Starting phenix.real_space_refine
on Tue Mar  3 17:09:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uz2_20950/03_2026/6uz2_20950.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uz2_20950/03_2026/6uz2_20950.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uz2_20950/03_2026/6uz2_20950.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uz2_20950/03_2026/6uz2_20950.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uz2_20950/03_2026/6uz2_20950.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uz2_20950/03_2026/6uz2_20950.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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      44      5.16       5
     C    4640      2.51       5
     N    1328      2.21       5
     O    1380      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7392
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 3694
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 210}
          Link IDs: {'PTRANS': 13, 'TRANS': 556}
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 749
          Unresolved non-hydrogen angles: 959
          Unresolved non-hydrogen dihedrals: 588
          Unresolved non-hydrogen chiralities: 79
          Planarities with less than four sites: {'GLU:plan': 21, 'ARG:plan': 21, 'ASP:plan': 17, 'PHE:plan': 6, 'ASN:plan1': 13, 'TYR:plan': 7, 'HIS:plan': 6, 'GLN:plan1': 10}
          Unresolved non-hydrogen planarities: 434
    Chain: "B"
      Number of atoms: 3698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 3698
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 209}
          Link IDs: {'PTRANS': 13, 'TRANS': 556}
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 745
          Unresolved non-hydrogen angles: 954
          Unresolved non-hydrogen dihedrals: 585
          Unresolved non-hydrogen chiralities: 79
          Planarities with less than four sites: {'GLU:plan': 20, 'ARG:plan': 21, 'ASP:plan': 17, 'PHE:plan': 6, 'ASN:plan1': 13, 'TYR:plan': 7, 'HIS:plan': 6, 'GLN:plan1': 10}
          Unresolved non-hydrogen planarities: 430
  Time building chain proxies: 1.88, per 1000 atoms: 0.25
  Number of scatterers: 7392
  At special positions: 0
  Unit cell: (72, 96, 131, 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      44     16.00
     O    1380      8.00
     N    1328      7.00
     C    4640      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: 0.80
  Conformation dependent library (CDL) restraints added in 290.7 milliseconds
  

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2132

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 5 sheets defined
      71.8% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 21
      Proline residue:  A  18  - end of helix
    Processing helix  chain 'A' and resid 24 through 47
    Processing helix  chain 'A' and resid 47 through 53
      removed outlier: 3.574A  pdb=" N   ASP A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 59
    Processing helix  chain 'A' and resid 62 through 109
      removed outlier: 3.712A  pdb=" N   TRP A  66 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
      Proline residue:  A  68  - end of helix
    Processing helix  chain 'A' and resid 113 through 118
    Processing helix  chain 'A' and resid 120 through 164
      removed outlier: 3.556A  pdb=" N   GLY A 155 " --> pdb=" O   ALA A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 196
      Proline residue:  A 176  - end of helix
      removed outlier: 3.755A  pdb=" N   MET A 196 " --> pdb=" O   ILE A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 221
      removed outlier: 5.028A  pdb=" N   LYS A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   GLU A 216 " --> pdb=" O   LYS A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 269
      removed outlier: 3.553A  pdb=" N   LYS A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   SER A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   ASP A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      removed outlier: 3.640A  pdb=" N   ALA A 262 " --> pdb=" O   ILE A 258 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   LEU A 263 " --> pdb=" O   ALA A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 276
    Processing helix  chain 'A' and resid 280 through 324
      Proline residue:  A 297  - end of helix
      removed outlier: 4.073A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ASN A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 390
      removed outlier: 3.834A  pdb=" N   ALA A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 411 through 418
    Processing helix  chain 'A' and resid 432 through 438
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 464
    Processing helix  chain 'A' and resid 468 through 472
      removed outlier: 3.687A  pdb=" N   ASP A 471 " --> pdb=" O   ASN A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 498
    Processing helix  chain 'A' and resid 512 through 527
    Processing helix  chain 'A' and resid 538 through 545
      removed outlier: 4.118A  pdb=" N   ALA A 545 " --> pdb=" O   THR A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 566
    Processing helix  chain 'A' and resid 570 through 574
      removed outlier: 3.521A  pdb=" N   ALA A 573 " --> pdb=" O   GLY A 570 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 17
    Processing helix  chain 'B' and resid 18 through 22
      Proline residue:  B  22  - end of helix
    Processing helix  chain 'B' and resid 23 through 53
      removed outlier: 3.861A  pdb=" N   LEU B  27 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   LYS B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 60 through 109
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 112 through 118
    Processing helix  chain 'B' and resid 120 through 164
    Processing helix  chain 'B' and resid 164 through 213
      Proline residue:  B 176  - end of helix
    Processing helix  chain 'B' and resid 213 through 221
    Processing helix  chain 'B' and resid 222 through 275
      removed outlier: 4.767A  pdb=" N   ASP B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      Proline residue:  B 253  - end of helix
      Proline residue:  B 273  - end of helix
    Processing helix  chain 'B' and resid 280 through 323
      removed outlier: 3.632A  pdb=" N   PHE B 288 " --> pdb=" O   ILE B 284 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
      removed outlier: 3.797A  pdb=" N   ASN B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE B 308 " --> pdb=" O   VAL B 304 " (cutoff:3.500A)
      removed outlier: 5.045A  pdb=" N   GLN B 309 " --> pdb=" O   ASN B 305 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   ARG B 310 " --> pdb=" O   ALA B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 390
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 412 through 419
    Processing helix  chain 'B' and resid 432 through 437
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 459 through 464
      removed outlier: 3.668A  pdb=" N   ASN B 464 " --> pdb=" O   MET B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 479
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 512 through 527
    Processing helix  chain 'B' and resid 540 through 545
      removed outlier: 3.677A  pdb=" N   LYS B 544 " --> pdb=" O   SER B 540 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   ALA B 545 " --> pdb=" O   THR B 541 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 540 through 545'
    Processing helix  chain 'B' and resid 561 through 567
    Processing helix  chain 'B' and resid 570 through 579
      removed outlier: 3.590A  pdb=" N   GLN B 574 " --> pdb=" O   GLY B 570 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 366
      removed outlier: 5.615A  pdb=" N   ARG A 360 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   PHE A 349 " --> pdb=" O   ARG A 360 " (cutoff:3.500A)
      removed outlier: 7.374A  pdb=" N   LEU A 364 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 5.311A  pdb=" N   ARG A 345 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ILE A 366 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
      removed outlier: 5.438A  pdb=" N   GLU A 343 " --> pdb=" O   ILE A 366 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   VAL A 347 " --> pdb=" O   GLU A 397 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   GLU A 397 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 371 through 374
    Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 422
      removed outlier: 5.311A  pdb=" N   ALA A 420 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 342 through 343
    Processing sheet with id=AA5, first strand: chain 'B' and resid 421 through 422
      removed outlier: 3.653A  pdb=" N   VAL B 422 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    586 hydrogen bonds defined for protein.
    1734 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: 1.17

  Time building geometry restraints manager: 0.95 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: 2498
        1.34 -     1.45: 996
        1.45 -     1.57: 3894
        1.57 -     1.69: 2
        1.69 -     1.81: 84
  Bond restraints: 7474
  Sorted by residual:
  bond pdb=" CG  ARG B 296 "
       pdb=" CD  ARG B 296 "
    ideal  model  delta    sigma   weight residual
    1.520  1.588 -0.068 3.00e-02 1.11e+03 5.18e+00
  bond pdb=" CG  ARG A 296 "
       pdb=" CD  ARG A 296 "
    ideal  model  delta    sigma   weight residual
    1.520  1.588 -0.068 3.00e-02 1.11e+03 5.15e+00
  bond pdb=" CB  TRP A  17 "
       pdb=" CG  TRP A  17 "
    ideal  model  delta    sigma   weight residual
    1.498  1.436  0.062 3.10e-02 1.04e+03 4.02e+00
  bond pdb=" CB  PHE A  13 "
       pdb=" CG  PHE A  13 "
    ideal  model  delta    sigma   weight residual
    1.502  1.459  0.043 2.30e-02 1.89e+03 3.52e+00
  bond pdb=" CB  TRP B  17 "
       pdb=" CG  TRP B  17 "
    ideal  model  delta    sigma   weight residual
    1.498  1.442  0.056 3.10e-02 1.04e+03 3.30e+00
  ... (remaining 7469 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 9918
        2.73 -     5.47: 230
        5.47 -     8.20: 31
        8.20 -    10.93: 8
       10.93 -    13.67: 8
  Bond angle restraints: 10195
  Sorted by residual:
  angle pdb=" N   HIS B 537 "
        pdb=" CA  HIS B 537 "
        pdb=" C   HIS B 537 "
      ideal   model   delta    sigma   weight residual
     112.59  100.04   12.55 1.22e+00 6.72e-01 1.06e+02
  angle pdb=" C   MET A 295 "
        pdb=" N   ARG A 296 "
        pdb=" CA  ARG A 296 "
      ideal   model   delta    sigma   weight residual
     119.83  112.91    6.92 1.11e+00 8.12e-01 3.88e+01
  angle pdb=" N   ALA B 536 "
        pdb=" CA  ALA B 536 "
        pdb=" C   ALA B 536 "
      ideal   model   delta    sigma   weight residual
     108.56  118.02   -9.46 1.74e+00 3.30e-01 2.95e+01
  angle pdb=" N   SER B 164 "
        pdb=" CA  SER B 164 "
        pdb=" C   SER B 164 "
      ideal   model   delta    sigma   weight residual
     107.93  116.15   -8.22 1.65e+00 3.67e-01 2.48e+01
  angle pdb=" N   TYR A 163 "
        pdb=" CA  TYR A 163 "
        pdb=" C   TYR A 163 "
      ideal   model   delta    sigma   weight residual
     111.36  116.32   -4.96 1.09e+00 8.42e-01 2.07e+01
  ... (remaining 10190 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.39: 3904
       13.39 -    26.77: 398
       26.77 -    40.16: 121
       40.16 -    53.54: 39
       53.54 -    66.93: 9
  Dihedral angle restraints: 4471
    sinusoidal: 1189
      harmonic: 3282
  Sorted by residual:
  dihedral pdb=" CA  GLU A 552 "
           pdb=" C   GLU A 552 "
           pdb=" N   ASP A 553 "
           pdb=" CA  ASP A 553 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.68   28.32     0      5.00e+00 4.00e-02 3.21e+01
  dihedral pdb=" CA  ALA A 457 "
           pdb=" C   ALA A 457 "
           pdb=" N   TYR A 458 "
           pdb=" CA  TYR A 458 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.96   28.04     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  LYS B 544 "
           pdb=" C   LYS B 544 "
           pdb=" N   ALA B 545 "
           pdb=" CA  ALA B 545 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.94   27.06     0      5.00e+00 4.00e-02 2.93e+01
  ... (remaining 4468 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 883
       0.048 -    0.096: 318
       0.096 -    0.143: 73
       0.143 -    0.191: 5
       0.191 -    0.239: 5
  Chirality restraints: 1284
  Sorted by residual:
  chirality pdb=" CA  VAL A 334 "
            pdb=" N   VAL A 334 "
            pdb=" C   VAL A 334 "
            pdb=" CB  VAL A 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CA  ALA B 536 "
            pdb=" N   ALA B 536 "
            pdb=" C   ALA B 536 "
            pdb=" CB  ALA B 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.25    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  TYR A 163 "
            pdb=" N   TYR A 163 "
            pdb=" C   TYR A 163 "
            pdb=" CB  TYR A 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 1281 not shown)

  Planarity restraints: 1327
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 262 "   -0.012 2.00e-02 2.50e+03   2.40e-02 5.77e+00
        pdb=" C   ALA B 262 "    0.042 2.00e-02 2.50e+03
        pdb=" O   ALA B 262 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LEU B 263 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 136 "   -0.011 2.00e-02 2.50e+03   2.31e-02 5.35e+00
        pdb=" C   ALA B 136 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ALA B 136 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   SER B 137 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 296 "    0.039 5.00e-02 4.00e+02   5.73e-02 5.26e+00
        pdb=" N   PRO B 297 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B 297 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 297 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1324 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1320
        2.74 -     3.28: 8957
        3.28 -     3.82: 12479
        3.82 -     4.36: 13927
        4.36 -     4.90: 22048
  Nonbonded interactions: 58731
  Sorted by model distance:
  nonbonded pdb=" O   ARG A  78 "
            pdb=" OG1 THR A  81 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   GLN B 256 "
            pdb=" OG  SER B 260 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   PRO A 297 "
            pdb=" OG  SER A 300 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   ALA A 175 "
            pdb=" OG  SER A 179 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   VAL A 135 "
            pdb=" OG  SER A 139 "
     model   vdw
     2.208 3.040
  ... (remaining 58726 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 11 through 148 or (resid 149 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 150 through 580))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.270
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     8.940
  Find NCS groups from input model:        0.100
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
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      :  0.009   0.068   7474  Z= 0.459
  Angle     :  1.131  13.667  10195  Z= 0.668
  Chirality :  0.051   0.239   1284
  Planarity :  0.005   0.057   1327
  Dihedral  : 13.781  66.927   2339
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 31.10
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 15.49 %
    Favored  : 84.33 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.70 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.29 (0.18), residues: 1136
  helix: -3.00 (0.14), residues: 715
  sheet: -3.18 (0.60), residues: 43
  loop : -4.28 (0.25), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 296 
 TYR   0.010   0.002   TYR A  83 
 PHE   0.040   0.004   PHE A 308 
 TRP   0.023   0.003   TRP A  91 
 HIS   0.009   0.002   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00864 ( 7474)
  covalent geometry    : angle       1.13148 (10195)
  hydrogen bonds       : bond        0.17148 (  586)
  hydrogen bonds       : angle       8.41066 ( 1734)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 246
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 LYS cc_start: 0.8540 (tptm) cc_final: 0.8230 (pttt)
REVERT: A  148 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7782 (tpp80)
REVERT: A  159 MET cc_start: 0.9199 (mmm) cc_final: 0.8524 (mmm)
REVERT: A  189 PHE cc_start: 0.8718 (m-10) cc_final: 0.8246 (m-80)
REVERT: A  190 ARG cc_start: 0.9025 (mtt180) cc_final: 0.8769 (mmp80)
REVERT: A  196 MET cc_start: 0.9023 (mmm) cc_final: 0.8611 (mmm)
REVERT: A  198 ASN cc_start: 0.9149 (m-40) cc_final: 0.8783 (p0)
REVERT: A  208 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8121 (mm-30)
REVERT: A  210 MET cc_start: 0.8939 (mmm) cc_final: 0.8546 (mtt)
REVERT: A  212 LYS cc_start: 0.9177 (mttt) cc_final: 0.8635 (mttm)
REVERT: A  230 PHE cc_start: 0.8652 (m-10) cc_final: 0.8353 (m-10)
REVERT: A  296 ARG cc_start: 0.5977 (mtt180) cc_final: 0.5144 (ttm170)
REVERT: B   98 MET cc_start: 0.9275 (ttm) cc_final: 0.8648 (tpp)
REVERT: B  171 LEU cc_start: 0.9173 (mt) cc_final: 0.8940 (mt)
REVERT: B  189 PHE cc_start: 0.8602 (m-10) cc_final: 0.8193 (t80)
REVERT: B  190 ARG cc_start: 0.9037 (mtt180) cc_final: 0.8716 (ptt180)
REVERT: B  191 ASN cc_start: 0.8431 (m-40) cc_final: 0.8063 (t0)
REVERT: B  196 MET cc_start: 0.8861 (mmm) cc_final: 0.8617 (tpp)
REVERT: B  210 MET cc_start: 0.8608 (tpt) cc_final: 0.8381 (tpt)
REVERT: B  296 ARG cc_start: 0.5595 (mtt180) cc_final: 0.4566 (ttm170)
REVERT: B  312 MET cc_start: 0.9242 (mmm) cc_final: 0.9026 (mmm)
  outliers start: 11
  outliers final: 5
  residues processed: 252
  average time/residue: 0.0815
  time to fit residues: 27.8882
Evaluate side-chains
  187 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 181
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:    0.0470
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:   30.0000
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    7.9990
   overall best weight:    3.4086

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

Flipped N/Q/H residues before XYZ refinement:
A  37 ASN
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 326 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.104681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.080510 restraints weight = 24756.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.082583 restraints weight = 15364.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.083974 restraints weight = 10907.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.085039 restraints weight = 8515.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.085708 restraints weight = 7031.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   7474  Z= 0.279
  Angle     :  0.808  10.895  10195  Z= 0.429
  Chirality :  0.047   0.151   1284
  Planarity :  0.005   0.058   1327
  Dihedral  :  5.675  24.358   1184
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.92 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.03 (0.22), residues: 1136
  helix: -1.20 (0.17), residues: 744
  sheet: -3.01 (0.84), residues: 32
  loop : -3.48 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  15 
 TYR   0.021   0.002   TYR A 268 
 PHE   0.047   0.003   PHE A 115 
 TRP   0.013   0.002   TRP B  66 
 HIS   0.009   0.003   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 ( 7474)
  covalent geometry    : angle       0.80825 (10195)
  hydrogen bonds       : bond        0.06596 (  586)
  hydrogen bonds       : angle       6.18855 ( 1734)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 PHE cc_start: 0.8404 (m-80) cc_final: 0.7928 (m-80)
REVERT: A  118 LYS cc_start: 0.8365 (tptm) cc_final: 0.8044 (pttt)
REVERT: A  125 LEU cc_start: 0.9418 (tt) cc_final: 0.8154 (tt)
REVERT: A  131 ASP cc_start: 0.8493 (m-30) cc_final: 0.8279 (m-30)
REVERT: A  154 ILE cc_start: 0.9486 (mt) cc_final: 0.9275 (mm)
REVERT: A  159 MET cc_start: 0.9378 (mmm) cc_final: 0.9011 (mmm)
REVERT: A  171 LEU cc_start: 0.9040 (mt) cc_final: 0.8772 (mt)
REVERT: A  189 PHE cc_start: 0.8480 (m-10) cc_final: 0.8226 (m-80)
REVERT: A  190 ARG cc_start: 0.8945 (mtt180) cc_final: 0.8684 (mmp80)
REVERT: A  196 MET cc_start: 0.8897 (mmm) cc_final: 0.8472 (tpp)
REVERT: A  198 ASN cc_start: 0.9148 (m-40) cc_final: 0.8776 (p0)
REVERT: A  208 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8096 (mm-30)
REVERT: A  212 LYS cc_start: 0.9137 (mttt) cc_final: 0.8635 (mttm)
REVERT: A  216 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8878 (pt0)
REVERT: A  226 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8503 (mm-30)
REVERT: A  288 PHE cc_start: 0.9085 (m-80) cc_final: 0.8865 (m-80)
REVERT: B   98 MET cc_start: 0.9374 (ttm) cc_final: 0.8537 (tpp)
REVERT: B  125 LEU cc_start: 0.8810 (mt) cc_final: 0.6791 (mt)
REVERT: B  144 ILE cc_start: 0.9143 (mt) cc_final: 0.8890 (mt)
REVERT: B  159 MET cc_start: 0.9183 (mmm) cc_final: 0.8782 (mmm)
REVERT: B  189 PHE cc_start: 0.8266 (m-10) cc_final: 0.8002 (t80)
REVERT: B  190 ARG cc_start: 0.9064 (mtt180) cc_final: 0.8673 (ptt180)
REVERT: B  191 ASN cc_start: 0.8342 (m-40) cc_final: 0.8039 (t0)
REVERT: B  210 MET cc_start: 0.8541 (tpt) cc_final: 0.8261 (ttt)
REVERT: B  214 HIS cc_start: 0.8279 (p-80) cc_final: 0.8067 (p-80)
REVERT: B  230 PHE cc_start: 0.8639 (m-10) cc_final: 0.7776 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 227
  average time/residue: 0.0666
  time to fit residues: 21.5227
Evaluate side-chains
  182 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 58 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9980
   chunk 44 optimal weight:    9.9990
   chunk 86 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 82 optimal weight:    0.8980
   chunk 52 optimal weight:   50.0000
   chunk 69 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 50 optimal weight:    5.9990
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 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 = 0.3872 r_free = 0.3872 target = 0.116497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.092422 restraints weight = 24547.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.094776 restraints weight = 14531.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.096417 restraints weight = 9841.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.097503 restraints weight = 7306.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.098309 restraints weight = 5850.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.4089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7474  Z= 0.158
  Angle     :  0.659   8.982  10195  Z= 0.348
  Chirality :  0.045   0.157   1284
  Planarity :  0.004   0.045   1327
  Dihedral  :  4.888  20.006   1184
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.55 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.24), residues: 1136
  helix:  0.11 (0.18), residues: 768
  sheet: -2.72 (0.86), residues: 32
  loop : -3.11 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 127 
 TYR   0.023   0.001   TYR A  87 
 PHE   0.031   0.002   PHE A 115 
 TRP   0.028   0.002   TRP B  66 
 HIS   0.007   0.002   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 7474)
  covalent geometry    : angle       0.65910 (10195)
  hydrogen bonds       : bond        0.05166 (  586)
  hydrogen bonds       : angle       5.23060 ( 1734)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 257
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.8465 (m-30) cc_final: 0.8247 (m-30)
REVERT: A   63 VAL cc_start: 0.9187 (p) cc_final: 0.8954 (m)
REVERT: A   98 MET cc_start: 0.8894 (tpp) cc_final: 0.8534 (tpp)
REVERT: A  118 LYS cc_start: 0.8061 (tptm) cc_final: 0.7823 (pttt)
REVERT: A  159 MET cc_start: 0.9114 (mmm) cc_final: 0.8167 (mmm)
REVERT: A  163 TYR cc_start: 0.8327 (m-80) cc_final: 0.7114 (m-80)
REVERT: A  198 ASN cc_start: 0.9168 (m-40) cc_final: 0.8808 (p0)
REVERT: A  208 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8358 (mm-30)
REVERT: A  216 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8777 (pt0)
REVERT: A  230 PHE cc_start: 0.8503 (m-80) cc_final: 0.7999 (m-10)
REVERT: A  261 LEU cc_start: 0.9537 (mt) cc_final: 0.9328 (mt)
REVERT: A  312 MET cc_start: 0.9205 (mmm) cc_final: 0.8442 (mmm)
REVERT: B   75 MET cc_start: 0.9083 (mmt) cc_final: 0.8755 (mmm)
REVERT: B   98 MET cc_start: 0.9304 (ttm) cc_final: 0.8440 (tpp)
REVERT: B  105 PHE cc_start: 0.8176 (m-10) cc_final: 0.7672 (m-10)
REVERT: B  159 MET cc_start: 0.8942 (mmm) cc_final: 0.8372 (mmm)
REVERT: B  163 TYR cc_start: 0.8188 (m-80) cc_final: 0.7065 (m-80)
REVERT: B  190 ARG cc_start: 0.8916 (mtt180) cc_final: 0.8511 (ptt180)
REVERT: B  197 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8575 (tm-30)
REVERT: B  200 MET cc_start: 0.8385 (mtm) cc_final: 0.7692 (mtt)
REVERT: B  240 GLN cc_start: 0.8967 (mt0) cc_final: 0.8553 (tt0)
REVERT: B  261 LEU cc_start: 0.9286 (mt) cc_final: 0.8895 (tp)
REVERT: B  320 THR cc_start: 0.9061 (p) cc_final: 0.8846 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 257
  average time/residue: 0.0688
  time to fit residues: 25.1939
Evaluate side-chains
  202 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 45 optimal weight:   30.0000
   chunk 84 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 0 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 119 GLN
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.117357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.093997 restraints weight = 24132.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.096201 restraints weight = 14803.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.097785 restraints weight = 10251.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.098822 restraints weight = 7714.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.099661 restraints weight = 6252.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.4988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7474  Z= 0.145
  Angle     :  0.608   9.923  10195  Z= 0.324
  Chirality :  0.044   0.270   1284
  Planarity :  0.004   0.042   1327
  Dihedral  :  4.472  18.615   1184
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.28 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.99 %
    Favored  : 95.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.25), residues: 1136
  helix:  0.60 (0.18), residues: 772
  sheet: -2.54 (0.89), residues: 32
  loop : -2.81 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 127 
 TYR   0.017   0.001   TYR B  87 
 PHE   0.039   0.002   PHE A 105 
 TRP   0.030   0.002   TRP B  66 
 HIS   0.004   0.002   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7474)
  covalent geometry    : angle       0.60819 (10195)
  hydrogen bonds       : bond        0.04839 (  586)
  hydrogen bonds       : angle       4.96135 ( 1734)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 255
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8852 (tpp) cc_final: 0.8211 (tpp)
REVERT: A  117 ASP cc_start: 0.7935 (m-30) cc_final: 0.7489 (t0)
REVERT: A  131 ASP cc_start: 0.8252 (m-30) cc_final: 0.8038 (m-30)
REVERT: A  159 MET cc_start: 0.8974 (mmm) cc_final: 0.8485 (mtp)
REVERT: A  163 TYR cc_start: 0.8297 (m-80) cc_final: 0.7579 (m-80)
REVERT: A  210 MET cc_start: 0.8581 (mtp) cc_final: 0.8183 (mmt)
REVERT: A  212 LYS cc_start: 0.8994 (mttt) cc_final: 0.8725 (tppt)
REVERT: A  216 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8711 (pt0)
REVERT: A  226 GLU cc_start: 0.8637 (tp30) cc_final: 0.6963 (tp30)
REVERT: A  230 PHE cc_start: 0.8176 (m-80) cc_final: 0.7929 (m-10)
REVERT: A  312 MET cc_start: 0.9050 (mmm) cc_final: 0.8293 (mmm)
REVERT: B   75 MET cc_start: 0.8935 (mmt) cc_final: 0.8667 (mmm)
REVERT: B   98 MET cc_start: 0.9179 (ttm) cc_final: 0.8244 (tpp)
REVERT: B  108 MET cc_start: 0.8658 (mtm) cc_final: 0.8331 (mtm)
REVERT: B  111 MET cc_start: 0.7847 (ttm) cc_final: 0.7610 (ttp)
REVERT: B  125 LEU cc_start: 0.9456 (tp) cc_final: 0.8676 (tp)
REVERT: B  131 ASP cc_start: 0.8178 (m-30) cc_final: 0.7966 (m-30)
REVERT: B  149 GLU cc_start: 0.8565 (mp0) cc_final: 0.7953 (mp0)
REVERT: B  159 MET cc_start: 0.8840 (mmm) cc_final: 0.8131 (mmm)
REVERT: B  163 TYR cc_start: 0.8237 (m-80) cc_final: 0.6877 (m-80)
REVERT: B  190 ARG cc_start: 0.8783 (mtt180) cc_final: 0.8302 (ptt180)
REVERT: B  197 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8486 (tm-30)
REVERT: B  208 GLU cc_start: 0.8386 (tp30) cc_final: 0.7742 (tp30)
REVERT: B  240 GLN cc_start: 0.8788 (mt0) cc_final: 0.8583 (tt0)
REVERT: B  257 LEU cc_start: 0.9356 (tt) cc_final: 0.9153 (tt)
REVERT: B  261 LEU cc_start: 0.9218 (mt) cc_final: 0.8797 (tp)
REVERT: B  296 ARG cc_start: 0.5721 (ttm170) cc_final: 0.4537 (ttt90)
REVERT: B  320 THR cc_start: 0.8975 (p) cc_final: 0.8769 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 256
  average time/residue: 0.0617
  time to fit residues: 22.8102
Evaluate side-chains
  203 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   chunk 101 optimal weight:   20.0000
   chunk 13 optimal weight:    4.9990
   chunk 93 optimal weight:   50.0000
   chunk 31 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 95 optimal weight:   30.0000
   chunk 85 optimal weight:    0.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 HIS
B 326 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.114422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.090509 restraints weight = 24541.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.092745 restraints weight = 14977.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.094268 restraints weight = 10316.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.095283 restraints weight = 7817.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.096067 restraints weight = 6346.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.5159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7474  Z= 0.201
  Angle     :  0.650   8.070  10195  Z= 0.347
  Chirality :  0.044   0.200   1284
  Planarity :  0.004   0.044   1327
  Dihedral  :  4.370  18.484   1184
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.37 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.25), residues: 1136
  helix:  0.74 (0.19), residues: 766
  sheet: -3.64 (0.72), residues: 25
  loop : -2.57 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 102 
 TYR   0.015   0.002   TYR B  83 
 PHE   0.050   0.003   PHE B 105 
 TRP   0.028   0.002   TRP B  66 
 HIS   0.003   0.002   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 7474)
  covalent geometry    : angle       0.65028 (10195)
  hydrogen bonds       : bond        0.05050 (  586)
  hydrogen bonds       : angle       5.02532 ( 1734)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.8311 (m-30) cc_final: 0.7974 (m-30)
REVERT: A   63 VAL cc_start: 0.9231 (p) cc_final: 0.8854 (m)
REVERT: A   98 MET cc_start: 0.8947 (tpp) cc_final: 0.8383 (tpp)
REVERT: A  115 PHE cc_start: 0.6865 (m-80) cc_final: 0.6429 (m-80)
REVERT: A  131 ASP cc_start: 0.8378 (m-30) cc_final: 0.8100 (m-30)
REVERT: A  209 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7991 (tm-30)
REVERT: A  210 MET cc_start: 0.8413 (mtp) cc_final: 0.8140 (mmt)
REVERT: A  211 LEU cc_start: 0.9557 (mt) cc_final: 0.9303 (mt)
REVERT: A  212 LYS cc_start: 0.8940 (mttt) cc_final: 0.8696 (tppt)
REVERT: A  216 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8717 (pt0)
REVERT: A  226 GLU cc_start: 0.8710 (tp30) cc_final: 0.7309 (tp30)
REVERT: A  288 PHE cc_start: 0.9133 (m-10) cc_final: 0.8914 (m-10)
REVERT: A  312 MET cc_start: 0.9157 (mmm) cc_final: 0.8528 (mmm)
REVERT: B   53 ASP cc_start: 0.7967 (p0) cc_final: 0.7656 (p0)
REVERT: B   54 ASP cc_start: 0.7751 (m-30) cc_final: 0.7217 (m-30)
REVERT: B   75 MET cc_start: 0.9049 (mmt) cc_final: 0.8797 (mmm)
REVERT: B   98 MET cc_start: 0.9159 (ttm) cc_final: 0.8441 (tpp)
REVERT: B  108 MET cc_start: 0.8742 (mtm) cc_final: 0.8423 (mtm)
REVERT: B  159 MET cc_start: 0.8992 (mmm) cc_final: 0.8592 (mmm)
REVERT: B  163 TYR cc_start: 0.8840 (m-80) cc_final: 0.8306 (m-80)
REVERT: B  190 ARG cc_start: 0.8941 (mtt180) cc_final: 0.8358 (ptt180)
REVERT: B  196 MET cc_start: 0.7195 (tpt) cc_final: 0.6994 (tpp)
REVERT: B  197 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8503 (tm-30)
REVERT: B  208 GLU cc_start: 0.8409 (tp30) cc_final: 0.7954 (tp30)
REVERT: B  261 LEU cc_start: 0.9327 (mt) cc_final: 0.8883 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.0629
  time to fit residues: 21.4843
Evaluate side-chains
  195 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 56 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 51 optimal weight:    9.9990
   chunk 108 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 98 optimal weight:    0.1980
   chunk 15 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 73 optimal weight:    0.9990
   chunk 54 optimal weight:    8.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 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 = 0.3872 r_free = 0.3872 target = 0.111307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.088168 restraints weight = 22982.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.090327 restraints weight = 14971.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.091895 restraints weight = 10805.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.093044 restraints weight = 8354.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.093799 restraints weight = 6845.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.5618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7474  Z= 0.144
  Angle     :  0.628   7.711  10195  Z= 0.333
  Chirality :  0.044   0.153   1284
  Planarity :  0.003   0.040   1327
  Dihedral  :  4.247  19.415   1184
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.93 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.26), residues: 1136
  helix:  0.90 (0.19), residues: 770
  sheet: -2.37 (0.92), residues: 32
  loop : -2.58 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 127 
 TYR   0.010   0.001   TYR B  87 
 PHE   0.035   0.002   PHE B 116 
 TRP   0.022   0.002   TRP B  66 
 HIS   0.004   0.002   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7474)
  covalent geometry    : angle       0.62802 (10195)
  hydrogen bonds       : bond        0.04673 (  586)
  hydrogen bonds       : angle       4.95429 ( 1734)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8982 (tpp) cc_final: 0.8347 (tpp)
REVERT: A  111 MET cc_start: 0.7780 (mtm) cc_final: 0.7415 (mtm)
REVERT: A  115 PHE cc_start: 0.6715 (m-80) cc_final: 0.5995 (m-80)
REVERT: A  163 TYR cc_start: 0.8588 (m-80) cc_final: 0.8075 (m-80)
REVERT: A  208 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8010 (mm-30)
REVERT: A  209 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7832 (tm-30)
REVERT: A  210 MET cc_start: 0.8566 (mtp) cc_final: 0.8166 (mmt)
REVERT: A  212 LYS cc_start: 0.8848 (mttt) cc_final: 0.8497 (tppt)
REVERT: A  226 GLU cc_start: 0.8740 (tp30) cc_final: 0.7983 (tp30)
REVERT: A  229 ARG cc_start: 0.9083 (mtt180) cc_final: 0.8791 (tpp80)
REVERT: A  296 ARG cc_start: 0.5264 (ttt180) cc_final: 0.5047 (ttt180)
REVERT: A  312 MET cc_start: 0.9150 (mmm) cc_final: 0.8370 (mmm)
REVERT: B   53 ASP cc_start: 0.7926 (p0) cc_final: 0.7642 (p0)
REVERT: B   64 LEU cc_start: 0.9078 (mp) cc_final: 0.8819 (mp)
REVERT: B   71 VAL cc_start: 0.9167 (t) cc_final: 0.8486 (t)
REVERT: B   75 MET cc_start: 0.8998 (mmt) cc_final: 0.8715 (mmm)
REVERT: B   98 MET cc_start: 0.9204 (ttm) cc_final: 0.8266 (tpp)
REVERT: B  100 MET cc_start: 0.8979 (mmm) cc_final: 0.8636 (tpt)
REVERT: B  108 MET cc_start: 0.8692 (mtm) cc_final: 0.8445 (mtm)
REVERT: B  125 LEU cc_start: 0.9465 (mt) cc_final: 0.9227 (mt)
REVERT: B  133 GLU cc_start: 0.9018 (tp30) cc_final: 0.8764 (mm-30)
REVERT: B  163 TYR cc_start: 0.8823 (m-80) cc_final: 0.8379 (m-80)
REVERT: B  190 ARG cc_start: 0.8881 (mtt180) cc_final: 0.8366 (ptt180)
REVERT: B  208 GLU cc_start: 0.8301 (tp30) cc_final: 0.7879 (tp30)
REVERT: B  230 PHE cc_start: 0.7586 (m-10) cc_final: 0.7345 (m-10)
REVERT: B  261 LEU cc_start: 0.9266 (mt) cc_final: 0.8910 (tp)
REVERT: B  288 PHE cc_start: 0.8873 (m-80) cc_final: 0.8641 (m-80)
REVERT: B  295 MET cc_start: 0.8956 (tpp) cc_final: 0.8610 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 248
  average time/residue: 0.0619
  time to fit residues: 22.1227
Evaluate side-chains
  197 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 87 optimal weight:    0.6980
   chunk 108 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9980
   chunk 38 optimal weight:   20.0000
   chunk 89 optimal weight:   30.0000
   chunk 26 optimal weight:    0.9990
   chunk 100 optimal weight:   20.0000
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.111144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.088067 restraints weight = 22975.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.090222 restraints weight = 15094.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.091746 restraints weight = 10880.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.092793 restraints weight = 8466.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.093689 restraints weight = 6989.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.5826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7474  Z= 0.161
  Angle     :  0.642   7.833  10195  Z= 0.337
  Chirality :  0.044   0.183   1284
  Planarity :  0.003   0.037   1327
  Dihedral  :  4.175  17.194   1184
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.93 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.26), residues: 1136
  helix:  0.93 (0.19), residues: 768
  sheet: -2.22 (0.94), residues: 32
  loop : -2.40 (0.36), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 101 
 TYR   0.014   0.001   TYR B  87 
 PHE   0.038   0.003   PHE B  56 
 TRP   0.015   0.001   TRP B  91 
 HIS   0.004   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7474)
  covalent geometry    : angle       0.64223 (10195)
  hydrogen bonds       : bond        0.04694 (  586)
  hydrogen bonds       : angle       4.90593 ( 1734)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9131 (m-80) cc_final: 0.8425 (m-80)
REVERT: A   60 ASP cc_start: 0.8225 (m-30) cc_final: 0.7898 (m-30)
REVERT: A   98 MET cc_start: 0.8977 (tpp) cc_final: 0.8288 (tpp)
REVERT: A  131 ASP cc_start: 0.8438 (m-30) cc_final: 0.8191 (m-30)
REVERT: A  209 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7666 (tm-30)
REVERT: A  210 MET cc_start: 0.8540 (mtp) cc_final: 0.8036 (mmt)
REVERT: A  212 LYS cc_start: 0.8890 (mttt) cc_final: 0.8554 (tppt)
REVERT: A  226 GLU cc_start: 0.8630 (tp30) cc_final: 0.7617 (tp30)
REVERT: A  296 ARG cc_start: 0.5244 (ttt180) cc_final: 0.4857 (ttt180)
REVERT: A  298 LEU cc_start: 0.9260 (mt) cc_final: 0.8975 (mt)
REVERT: A  312 MET cc_start: 0.9059 (mmm) cc_final: 0.8347 (mmm)
REVERT: B   53 ASP cc_start: 0.7796 (p0) cc_final: 0.7428 (p0)
REVERT: B   98 MET cc_start: 0.9217 (ttm) cc_final: 0.8178 (tpp)
REVERT: B  100 MET cc_start: 0.8851 (mmm) cc_final: 0.8431 (tpt)
REVERT: B  111 MET cc_start: 0.7994 (ttt) cc_final: 0.7188 (tmm)
REVERT: B  131 ASP cc_start: 0.8374 (m-30) cc_final: 0.8094 (m-30)
REVERT: B  190 ARG cc_start: 0.8935 (mtt180) cc_final: 0.8398 (ptt180)
REVERT: B  208 GLU cc_start: 0.8172 (tp30) cc_final: 0.7837 (tp30)
REVERT: B  261 LEU cc_start: 0.9304 (mt) cc_final: 0.8926 (tp)
REVERT: B  288 PHE cc_start: 0.8923 (m-80) cc_final: 0.8685 (m-80)
REVERT: B  295 MET cc_start: 0.8926 (tpp) cc_final: 0.8502 (tmm)
REVERT: B  296 ARG cc_start: 0.5366 (ttm170) cc_final: 0.5030 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.0592
  time to fit residues: 20.1807
Evaluate side-chains
  200 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 66 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 40 optimal weight:    8.9990
   chunk 50 optimal weight:    9.9990
   chunk 97 optimal weight:    9.9990
   chunk 91 optimal weight:    0.1980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B 107 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.111740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.087690 restraints weight = 22659.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.089918 restraints weight = 14832.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.091508 restraints weight = 10720.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.092754 restraints weight = 8296.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.093664 restraints weight = 6770.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.6074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7474  Z= 0.141
  Angle     :  0.654   8.823  10195  Z= 0.337
  Chirality :  0.044   0.197   1284
  Planarity :  0.003   0.041   1327
  Dihedral  :  4.110  19.532   1184
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.67 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.26), residues: 1136
  helix:  0.98 (0.19), residues: 777
  sheet: -2.17 (0.94), residues: 32
  loop : -2.43 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 127 
 TYR   0.014   0.001   TYR A 268 
 PHE   0.030   0.002   PHE B 116 
 TRP   0.017   0.001   TRP B  91 
 HIS   0.003   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 7474)
  covalent geometry    : angle       0.65439 (10195)
  hydrogen bonds       : bond        0.04535 (  586)
  hydrogen bonds       : angle       4.82061 ( 1734)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8919 (tpp) cc_final: 0.8295 (tpp)
REVERT: A  108 MET cc_start: 0.8969 (mtm) cc_final: 0.8687 (mtm)
REVERT: A  131 ASP cc_start: 0.8347 (m-30) cc_final: 0.8143 (m-30)
REVERT: A  212 LYS cc_start: 0.8854 (mttt) cc_final: 0.8566 (tppt)
REVERT: A  229 ARG cc_start: 0.9047 (mtt180) cc_final: 0.8841 (tpp80)
REVERT: A  294 LEU cc_start: 0.9404 (tp) cc_final: 0.9181 (tp)
REVERT: A  296 ARG cc_start: 0.5227 (ttt180) cc_final: 0.4907 (ttt180)
REVERT: A  298 LEU cc_start: 0.9259 (mt) cc_final: 0.8950 (mt)
REVERT: A  312 MET cc_start: 0.8985 (mmm) cc_final: 0.8272 (mmm)
REVERT: B   98 MET cc_start: 0.9171 (ttm) cc_final: 0.8162 (tpp)
REVERT: B  100 MET cc_start: 0.8777 (mmm) cc_final: 0.8373 (tpt)
REVERT: B  131 ASP cc_start: 0.8264 (m-30) cc_final: 0.8022 (m-30)
REVERT: B  190 ARG cc_start: 0.8904 (mtt180) cc_final: 0.8374 (ptt180)
REVERT: B  208 GLU cc_start: 0.7935 (tp30) cc_final: 0.7565 (tp30)
REVERT: B  257 LEU cc_start: 0.9271 (tt) cc_final: 0.9062 (tt)
REVERT: B  288 PHE cc_start: 0.8846 (m-80) cc_final: 0.8621 (m-80)
REVERT: B  295 MET cc_start: 0.8873 (tpp) cc_final: 0.8412 (tmm)
REVERT: B  296 ARG cc_start: 0.5245 (ttm170) cc_final: 0.4810 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.0611
  time to fit residues: 21.2751
Evaluate side-chains
  201 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 28 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   chunk 108 optimal weight:    5.9990
   chunk 73 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 106 optimal weight:   20.0000
   chunk 27 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 87 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.113410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.090309 restraints weight = 22608.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.092506 restraints weight = 14838.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.094003 restraints weight = 10744.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.095244 restraints weight = 8380.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.096056 restraints weight = 6870.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.6359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7474  Z= 0.152
  Angle     :  0.671  12.285  10195  Z= 0.345
  Chirality :  0.044   0.174   1284
  Planarity :  0.004   0.043   1327
  Dihedral  :  4.050  20.587   1184
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.84 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.26), residues: 1136
  helix:  1.00 (0.19), residues: 784
  sheet: -2.15 (0.94), residues: 32
  loop : -2.37 (0.37), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 102 
 TYR   0.013   0.001   TYR A 163 
 PHE   0.029   0.002   PHE A 230 
 TRP   0.015   0.001   TRP A  91 
 HIS   0.004   0.002   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7474)
  covalent geometry    : angle       0.67060 (10195)
  hydrogen bonds       : bond        0.04552 (  586)
  hydrogen bonds       : angle       4.80604 ( 1734)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9127 (m-80) cc_final: 0.8559 (m-80)
REVERT: A  108 MET cc_start: 0.9157 (mtm) cc_final: 0.8382 (mtp)
REVERT: A  131 ASP cc_start: 0.8418 (m-30) cc_final: 0.8182 (m-30)
REVERT: A  212 LYS cc_start: 0.8816 (mttt) cc_final: 0.8608 (tppt)
REVERT: A  294 LEU cc_start: 0.9412 (tp) cc_final: 0.9182 (tp)
REVERT: A  296 ARG cc_start: 0.5149 (ttt180) cc_final: 0.4845 (ttt180)
REVERT: A  298 LEU cc_start: 0.9272 (mt) cc_final: 0.8985 (mt)
REVERT: A  312 MET cc_start: 0.9015 (mmm) cc_final: 0.8323 (mmm)
REVERT: B   98 MET cc_start: 0.8993 (ttt) cc_final: 0.8151 (tmm)
REVERT: B  131 ASP cc_start: 0.8213 (m-30) cc_final: 0.8001 (m-30)
REVERT: B  190 ARG cc_start: 0.8938 (mtt180) cc_final: 0.8367 (ptt180)
REVERT: B  208 GLU cc_start: 0.7833 (tp30) cc_final: 0.7570 (tp30)
REVERT: B  228 LYS cc_start: 0.9331 (mttt) cc_final: 0.8903 (tttt)
REVERT: B  288 PHE cc_start: 0.8946 (m-80) cc_final: 0.8696 (m-80)
REVERT: B  295 MET cc_start: 0.8871 (tpp) cc_final: 0.8467 (tmm)
REVERT: B  296 ARG cc_start: 0.5293 (ttm170) cc_final: 0.4839 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.0624
  time to fit residues: 21.2424
Evaluate side-chains
  197 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:   30.0000
   chunk 10 optimal weight:    4.9990
   chunk 54 optimal weight:   20.0000
   chunk 64 optimal weight:    1.9990
   chunk 26 optimal weight:    0.3980
   chunk 38 optimal weight:   30.0000
   chunk 93 optimal weight:   40.0000
   chunk 39 optimal weight:   40.0000
   chunk 55 optimal weight:    1.9990
   chunk 32 optimal weight:   20.0000
   chunk 31 optimal weight:    0.7980
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
B 107 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.113790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.087257 restraints weight = 23444.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.089525 restraints weight = 15146.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.091152 restraints weight = 10879.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.092275 restraints weight = 8451.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.092945 restraints weight = 6996.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.6286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7474  Z= 0.197
  Angle     :  0.721   8.274  10195  Z= 0.379
  Chirality :  0.045   0.187   1284
  Planarity :  0.004   0.042   1327
  Dihedral  :  4.233  21.954   1184
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.28 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.26), residues: 1136
  helix:  0.90 (0.19), residues: 778
  sheet: -2.75 (0.91), residues: 30
  loop : -2.41 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 102 
 TYR   0.032   0.002   TYR A 163 
 PHE   0.037   0.003   PHE A 230 
 TRP   0.022   0.002   TRP B  91 
 HIS   0.004   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 7474)
  covalent geometry    : angle       0.72107 (10195)
  hydrogen bonds       : bond        0.04969 (  586)
  hydrogen bonds       : angle       5.07514 ( 1734)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.8266 (m-30) cc_final: 0.8011 (m-30)
REVERT: A   98 MET cc_start: 0.9043 (tpp) cc_final: 0.8777 (tpp)
REVERT: A  131 ASP cc_start: 0.8459 (m-30) cc_final: 0.8180 (m-30)
REVERT: A  212 LYS cc_start: 0.8893 (mttt) cc_final: 0.8631 (tppt)
REVERT: A  294 LEU cc_start: 0.9460 (tp) cc_final: 0.9195 (tp)
REVERT: A  296 ARG cc_start: 0.5105 (ttt180) cc_final: 0.4425 (ttt180)
REVERT: A  298 LEU cc_start: 0.9277 (mt) cc_final: 0.8975 (mt)
REVERT: A  312 MET cc_start: 0.9129 (mmm) cc_final: 0.8742 (mmm)
REVERT: B   98 MET cc_start: 0.9140 (ttt) cc_final: 0.8145 (tmm)
REVERT: B  131 ASP cc_start: 0.8246 (m-30) cc_final: 0.7993 (m-30)
REVERT: B  190 ARG cc_start: 0.8995 (mtt180) cc_final: 0.8385 (ptt180)
REVERT: B  228 LYS cc_start: 0.9353 (mttt) cc_final: 0.9030 (tttt)
REVERT: B  295 MET cc_start: 0.8971 (tpp) cc_final: 0.8634 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 227
  average time/residue: 0.0616
  time to fit residues: 20.3481
Evaluate side-chains
  183 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 14 optimal weight:    0.8980
   chunk 1 optimal weight:    0.2980
   chunk 30 optimal weight:    0.9980
   chunk 44 optimal weight:   20.0000
   chunk 92 optimal weight:   30.0000
   chunk 67 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 90 optimal weight:    5.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 223 GLN
B 107 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.113462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.088039 restraints weight = 22982.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.090229 restraints weight = 15030.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.091849 restraints weight = 10885.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.092900 restraints weight = 8463.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.093693 restraints weight = 7022.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.6633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7474  Z= 0.149
  Angle     :  0.700   8.889  10195  Z= 0.363
  Chirality :  0.045   0.171   1284
  Planarity :  0.004   0.044   1327
  Dihedral  :  4.112  18.032   1184
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.28 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.26), residues: 1136
  helix:  0.93 (0.19), residues: 781
  sheet: -2.73 (0.91), residues: 30
  loop : -2.37 (0.37), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 229 
 TYR   0.018   0.001   TYR A 163 
 PHE   0.033   0.003   PHE A 105 
 TRP   0.020   0.001   TRP B  91 
 HIS   0.006   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7474)
  covalent geometry    : angle       0.69952 (10195)
  hydrogen bonds       : bond        0.04624 (  586)
  hydrogen bonds       : angle       4.92921 ( 1734)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1223.45 seconds
wall clock time: 21 minutes 46.31 seconds (1306.31 seconds total)