Starting phenix.real_space_refine
on Tue Mar 11 14:29:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bp3_30143/03_2025/7bp3_30143.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bp3_30143/03_2025/7bp3_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_30143/03_2025/7bp3_30143.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bp3_30143/03_2025/7bp3_30143.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bp3_30143/03_2025/7bp3_30143.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bp3_30143/03_2025/7bp3_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-5624/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: 5.48, per 1000 atoms: 0.90
  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: 1.45
  Conformation dependent library (CDL) restraints added in 935.0 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: 0.53
  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: 1.57

  Time building geometry restraints manager: 1.72 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.540
  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:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     19.060
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.010
-------------------------------------------------------------------------------
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  : 0.654 
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: 0.1772
  time to fit residues: 60.0442
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  : 0.629 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.133651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.121801 restraints weight = 14223.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.125083 restraints weight = 7536.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.127277 restraints weight = 4561.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
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  : 0.679 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 SER cc_start: 0.8831 (t) cc_final: 0.8386 (t)
REVERT: A   34 TYR cc_start: 0.8251 (t80) cc_final: 0.7947 (t80)
REVERT: A   40 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7933 (t)
REVERT: A   52 HIS cc_start: 0.6919 (p-80) cc_final: 0.5780 (m170)
REVERT: A   65 MET cc_start: 0.8468 (ttm) cc_final: 0.8186 (ttm)
REVERT: A  127 ASN cc_start: 0.9234 (t0) cc_final: 0.8996 (t0)
REVERT: A  129 GLN cc_start: 0.8483 (tp40) cc_final: 0.8133 (tp40)
REVERT: A  151 MET cc_start: 0.7214 (mmp) cc_final: 0.6226 (mmt)
REVERT: A  166 GLN cc_start: 0.8407 (mm110) cc_final: 0.7889 (mm110)
REVERT: A  169 PHE cc_start: 0.8056 (m-10) cc_final: 0.7793 (m-80)
REVERT: A  175 LYS cc_start: 0.5850 (mptt) cc_final: 0.5334 (pttt)
REVERT: A  244 HIS cc_start: 0.7539 (OUTLIER) cc_final: 0.7291 (t70)
REVERT: A  274 ASP cc_start: 0.8533 (t0) cc_final: 0.8284 (t0)
REVERT: A  289 MET cc_start: 0.8383 (ppp) cc_final: 0.7822 (tmm)
REVERT: A  294 MET cc_start: 0.8872 (tmm) cc_final: 0.8624 (tmm)
REVERT: A  331 CYS cc_start: 0.7307 (p) cc_final: 0.7059 (p)
REVERT: A  404 LYS cc_start: 0.8120 (mptt) cc_final: 0.7472 (mtpt)
REVERT: A  430 ARG cc_start: 0.7808 (mtt-85) cc_final: 0.7374 (tmt170)
REVERT: B   52 HIS cc_start: 0.7029 (p-80) cc_final: 0.6137 (m-70)
REVERT: B  120 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8263 (t)
REVERT: B  127 ASN cc_start: 0.9405 (t0) cc_final: 0.8815 (t0)
REVERT: B  134 ILE cc_start: 0.9026 (mm) cc_final: 0.8823 (tp)
REVERT: B  184 LEU cc_start: 0.8522 (mp) cc_final: 0.8300 (mt)
REVERT: B  196 ARG cc_start: 0.5958 (ttt180) cc_final: 0.5096 (tpt170)
REVERT: B  242 PHE cc_start: 0.7847 (m-10) cc_final: 0.7031 (p90)
REVERT: B  248 LEU cc_start: 0.8652 (tp) cc_final: 0.8449 (tp)
REVERT: B  315 TYR cc_start: 0.8314 (m-10) cc_final: 0.8014 (m-10)
REVERT: B  408 MET cc_start: 0.5635 (ttp) cc_final: 0.5211 (tmm)
  outliers start: 34
  outliers final: 15
  residues processed: 208
  average time/residue: 0.1440
  time to fit residues: 41.0519
Evaluate side-chains
  181 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 163
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
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   40 VAL
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 33 optimal weight:    0.0270
   chunk 59 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.4044

-------------------------------------------------------------------------------
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**
A 425 ASN
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 425 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.139862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.127748 restraints weight = 14015.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.131040 restraints weight = 7308.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.133195 restraints weight = 4356.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.3925

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= 0.224
  Angle     :  0.719  10.216   8470  Z= 0.359
  Chirality :  0.043   0.163    960
  Planarity :  0.005   0.054   1042
  Dihedral  :  5.458  26.679    850
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 24.69 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.29), residues: 780
  helix: -0.24 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -3.98 (0.42), 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   0.051   0.002   PHE B 284 
 TYR   0.013   0.001   TYR B 167 
 ARG   0.004   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
  200 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 172
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8162 (t80) cc_final: 0.7943 (t80)
REVERT: A   52 HIS cc_start: 0.6675 (p-80) cc_final: 0.5288 (m-70)
REVERT: A  129 GLN cc_start: 0.8521 (tp40) cc_final: 0.8169 (tp40)
REVERT: A  151 MET cc_start: 0.6924 (mmp) cc_final: 0.5852 (mmt)
REVERT: A  166 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8113 (mm-40)
REVERT: A  175 LYS cc_start: 0.5685 (mptt) cc_final: 0.5211 (pttt)
REVERT: A  274 ASP cc_start: 0.8513 (t0) cc_final: 0.8254 (t0)
REVERT: A  289 MET cc_start: 0.8305 (ppp) cc_final: 0.7958 (tmm)
REVERT: A  312 ARG cc_start: 0.7558 (mmt180) cc_final: 0.7099 (mtt180)
REVERT: A  404 LYS cc_start: 0.8171 (mptt) cc_final: 0.7547 (mtpt)
REVERT: A  413 ILE cc_start: 0.8974 (tt) cc_final: 0.8764 (tt)
REVERT: A  430 ARG cc_start: 0.7668 (mtt-85) cc_final: 0.7450 (tmt170)
REVERT: A  431 LEU cc_start: 0.8622 (pp) cc_final: 0.8326 (mt)
REVERT: B   40 VAL cc_start: 0.8351 (m) cc_final: 0.8141 (p)
REVERT: B   52 HIS cc_start: 0.7078 (p-80) cc_final: 0.6070 (m-70)
REVERT: B  127 ASN cc_start: 0.9422 (t0) cc_final: 0.8761 (t0)
REVERT: B  129 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8398 (tm-30)
REVERT: B  196 ARG cc_start: 0.5779 (ttt180) cc_final: 0.5171 (tpt170)
REVERT: B  242 PHE cc_start: 0.7835 (m-10) cc_final: 0.7103 (p90)
REVERT: B  315 TYR cc_start: 0.8264 (m-10) cc_final: 0.7954 (m-10)
REVERT: B  408 MET cc_start: 0.5589 (ttp) cc_final: 0.5147 (tmm)
  outliers start: 28
  outliers final: 15
  residues processed: 186
  average time/residue: 0.1465
  time to fit residues: 36.9408
Evaluate side-chains
  169 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 154
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
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  356 SER
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  113 TYR
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  167 TYR
Chi-restraints excluded: chain B residue  174 TRP
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 56 optimal weight:   20.0000
   chunk 77 optimal weight:    2.9990
   chunk 35 optimal weight:    9.9990
   chunk 48 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   chunk 16 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 46 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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**
B 254 ASN
** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.136232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.124245 restraints weight = 14216.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.127409 restraints weight = 7527.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.129496 restraints weight = 4566.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.4328

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= 0.283
  Angle     :  0.752   9.162   8470  Z= 0.381
  Chirality :  0.045   0.148    960
  Planarity :  0.005   0.051   1042
  Dihedral  :  5.474  25.332    850
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 26.41 %
    Favored  : 67.97 %
  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: -1.02 (0.30), residues: 780
  helix:  0.10 (0.21), residues: 630
  sheet:  None (None), residues: 0
  loop : -3.78 (0.44), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B  60 
 HIS   0.007   0.003   HIS A  52 
 PHE   0.047   0.002   PHE B 284 
 TYR   0.017   0.002   TYR B 167 
 ARG   0.004   0.000   ARG A 245 

*********************** 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
  209 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 173
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7963 (t)
REVERT: A   52 HIS cc_start: 0.6777 (p-80) cc_final: 0.5073 (m170)
REVERT: A   57 GLU cc_start: 0.8479 (mp0) cc_final: 0.8259 (mp0)
REVERT: A  129 GLN cc_start: 0.8620 (tp40) cc_final: 0.8313 (tp40)
REVERT: A  151 MET cc_start: 0.7012 (mmp) cc_final: 0.5900 (mmt)
REVERT: A  168 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.5889 (tt)
REVERT: A  169 PHE cc_start: 0.7937 (m-80) cc_final: 0.7680 (m-80)
REVERT: A  175 LYS cc_start: 0.5718 (mptt) cc_final: 0.5148 (pttt)
REVERT: A  274 ASP cc_start: 0.8514 (t0) cc_final: 0.8272 (t0)
REVERT: A  289 MET cc_start: 0.8244 (ppp) cc_final: 0.7909 (tmm)
REVERT: A  312 ARG cc_start: 0.7548 (mmt180) cc_final: 0.7142 (mtt180)
REVERT: A  319 PHE cc_start: 0.7738 (t80) cc_final: 0.7092 (t80)
REVERT: A  331 CYS cc_start: 0.7240 (p) cc_final: 0.7034 (p)
REVERT: A  404 LYS cc_start: 0.8171 (mptt) cc_final: 0.7561 (mtpt)
REVERT: B   20 TRP cc_start: 0.8709 (p-90) cc_final: 0.8058 (p-90)
REVERT: B   40 VAL cc_start: 0.8433 (m) cc_final: 0.8169 (p)
REVERT: B   52 HIS cc_start: 0.7052 (p-80) cc_final: 0.5966 (m-70)
REVERT: B  120 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8162 (t)
REVERT: B  126 PHE cc_start: 0.8225 (t80) cc_final: 0.7927 (t80)
REVERT: B  127 ASN cc_start: 0.9445 (t0) cc_final: 0.9240 (t0)
REVERT: B  129 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8405 (tm-30)
REVERT: B  168 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6194 (mt)
REVERT: B  196 ARG cc_start: 0.5964 (ttt180) cc_final: 0.5352 (tpt170)
REVERT: B  242 PHE cc_start: 0.7908 (m-10) cc_final: 0.6957 (p90)
REVERT: B  289 MET cc_start: 0.8632 (ppp) cc_final: 0.8277 (ppp)
REVERT: B  315 TYR cc_start: 0.8355 (m-10) cc_final: 0.7955 (m-10)
REVERT: B  408 MET cc_start: 0.5655 (ttp) cc_final: 0.5166 (tmm)
  outliers start: 36
  outliers final: 22
  residues processed: 192
  average time/residue: 0.1451
  time to fit residues: 37.7680
Evaluate side-chains
  181 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   61 ILE
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  195 MET
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  428 ASN
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   98 LEU
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  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  241 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0770
   chunk 62 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    1.0146

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.139002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.126692 restraints weight = 14085.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.130000 restraints weight = 7700.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.132275 restraints weight = 4733.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.4814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6244  Z= 0.212
  Angle     :  0.732  11.284   8470  Z= 0.357
  Chirality :  0.044   0.175    960
  Planarity :  0.005   0.052   1042
  Dihedral  :  5.234  26.664    850
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 30.62 %
    Favored  : 64.06 %
  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: -0.74 (0.30), residues: 780
  helix:  0.29 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -3.61 (0.45), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   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 B 167 
 ARG   0.004   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
  204 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 170
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8214 (t80) cc_final: 0.7850 (t80)
REVERT: A   52 HIS cc_start: 0.6774 (p-80) cc_final: 0.4977 (m170)
REVERT: A   57 GLU cc_start: 0.8419 (mp0) cc_final: 0.8211 (mp0)
REVERT: A  129 GLN cc_start: 0.8619 (tp40) cc_final: 0.8288 (tp40)
REVERT: A  169 PHE cc_start: 0.7863 (m-80) cc_final: 0.7541 (m-80)
REVERT: A  175 LYS cc_start: 0.5646 (mptt) cc_final: 0.5133 (pttt)
REVERT: A  274 ASP cc_start: 0.8510 (t0) cc_final: 0.8274 (t0)
REVERT: A  289 MET cc_start: 0.8082 (ppp) cc_final: 0.7813 (ppp)
REVERT: A  404 LYS cc_start: 0.8122 (mptt) cc_final: 0.7528 (mtpt)
REVERT: A  431 LEU cc_start: 0.9037 (mt) cc_final: 0.8750 (mm)
REVERT: B   52 HIS cc_start: 0.7140 (p-80) cc_final: 0.5875 (m-70)
REVERT: B  126 PHE cc_start: 0.8279 (t80) cc_final: 0.8070 (t80)
REVERT: B  127 ASN cc_start: 0.9417 (t0) cc_final: 0.9183 (t0)
REVERT: B  129 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8437 (tm-30)
REVERT: B  196 ARG cc_start: 0.5893 (ttt180) cc_final: 0.5397 (tpt170)
REVERT: B  242 PHE cc_start: 0.7893 (m-10) cc_final: 0.6881 (p90)
REVERT: B  279 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8027 (tm-30)
REVERT: B  289 MET cc_start: 0.8603 (ppp) cc_final: 0.8240 (ppp)
REVERT: B  315 TYR cc_start: 0.8239 (m-10) cc_final: 0.7887 (m-10)
REVERT: B  406 MET cc_start: 0.7987 (tmm) cc_final: 0.7071 (tmm)
REVERT: B  408 MET cc_start: 0.5702 (ttp) cc_final: 0.5159 (tmm)
REVERT: B  443 GLN cc_start: 0.6313 (OUTLIER) cc_final: 0.5737 (mm110)
  outliers start: 34
  outliers final: 14
  residues processed: 186
  average time/residue: 0.1478
  time to fit residues: 37.9200
Evaluate side-chains
  163 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
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  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  356 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain B residue   32 PHE
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  399 LEU
Chi-restraints excluded: chain B residue  443 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 20 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 32 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 46 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 64 optimal weight:    9.9990
   overall best weight:    1.5784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.137906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.126191 restraints weight = 14340.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.129370 restraints weight = 7931.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.131510 restraints weight = 4933.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.5129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6244  Z= 0.229
  Angle     :  0.753  11.388   8470  Z= 0.366
  Chirality :  0.045   0.271    960
  Planarity :  0.005   0.050   1042
  Dihedral  :  5.233  26.961    850
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 31.25 %
    Favored  : 64.69 %
  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: -0.52 (0.31), residues: 780
  helix:  0.41 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -3.45 (0.48), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B  60 
 HIS   0.008   0.002   HIS A  52 
 PHE   0.046   0.002   PHE B 284 
 TYR   0.016   0.001   TYR B 167 
 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
  189 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 163
  time to evaluate  : 0.607 
Fit side-chains
REVERT: A   34 TYR cc_start: 0.8146 (t80) cc_final: 0.7928 (t80)
REVERT: A   52 HIS cc_start: 0.6813 (p-80) cc_final: 0.4973 (m170)
REVERT: A   57 GLU cc_start: 0.8364 (mp0) cc_final: 0.8132 (mp0)
REVERT: A  129 GLN cc_start: 0.8563 (tp40) cc_final: 0.8215 (tp40)
REVERT: A  169 PHE cc_start: 0.7999 (m-80) cc_final: 0.7661 (m-80)
REVERT: A  175 LYS cc_start: 0.5924 (mptt) cc_final: 0.5371 (pttt)
REVERT: A  274 ASP cc_start: 0.8535 (t0) cc_final: 0.8305 (t0)
REVERT: A  289 MET cc_start: 0.8118 (ppp) cc_final: 0.7663 (ppp)
REVERT: A  299 SER cc_start: 0.8664 (m) cc_final: 0.8306 (p)
REVERT: A  322 MET cc_start: 0.8052 (ppp) cc_final: 0.7695 (ppp)
REVERT: A  404 LYS cc_start: 0.8100 (mptt) cc_final: 0.7492 (mtpt)
REVERT: A  431 LEU cc_start: 0.9110 (mt) cc_final: 0.8869 (mm)
REVERT: B   52 HIS cc_start: 0.7174 (p-80) cc_final: 0.5810 (m-70)
REVERT: B  126 PHE cc_start: 0.8329 (t80) cc_final: 0.8037 (t80)
REVERT: B  129 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8430 (tm-30)
REVERT: B  196 ARG cc_start: 0.5958 (ttt180) cc_final: 0.5551 (tpt170)
REVERT: B  242 PHE cc_start: 0.7925 (m-10) cc_final: 0.6977 (p90)
REVERT: B  266 ILE cc_start: 0.9554 (OUTLIER) cc_final: 0.9300 (mp)
REVERT: B  289 MET cc_start: 0.8617 (ppp) cc_final: 0.8287 (ppp)
REVERT: B  315 TYR cc_start: 0.8220 (m-10) cc_final: 0.7879 (m-10)
REVERT: B  363 MET cc_start: 0.8922 (tpp) cc_final: 0.8389 (tpp)
REVERT: B  408 MET cc_start: 0.5626 (ttp) cc_final: 0.5179 (tmm)
REVERT: B  443 GLN cc_start: 0.6319 (OUTLIER) cc_final: 0.5696 (mm110)
REVERT: B  444 LYS cc_start: 0.5825 (ttpp) cc_final: 0.5622 (ttpt)
  outliers start: 26
  outliers final: 19
  residues processed: 178
  average time/residue: 0.1448
  time to fit residues: 35.4907
Evaluate side-chains
  171 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
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  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  356 SER
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 A residue  444 LYS
Chi-restraints excluded: chain B residue  112 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  266 ILE
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  399 LEU
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 66 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   chunk 11 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 1 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 51 optimal weight:    7.9990
   overall best weight:    1.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.138057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.125795 restraints weight = 14461.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.129112 restraints weight = 7973.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.131367 restraints weight = 4954.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.5330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6244  Z= 0.226
  Angle     :  0.744   9.691   8470  Z= 0.361
  Chirality :  0.044   0.184    960
  Planarity :  0.005   0.047   1042
  Dihedral  :  5.147  27.316    850
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 32.97 %
    Favored  : 62.50 %
  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: -0.35 (0.31), residues: 780
  helix:  0.53 (0.21), residues: 626
  sheet:  None (None), residues: 0
  loop : -3.24 (0.51), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B  60 
 HIS   0.008   0.002   HIS A  52 
 PHE   0.042   0.002   PHE B 284 
 TYR   0.015   0.001   TYR B 167 
 ARG   0.001   0.000   ARG B 436 

*********************** 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
  179 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A   34 TYR cc_start: 0.8187 (t80) cc_final: 0.7791 (t80)
REVERT: A   52 HIS cc_start: 0.6825 (p-80) cc_final: 0.4851 (m170)
REVERT: A   57 GLU cc_start: 0.8374 (mp0) cc_final: 0.8117 (mp0)
REVERT: A  129 GLN cc_start: 0.8556 (tp40) cc_final: 0.8282 (tp40)
REVERT: A  169 PHE cc_start: 0.8035 (m-80) cc_final: 0.7681 (m-80)
REVERT: A  175 LYS cc_start: 0.5895 (mptt) cc_final: 0.5361 (pttt)
REVERT: A  274 ASP cc_start: 0.8616 (t0) cc_final: 0.8350 (t0)
REVERT: A  289 MET cc_start: 0.8074 (ppp) cc_final: 0.7566 (ppp)
REVERT: A  299 SER cc_start: 0.8715 (m) cc_final: 0.8348 (p)
REVERT: A  322 MET cc_start: 0.8072 (ppp) cc_final: 0.7709 (ppp)
REVERT: A  404 LYS cc_start: 0.8114 (mptt) cc_final: 0.7510 (mttt)
REVERT: A  431 LEU cc_start: 0.9154 (mt) cc_final: 0.8932 (mm)
REVERT: B   52 HIS cc_start: 0.7363 (p-80) cc_final: 0.5914 (m170)
REVERT: B  126 PHE cc_start: 0.8364 (t80) cc_final: 0.8051 (t80)
REVERT: B  168 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.5693 (tt)
REVERT: B  196 ARG cc_start: 0.5975 (ttt180) cc_final: 0.5555 (tpt170)
REVERT: B  279 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8178 (tm-30)
REVERT: B  289 MET cc_start: 0.8620 (ppp) cc_final: 0.8260 (ppp)
REVERT: B  315 TYR cc_start: 0.8186 (m-10) cc_final: 0.7911 (m-10)
REVERT: B  363 MET cc_start: 0.8991 (tpp) cc_final: 0.8659 (tpp)
REVERT: B  408 MET cc_start: 0.5666 (ttp) cc_final: 0.5208 (tmm)
REVERT: B  443 GLN cc_start: 0.6288 (OUTLIER) cc_final: 0.5676 (mm110)
  outliers start: 29
  outliers final: 20
  residues processed: 166
  average time/residue: 0.1450
  time to fit residues: 33.2257
Evaluate side-chains
  167 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
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   61 ILE
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  356 SER
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  112 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  399 LEU
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 75 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0670
   chunk 62 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 39 optimal weight:    0.4980
   chunk 32 optimal weight:    0.0670
   chunk 28 optimal weight:    9.9990
   chunk 6 optimal weight:    0.4980
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.4256

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

Flipped N/Q/H residues before XYZ refinement:
B 328 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.143965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.131948 restraints weight = 14993.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.135144 restraints weight = 8474.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.137312 restraints weight = 5352.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.5679

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= 0.200
  Angle     :  0.746  11.452   8470  Z= 0.356
  Chirality :  0.044   0.171    960
  Planarity :  0.004   0.048   1042
  Dihedral  :  5.020  28.219    850
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 35.00 %
    Favored  : 62.34 %
  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: -0.24 (0.31), residues: 780
  helix:  0.63 (0.21), residues: 624
  sheet:  None (None), residues: 0
  loop : -3.30 (0.50), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B  60 
 HIS   0.007   0.002   HIS A  52 
 PHE   0.030   0.001   PHE B 284 
 TYR   0.011   0.001   TYR A 343 
 ARG   0.002   0.000   ARG B 297 

*********************** 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
  181 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 164
  time to evaluate  : 0.635 
Fit side-chains
REVERT: A   34 TYR cc_start: 0.8220 (t80) cc_final: 0.7757 (t80)
REVERT: A   57 GLU cc_start: 0.8339 (mp0) cc_final: 0.8116 (mp0)
REVERT: A  129 GLN cc_start: 0.8558 (tp40) cc_final: 0.8269 (tp40)
REVERT: A  166 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7040 (mm-40)
REVERT: A  169 PHE cc_start: 0.7785 (m-80) cc_final: 0.7336 (m-80)
REVERT: A  174 TRP cc_start: 0.6385 (OUTLIER) cc_final: 0.5770 (m-10)
REVERT: A  175 LYS cc_start: 0.5914 (mptt) cc_final: 0.5400 (pttt)
REVERT: A  274 ASP cc_start: 0.8557 (t0) cc_final: 0.8284 (t0)
REVERT: A  289 MET cc_start: 0.8021 (ppp) cc_final: 0.7404 (ppp)
REVERT: A  299 SER cc_start: 0.8590 (m) cc_final: 0.8266 (p)
REVERT: A  322 MET cc_start: 0.8007 (ppp) cc_final: 0.7636 (ppp)
REVERT: A  404 LYS cc_start: 0.8047 (mptt) cc_final: 0.7477 (mttt)
REVERT: B  124 LEU cc_start: 0.9038 (tp) cc_final: 0.8678 (tt)
REVERT: B  126 PHE cc_start: 0.8369 (t80) cc_final: 0.7976 (t80)
REVERT: B  196 ARG cc_start: 0.5832 (ttt180) cc_final: 0.5575 (tpp80)
REVERT: B  289 MET cc_start: 0.8491 (ppp) cc_final: 0.8159 (ppp)
REVERT: B  315 TYR cc_start: 0.8138 (m-10) cc_final: 0.7904 (m-10)
REVERT: B  408 MET cc_start: 0.5501 (ttp) cc_final: 0.5158 (tmm)
  outliers start: 17
  outliers final: 12
  residues processed: 174
  average time/residue: 0.1470
  time to fit residues: 35.0698
Evaluate side-chains
  162 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 149
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
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  356 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  158 LEU
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  399 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 56 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9990
   chunk 76 optimal weight:    8.9990
   chunk 69 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 275 GLN
B  48 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.139979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.127951 restraints weight = 14832.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.131259 restraints weight = 8074.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.133468 restraints weight = 4985.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.5829

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= 0.224
  Angle     :  0.788  10.447   8470  Z= 0.380
  Chirality :  0.045   0.212    960
  Planarity :  0.005   0.048   1042
  Dihedral  :  5.030  28.786    850
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 36.09 %
    Favored  : 61.09 %
  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: -0.20 (0.31), residues: 780
  helix:  0.66 (0.21), residues: 624
  sheet:  None (None), residues: 0
  loop : -3.30 (0.50), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  20 
 HIS   0.007   0.002   HIS A  52 
 PHE   0.037   0.002   PHE B 284 
 TYR   0.012   0.001   TYR B 167 
 ARG   0.001   0.000   ARG B 436 

*********************** 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
  170 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8278 (t80) cc_final: 0.7702 (t80)
REVERT: A   43 PHE cc_start: 0.6870 (m-80) cc_final: 0.6240 (m-80)
REVERT: A  129 GLN cc_start: 0.8564 (tp40) cc_final: 0.8268 (tp40)
REVERT: A  166 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7669 (mm-40)
REVERT: A  168 LEU cc_start: 0.6230 (tp) cc_final: 0.5190 (tt)
REVERT: A  169 PHE cc_start: 0.7992 (m-80) cc_final: 0.7694 (m-80)
REVERT: A  175 LYS cc_start: 0.5929 (mptt) cc_final: 0.5291 (pttt)
REVERT: A  274 ASP cc_start: 0.8623 (t0) cc_final: 0.8340 (t0)
REVERT: A  299 SER cc_start: 0.8695 (m) cc_final: 0.8340 (p)
REVERT: A  322 MET cc_start: 0.8140 (ppp) cc_final: 0.7748 (ppp)
REVERT: A  404 LYS cc_start: 0.8040 (mptt) cc_final: 0.7459 (mttt)
REVERT: A  431 LEU cc_start: 0.8780 (mm) cc_final: 0.8517 (mm)
REVERT: B  124 LEU cc_start: 0.9053 (tp) cc_final: 0.8736 (tt)
REVERT: B  126 PHE cc_start: 0.8369 (t80) cc_final: 0.7988 (t80)
REVERT: B  151 MET cc_start: 0.7253 (mmp) cc_final: 0.6951 (tpp)
REVERT: B  168 LEU cc_start: 0.6592 (tp) cc_final: 0.5346 (tt)
REVERT: B  196 ARG cc_start: 0.5940 (ttt180) cc_final: 0.5578 (tpt170)
REVERT: B  274 ASP cc_start: 0.8103 (t0) cc_final: 0.7897 (t0)
REVERT: B  289 MET cc_start: 0.8572 (ppp) cc_final: 0.8201 (ppp)
REVERT: B  315 TYR cc_start: 0.8200 (m-10) cc_final: 0.7932 (m-10)
REVERT: B  408 MET cc_start: 0.5674 (ttp) cc_final: 0.5224 (tmm)
REVERT: B  443 GLN cc_start: 0.5996 (OUTLIER) cc_final: 0.5447 (mm110)
  outliers start: 18
  outliers final: 13
  residues processed: 163
  average time/residue: 0.1496
  time to fit residues: 33.4753
Evaluate side-chains
  159 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue  167 TYR
Chi-restraints excluded: chain A residue  174 TRP
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   60 TRP
Chi-restraints excluded: chain B residue  112 LEU
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  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:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 324 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.134628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.122564 restraints weight = 14176.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.125710 restraints weight = 7948.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.127825 restraints weight = 5000.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.5684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   6244  Z= 0.334
  Angle     :  0.856  10.034   8470  Z= 0.424
  Chirality :  0.048   0.225    960
  Planarity :  0.005   0.049   1042
  Dihedral  :  5.321  29.677    850
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 37.50 %
    Favored  : 59.84 %
  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: -0.42 (0.31), residues: 780
  helix:  0.48 (0.21), residues: 626
  sheet:  None (None), residues: 0
  loop : -3.30 (0.51), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  60 
 HIS   0.008   0.002   HIS A  52 
 PHE   0.048   0.002   PHE B 284 
 TYR   0.021   0.002   TYR A 140 
 ARG   0.002   0.000   ARG A 446 

********************** 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
  163 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8256 (t80) cc_final: 0.7996 (t80)
REVERT: A   52 HIS cc_start: 0.6945 (p-80) cc_final: 0.4669 (m170)
REVERT: A  129 GLN cc_start: 0.8618 (tp40) cc_final: 0.8349 (tp40)
REVERT: A  164 PHE cc_start: 0.6339 (m-80) cc_final: 0.6130 (m-80)
REVERT: A  166 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7701 (mm-40)
REVERT: A  175 LYS cc_start: 0.5943 (mptt) cc_final: 0.5236 (pttt)
REVERT: A  274 ASP cc_start: 0.8633 (t0) cc_final: 0.8369 (t0)
REVERT: A  299 SER cc_start: 0.8733 (m) cc_final: 0.8376 (p)
REVERT: A  322 MET cc_start: 0.8221 (ppp) cc_final: 0.7882 (ppp)
REVERT: A  404 LYS cc_start: 0.8044 (mptt) cc_final: 0.7457 (mttt)
REVERT: B  102 LEU cc_start: 0.8403 (tt) cc_final: 0.8058 (tt)
REVERT: B  126 PHE cc_start: 0.8368 (t80) cc_final: 0.8023 (t80)
REVERT: B  196 ARG cc_start: 0.6208 (ttt180) cc_final: 0.5642 (tpt170)
REVERT: B  289 MET cc_start: 0.8709 (ppp) cc_final: 0.8408 (ppp)
REVERT: B  315 TYR cc_start: 0.8284 (m-10) cc_final: 0.7956 (m-10)
REVERT: B  408 MET cc_start: 0.5605 (ttp) cc_final: 0.5156 (tmm)
REVERT: B  443 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.5891 (mm110)
  outliers start: 17
  outliers final: 13
  residues processed: 154
  average time/residue: 0.1464
  time to fit residues: 30.8935
Evaluate side-chains
  154 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
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   61 ILE
Chi-restraints excluded: chain A residue  167 TYR
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain B residue  112 LEU
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  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 34 optimal weight:    8.9990
   chunk 71 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 18 optimal weight:    0.2980
   overall best weight:    2.2386

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

Flipped N/Q/H residues before XYZ refinement:
B  48 GLN
B 328 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.135917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.123442 restraints weight = 14444.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.126790 restraints weight = 8089.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.129012 restraints weight = 5067.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.5869

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= 0.262
  Angle     :  0.836  10.390   8470  Z= 0.405
  Chirality :  0.046   0.172    960
  Planarity :  0.005   0.049   1042
  Dihedral  :  5.315  30.753    850
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 37.50 %
    Favored  : 59.84 %
  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: -0.34 (0.31), residues: 780
  helix:  0.55 (0.21), residues: 626
  sheet:  None (None), residues: 0
  loop : -3.31 (0.49), 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   0.056   0.002   PHE A 169 
 TYR   0.016   0.001   TYR B 167 
 ARG   0.002   0.000   ARG B 297 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1875.39 seconds
wall clock time: 33 minutes 32.02 seconds (2012.02 seconds total)