76 (0.43), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A  20 
 HIS   0.007   0.002   HIS A  52 
 PHE   0.033   0.001   PHE B 284 
 TYR   0.014   0.001   TYR A 343 
 ARG   0.003   0.000   ARG A 196 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1453.90 seconds
wall clock time: 27 minutes 28.31 seconds (1648.31 seconds total)