Starting phenix.real_space_refine
on Thu Jul 31 16:05:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j90_36083/07_2025/8j90_36083.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j90_36083/07_2025/8j90_36083.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j90_36083/07_2025/8j90_36083.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j90_36083/07_2025/8j90_36083.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j90_36083/07_2025/8j90_36083.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j90_36083/07_2025/8j90_36083.cif"
  }
  resolution = 4.71
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 54 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P     222      5.49       5
     S      33      5.16       5
     C    8093      2.51       5
     N    2543      2.21       5
     O    2990      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13881
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 598
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 2, 'TRANS': 71}
    Chain: "B"
      Number of atoms: 636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 636
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 676
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 3, 'TRANS': 84}
    Chain: "D"
      Number of atoms: 703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 703
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 3, 'TRANS': 86}
    Chain: "E"
      Number of atoms: 621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 621
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "F"
      Number of atoms: 676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 676
          Classifications: {'peptide': 84}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    Chain: "G"
      Number of atoms: 635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 635
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 3, 'TRANS': 78}
    Chain: "H"
      Number of atoms: 703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 703
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 3, 'TRANS': 86}
    Chain: "I"
      Number of atoms: 2260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 2260
          Classifications: {'DNA': 111}
          Link IDs: {'rna3p': 110}
    Chain: "J"
      Number of atoms: 2291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 2291
          Classifications: {'DNA': 111}
          Link IDs: {'rna3p': 110}
    Chain: "K"
      Number of atoms: 4082
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 504, 4082
          Classifications: {'peptide': 504}
          Link IDs: {'PTRANS': 19, 'TRANS': 484}
          Chain breaks: 4
  Time building chain proxies: 8.48, per 1000 atoms: 0.61
  Number of scatterers: 13881
  At special positions: 0
  Unit cell: (118.72, 130.38, 127.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      33     16.00
     P     222     15.00
     O    2990      8.00
     N    2543      7.00
     C    8093      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: 3.53
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2180

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 11 sheets defined
      69.1% alpha, 4.6% beta
      109 base pairs and 181 stacking pairs defined.
    Time for finding SS restraints: 6.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.789A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.501A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.787A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 26 through 30
    Processing helix  chain 'C' and resid 35 through 47
    Processing helix  chain 'C' and resid 55 through 82
    Processing helix  chain 'C' and resid 88 through 99
    Processing helix  chain 'C' and resid 99 through 106
    Processing helix  chain 'D' and resid 62 through 74
    Processing helix  chain 'D' and resid 80 through 109
    Processing helix  chain 'D' and resid 115 through 127
    Processing helix  chain 'D' and resid 128 through 149
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 4.405A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.591A  pdb=" N   ASN F  64 " --> pdb=" O   ILE F  60 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   VAL F  65 " --> pdb=" O   PHE F  61 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 35 through 47
    Processing helix  chain 'G' and resid 55 through 83
    Processing helix  chain 'G' and resid 88 through 99
    Processing helix  chain 'G' and resid 99 through 106
    Processing helix  chain 'H' and resid 62 through 74
    Processing helix  chain 'H' and resid 80 through 109
    Processing helix  chain 'H' and resid 115 through 127
    Processing helix  chain 'H' and resid 128 through 149
    Processing helix  chain 'K' and resid 185 through 193
    Processing helix  chain 'K' and resid 203 through 219
    Processing helix  chain 'K' and resid 233 through 247
      removed outlier: 4.005A  pdb=" N   HIS K 243 " --> pdb=" O   GLY K 239 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   LEU K 244 " --> pdb=" O   PHE K 240 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS K 245 " --> pdb=" O   LEU K 241 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 258 through 260
      No H-bonds generated for 'chain 'K' and resid 258 through 260'
    Processing helix  chain 'K' and resid 261 through 273
    Processing helix  chain 'K' and resid 284 through 295
    Processing helix  chain 'K' and resid 311 through 317
    Processing helix  chain 'K' and resid 317 through 323
      removed outlier: 3.816A  pdb=" N   ARG K 323 " --> pdb=" O   LYS K 319 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 334 through 338
      removed outlier: 3.532A  pdb=" N   LEU K 338 " --> pdb=" O   GLY K 335 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 343 through 350
      removed outlier: 3.641A  pdb=" N   ARG K 347 " --> pdb=" O   CYS K 343 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 369 through 380
    Processing helix  chain 'K' and resid 389 through 394
      removed outlier: 3.946A  pdb=" N   SER K 392 " --> pdb=" O   GLU K 389 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   TRP K 393 " --> pdb=" O   PHE K 390 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   PHE K 394 " --> pdb=" O   GLU K 391 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 389 through 394'
    Processing helix  chain 'K' and resid 408 through 420
      removed outlier: 4.301A  pdb=" N   ALA K 414 " --> pdb=" O   GLU K 410 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   LEU K 420 " --> pdb=" O   VAL K 416 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 420 through 428
      Proline residue:  K 426  - end of helix
    Processing helix  chain 'K' and resid 453 through 465
      removed outlier: 3.868A  pdb=" N   ASN K 465 " --> pdb=" O   GLU K 461 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 467 through 476
    Processing helix  chain 'K' and resid 488 through 499
    Processing helix  chain 'K' and resid 500 through 508
      removed outlier: 3.849A  pdb=" N   GLN K 504 " --> pdb=" O   PRO K 500 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 515 through 523
      removed outlier: 3.899A  pdb=" N   ILE K 519 " --> pdb=" O   PRO K 515 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   CYS K 523 " --> pdb=" O   ILE K 519 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 523 through 540
      removed outlier: 3.523A  pdb=" N   ARG K 527 " --> pdb=" O   CYS K 523 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 549 through 563
      removed outlier: 4.293A  pdb=" N   ILE K 555 " --> pdb=" O   LYS K 551 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 575 through 588
    Processing helix  chain 'K' and resid 601 through 606
      removed outlier: 3.550A  pdb=" N   GLY K 604 " --> pdb=" O   ARG K 601 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LEU K 605 " --> pdb=" O   ALA K 602 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLY K 606 " --> pdb=" O   GLY K 603 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 601 through 606'
    Processing helix  chain 'K' and resid 623 through 636
      removed outlier: 4.744A  pdb=" N   CYS K 634 " --> pdb=" O   ALA K 630 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 653 through 674
      removed outlier: 3.845A  pdb=" N   ARG K 657 " --> pdb=" O   SER K 653 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 714 through 722
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.719A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 52
      removed outlier: 6.494A  pdb=" N   ARG C  51 " --> pdb=" O   ILE D 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 110 through 111
      removed outlier: 7.084A  pdb=" N   THR C 110 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'G' and resid 86 through 87
    Processing sheet with id=AA8, first strand: chain 'K' and resid 223 through 225
    Processing sheet with id=AA9, first strand: chain 'K' and resid 278 through 281
      removed outlier: 4.029A  pdb=" N   SER K 310 " --> pdb=" O   TYR K 281 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   TYR K 253 " --> pdb=" O   VAL K 307 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   THR K 309 " --> pdb=" O   TYR K 253 " (cutoff:3.500A)
      removed outlier: 5.638A  pdb=" N   VAL K 255 " --> pdb=" O   THR K 309 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'K' and resid 644 through 647
      removed outlier: 3.923A  pdb=" N   VAL K 645 " --> pdb=" O   LYS K 444 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'K' and resid 569 through 570
      removed outlier: 8.317A  pdb=" N   LEU K 598 " --> pdb=" O   VAL K 543 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ILE K 545 " --> pdb=" O   LEU K 598 " (cutoff:3.500A)
      removed outlier: 5.697A  pdb=" N   LEU K 544 " --> pdb=" O   ILE K 616 " (cutoff:3.500A)

    577 hydrogen bonds defined for protein.
    1710 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      284 hydrogen bonds
      568 hydrogen bond angles
      0 basepair planarities
      109 basepair parallelities
      181 stacking parallelities
  Total time for adding SS restraints: 7.89

  Time building geometry restraints manager: 4.23 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1829
        1.31 -     1.44: 4870
        1.44 -     1.56: 7386
        1.56 -     1.69: 442
        1.69 -     1.81: 55
  Bond restraints: 14582
  Sorted by residual:
  bond pdb=" C   THR A  80 "
       pdb=" O   THR A  80 "
    ideal  model  delta    sigma   weight residual
    1.234  1.185  0.049 1.16e-02 7.43e+03 1.76e+01
  bond pdb=" CA  LYS K 233 "
       pdb=" C   LYS K 233 "
    ideal  model  delta    sigma   weight residual
    1.520  1.464  0.055 1.40e-02 5.10e+03 1.57e+01
  bond pdb=" CA  TYR K 511 "
       pdb=" C   TYR K 511 "
    ideal  model  delta    sigma   weight residual
    1.524  1.475  0.049 1.28e-02 6.10e+03 1.49e+01
  bond pdb=" CA  THR A  80 "
       pdb=" C   THR A  80 "
    ideal  model  delta    sigma   weight residual
    1.528  1.481  0.048 1.28e-02 6.10e+03 1.40e+01
  bond pdb=" CA  ARG B  95 "
       pdb=" C   ARG B  95 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.044 1.17e-02 7.31e+03 1.39e+01
  ... (remaining 14577 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.43: 20511
        4.43 -     8.87: 97
        8.87 -    13.30: 7
       13.30 -    17.73: 1
       17.73 -    22.17: 1
  Bond angle restraints: 20617
  Sorted by residual:
  angle pdb=" N   GLY K 509 "
        pdb=" CA  GLY K 509 "
        pdb=" C   GLY K 509 "
      ideal   model   delta    sigma   weight residual
     114.95   92.78   22.17 1.41e+00 5.03e-01 2.47e+02
  angle pdb=" N   GLN K 504 "
        pdb=" CA  GLN K 504 "
        pdb=" C   GLN K 504 "
      ideal   model   delta    sigma   weight residual
     111.03   98.83   12.20 1.11e+00 8.12e-01 1.21e+02
  angle pdb=" N   LEU K 231 "
        pdb=" CA  LEU K 231 "
        pdb=" C   LEU K 231 "
      ideal   model   delta    sigma   weight residual
     111.07  101.86    9.21 1.07e+00 8.73e-01 7.41e+01
  angle pdb=" N   TYR K 511 "
        pdb=" CA  TYR K 511 "
        pdb=" C   TYR K 511 "
      ideal   model   delta    sigma   weight residual
     111.02  101.59    9.43 1.22e+00 6.72e-01 5.98e+01
  angle pdb=" N   THR A  80 "
        pdb=" CA  THR A  80 "
        pdb=" C   THR A  80 "
      ideal   model   delta    sigma   weight residual
     109.86  121.17  -11.31 1.55e+00 4.16e-01 5.33e+01
  ... (remaining 20612 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.99: 6741
       26.99 -    53.98: 1202
       53.98 -    80.97: 260
       80.97 -   107.96: 7
      107.96 -   134.95: 1
  Dihedral angle restraints: 8211
    sinusoidal: 4840
      harmonic: 3371
  Sorted by residual:
  dihedral pdb=" CA  THR K 453 "
           pdb=" C   THR K 453 "
           pdb=" N   ASP K 454 "
           pdb=" CA  ASP K 454 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.44  -26.56     0      5.00e+00 4.00e-02 2.82e+01
  dihedral pdb=" CA  LYS K 344 "
           pdb=" C   LYS K 344 "
           pdb=" N   LEU K 345 "
           pdb=" CA  LEU K 345 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.78   22.22     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  TYR K 325 "
           pdb=" C   TYR K 325 "
           pdb=" N   PRO K 326 "
           pdb=" CA  PRO K 326 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.81   21.19     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 8208 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 2166
       0.080 -    0.160: 157
       0.160 -    0.240: 11
       0.240 -    0.321: 2
       0.321 -    0.401: 2
  Chirality restraints: 2338
  Sorted by residual:
  chirality pdb=" CA  GLN K 228 "
            pdb=" N   GLN K 228 "
            pdb=" C   GLN K 228 "
            pdb=" CB  GLN K 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.01e+00
  chirality pdb=" CA  THR A  80 "
            pdb=" N   THR A  80 "
            pdb=" C   THR A  80 "
            pdb=" CB  THR A  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.20    0.33 2.00e-01 2.50e+01 2.73e+00
  chirality pdb=" CA  ASP K 227 "
            pdb=" N   ASP K 227 "
            pdb=" C   ASP K 227 "
            pdb=" CB  ASP K 227 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.32e+00
  ... (remaining 2335 not shown)

  Planarity restraints: 1836
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY K 230 "   -0.015 2.00e-02 2.50e+03   3.13e-02 9.78e+00
        pdb=" C   GLY K 230 "    0.054 2.00e-02 2.50e+03
        pdb=" O   GLY K 230 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU K 231 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP K 373 "   -0.023 2.00e-02 2.50e+03   1.75e-02 7.69e+00
        pdb=" CG  TRP K 373 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 TRP K 373 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP K 373 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP K 373 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP K 373 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP K 373 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP K 373 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP K 373 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP K 373 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE G  42 "   -0.015 2.00e-02 2.50e+03   1.95e-02 6.63e+00
        pdb=" CG  PHE G  42 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 PHE G  42 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE G  42 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 PHE G  42 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE G  42 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE G  42 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1833 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.21: 12
        2.21 -     2.88: 4832
        2.88 -     3.55: 22771
        3.55 -     4.23: 36049
        4.23 -     4.90: 54027
  Nonbonded interactions: 117691
  Sorted by model distance:
  nonbonded pdb=" CE1 HIS K 282 "
            pdb=" CB  SER K 310 "
     model   vdw
     1.534 3.660
  nonbonded pdb=" O   LEU B  90 "
            pdb=" O   ARG B  95 "
     model   vdw
     1.843 3.040
  nonbonded pdb=" CA  GLY K 505 "
            pdb=" OD2 ASP K 508 "
     model   vdw
     1.903 3.440
  nonbonded pdb=" NZ  LYS K 233 "
            pdb=" O   THR K 361 "
     model   vdw
     1.931 3.120
  nonbonded pdb=" O   ARG G  51 "
            pdb=" OG1 THR H 113 "
     model   vdw
     2.101 3.040
  ... (remaining 117686 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 'E' and resid 61 through 134)
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 23 through 101)
}
ncs_group {
  reference = (chain 'C' and resid 32 through 113)
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.610
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     40.990
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.070
  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:             0.010
  Load rotamer database and sin/cos tables:3.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6771
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  14582  Z= 0.244
  Angle     :  0.842  22.166  20617  Z= 0.491
  Chirality :  0.046   0.401   2338
  Planarity :  0.006   0.066   1836
  Dihedral  : 24.019 134.951   6031
  Min Nonbonded Distance : 1.534

Molprobity Statistics.
  All-atom Clashscore : 23.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  1.00 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.25), residues: 1142
  helix:  0.43 (0.18), residues: 765
  sheet: -1.33 (0.60), residues: 64
  loop : -0.92 (0.37), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.003   TRP K 373 
 HIS   0.011   0.001   HIS K 455 
 PHE   0.045   0.002   PHE G  42 
 TYR   0.021   0.002   TYR K 663 
 ARG   0.014   0.001   ARG K 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10711 (  861)
  hydrogen bonds       : angle       5.17276 ( 2278)
  covalent geometry    : bond        0.00451 (14582)
  covalent geometry    : angle       0.84201 (20617)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  494 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 491
  time to evaluate  : 1.334 
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   62 ILE cc_start: 0.7989 (pt) cc_final: 0.7644 (mt)
REVERT: A   64 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7909 (mttp)
REVERT: A   80 THR cc_start: 0.8557 (p) cc_final: 0.8238 (p)
REVERT: A   86 SER cc_start: 0.8211 (m) cc_final: 0.7551 (t)
REVERT: A   89 VAL cc_start: 0.7749 (t) cc_final: 0.7466 (m)
REVERT: A  109 LEU cc_start: 0.8866 (tp) cc_final: 0.8600 (tp)
REVERT: A  118 THR cc_start: 0.8376 (m) cc_final: 0.8045 (m)
REVERT: A  133 GLU cc_start: 0.6612 (pm20) cc_final: 0.6385 (pt0)
REVERT: B   27 GLN cc_start: 0.7313 (mm-40) cc_final: 0.7110 (tt0)
REVERT: B   31 LYS cc_start: 0.8720 (tttt) cc_final: 0.8476 (mmtm)
REVERT: B   45 ARG cc_start: 0.6727 (tpt170) cc_final: 0.6522 (mmm160)
REVERT: B   49 LEU cc_start: 0.9000 (mp) cc_final: 0.8727 (tt)
REVERT: B   84 MET cc_start: 0.7224 (tpt) cc_final: 0.6515 (mmm)
REVERT: B   88 TYR cc_start: 0.6724 (m-80) cc_final: 0.6190 (m-80)
REVERT: B   91 LYS cc_start: 0.7818 (tmmt) cc_final: 0.7447 (tttt)
REVERT: C   28 MET cc_start: 0.5940 (mtm) cc_final: 0.5198 (ttp)
REVERT: C   42 PHE cc_start: 0.7579 (m-10) cc_final: 0.7284 (m-80)
REVERT: C   98 ASN cc_start: 0.7733 (m-40) cc_final: 0.7531 (t0)
REVERT: D   62 TYR cc_start: 0.7562 (m-10) cc_final: 0.7098 (m-10)
REVERT: D   63 LYS cc_start: 0.7569 (mptt) cc_final: 0.7163 (mmmm)
REVERT: D   91 ILE cc_start: 0.8204 (mm) cc_final: 0.7911 (mm)
REVERT: D  112 PRO cc_start: 0.8156 (Cg_exo) cc_final: 0.7831 (Cg_endo)
REVERT: D  130 GLU cc_start: 0.7793 (mp0) cc_final: 0.7256 (mt-10)
REVERT: E   73 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7942 (tm-30)
REVERT: E   79 LYS cc_start: 0.7157 (tmtt) cc_final: 0.6418 (mmtp)
REVERT: E   94 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7874 (mt-10)
REVERT: F   22 LEU cc_start: 0.7228 (tt) cc_final: 0.6985 (pp)
REVERT: F   30 THR cc_start: 0.7357 (p) cc_final: 0.7080 (t)
REVERT: G   34 PHE cc_start: 0.5253 (m-10) cc_final: 0.4813 (m-80)
REVERT: G   42 PHE cc_start: 0.7250 (m-80) cc_final: 0.6938 (m-80)
REVERT: H  110 LYS cc_start: 0.6715 (tptt) cc_final: 0.6180 (ttmt)
REVERT: H  125 LEU cc_start: 0.9147 (tt) cc_final: 0.8288 (tt)
REVERT: H  127 LEU cc_start: 0.7947 (mm) cc_final: 0.7621 (mp)
REVERT: K  241 LEU cc_start: 0.8096 (mm) cc_final: 0.7835 (mm)
REVERT: K  249 LEU cc_start: 0.8247 (mt) cc_final: 0.7784 (tp)
REVERT: K  253 TYR cc_start: 0.6356 (m-80) cc_final: 0.5353 (m-10)
REVERT: K  254 LEU cc_start: 0.7308 (tp) cc_final: 0.6870 (tp)
REVERT: K  324 HIS cc_start: 0.6129 (m90) cc_final: 0.5764 (t-170)
REVERT: K  329 TYR cc_start: 0.7325 (m-80) cc_final: 0.6659 (t80)
REVERT: K  352 LEU cc_start: 0.7898 (mt) cc_final: 0.7511 (tp)
REVERT: K  373 TRP cc_start: 0.6790 (t-100) cc_final: 0.6201 (t-100)
REVERT: K  382 ASP cc_start: 0.6786 (m-30) cc_final: 0.6384 (m-30)
REVERT: K  384 PHE cc_start: 0.8174 (m-80) cc_final: 0.7613 (m-80)
REVERT: K  459 PHE cc_start: 0.7264 (m-10) cc_final: 0.7042 (m-80)
REVERT: K  468 LEU cc_start: 0.8389 (tp) cc_final: 0.7951 (tp)
REVERT: K  557 ASP cc_start: 0.8072 (t0) cc_final: 0.7637 (t70)
REVERT: K  569 ARG cc_start: 0.6738 (ttt90) cc_final: 0.6049 (ttm-80)
REVERT: K  618 TYR cc_start: 0.7568 (t80) cc_final: 0.6966 (t80)
REVERT: K  621 ASP cc_start: 0.7324 (t0) cc_final: 0.6952 (m-30)
REVERT: K  623 ASN cc_start: 0.8221 (t0) cc_final: 0.7983 (t0)
REVERT: K  631 MET cc_start: 0.6804 (ppp) cc_final: 0.6599 (tpt)
REVERT: K  636 ARG cc_start: 0.5498 (ttt90) cc_final: 0.5272 (tmt170)
REVERT: K  748 TRP cc_start: 0.5448 (p-90) cc_final: 0.5222 (p-90)
REVERT: K  755 SER cc_start: 0.7445 (p) cc_final: 0.7226 (t)
  outliers start: 3
  outliers final: 0
  residues processed: 493
  average time/residue: 0.3552
  time to fit residues: 232.7298
Evaluate side-chains
  268 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:    8.9990
   chunk 102 optimal weight:    8.9990
   chunk 56 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 54 optimal weight:    4.9990
   chunk 105 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 64 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 122 optimal weight:    0.9980
   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  85 GLN
C  33 GLN
** D  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  82 ASN
G  98 ASN
** H  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 219 ASN
** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 377 ASN
K 421 HIS
** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 496 ASN
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 675 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.069670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.051821 restraints weight = 77711.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.053336 restraints weight = 43171.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.054311 restraints weight = 29397.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14582  Z= 0.178
  Angle     :  0.696   8.598  20617  Z= 0.385
  Chirality :  0.042   0.233   2338
  Planarity :  0.005   0.048   1836
  Dihedral  : 28.308 137.830   3682
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 15.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  7.88 %
    Favored  : 91.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.24), residues: 1142
  helix:  0.70 (0.18), residues: 774
  sheet: -0.27 (0.76), residues: 49
  loop : -1.08 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP K 373 
 HIS   0.014   0.002   HIS B  75 
 PHE   0.032   0.002   PHE K 596 
 TYR   0.019   0.002   TYR C  48 
 ARG   0.011   0.001   ARG F  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04525 (  861)
  hydrogen bonds       : angle       4.19857 ( 2278)
  covalent geometry    : bond        0.00394 (14582)
  covalent geometry    : angle       0.69561 (20617)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 316
  time to evaluate  : 1.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 PHE cc_start: 0.7642 (t80) cc_final: 0.7302 (t80)
REVERT: A   86 SER cc_start: 0.8429 (m) cc_final: 0.8067 (t)
REVERT: A  118 THR cc_start: 0.8754 (m) cc_final: 0.8277 (m)
REVERT: A  133 GLU cc_start: 0.6602 (pm20) cc_final: 0.5796 (pt0)
REVERT: B   64 ASN cc_start: 0.7298 (t0) cc_final: 0.7082 (t0)
REVERT: B   88 TYR cc_start: 0.7033 (m-80) cc_final: 0.5957 (m-80)
REVERT: B   91 LYS cc_start: 0.7855 (tmmt) cc_final: 0.7280 (tttt)
REVERT: B   98 TYR cc_start: 0.6946 (m-10) cc_final: 0.6284 (m-10)
REVERT: C   28 MET cc_start: 0.5047 (mtm) cc_final: 0.4073 (ttp)
REVERT: C   42 PHE cc_start: 0.7334 (m-10) cc_final: 0.7096 (m-80)
REVERT: C   98 ASN cc_start: 0.7813 (m-40) cc_final: 0.7297 (t0)
REVERT: D   63 LYS cc_start: 0.7333 (mptt) cc_final: 0.6606 (mmmt)
REVERT: D  110 LYS cc_start: 0.6905 (mmtt) cc_final: 0.6317 (mtpp)
REVERT: D  111 LYS cc_start: 0.8167 (tptt) cc_final: 0.7530 (tptt)
REVERT: D  130 GLU cc_start: 0.7767 (mp0) cc_final: 0.7093 (mt-10)
REVERT: E   79 LYS cc_start: 0.6914 (tmtt) cc_final: 0.6521 (mmtt)
REVERT: F   21 VAL cc_start: 0.6295 (t) cc_final: 0.4476 (m)
REVERT: G   47 ARG cc_start: 0.7952 (mmm-85) cc_final: 0.7584 (mmm-85)
REVERT: G   83 LYS cc_start: 0.8036 (mmmm) cc_final: 0.6910 (ptpp)
REVERT: H  125 LEU cc_start: 0.8646 (tt) cc_final: 0.8415 (tt)
REVERT: K  224 ILE cc_start: 0.8511 (mp) cc_final: 0.8109 (mm)
REVERT: K  229 MET cc_start: 0.4994 (ptt) cc_final: 0.4637 (ptt)
REVERT: K  249 LEU cc_start: 0.8263 (mt) cc_final: 0.7848 (tp)
REVERT: K  281 TYR cc_start: 0.7264 (t80) cc_final: 0.6226 (t80)
REVERT: K  282 HIS cc_start: 0.5260 (m90) cc_final: 0.4944 (m-70)
REVERT: K  315 MET cc_start: 0.7142 (tpp) cc_final: 0.6904 (tpp)
REVERT: K  321 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6773 (mm)
REVERT: K  373 TRP cc_start: 0.6610 (t-100) cc_final: 0.6115 (t-100)
REVERT: K  382 ASP cc_start: 0.6720 (m-30) cc_final: 0.6394 (m-30)
REVERT: K  384 PHE cc_start: 0.8360 (m-80) cc_final: 0.7936 (m-80)
REVERT: K  468 LEU cc_start: 0.8122 (tp) cc_final: 0.7699 (tt)
REVERT: K  553 LEU cc_start: 0.7449 (mp) cc_final: 0.7050 (mp)
REVERT: K  557 ASP cc_start: 0.7965 (t0) cc_final: 0.7479 (t70)
REVERT: K  570 ILE cc_start: 0.6712 (mm) cc_final: 0.6497 (mp)
REVERT: K  621 ASP cc_start: 0.7455 (t0) cc_final: 0.7067 (m-30)
REVERT: K  623 ASN cc_start: 0.7945 (t0) cc_final: 0.7583 (t0)
REVERT: K  748 TRP cc_start: 0.5613 (p-90) cc_final: 0.5403 (p-90)
REVERT: K  755 SER cc_start: 0.7205 (p) cc_final: 0.6970 (t)
  outliers start: 10
  outliers final: 1
  residues processed: 322
  average time/residue: 0.2873
  time to fit residues: 130.5323
Evaluate side-chains
  219 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 217
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 86 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 94 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0770
   chunk 134 optimal weight:    0.0870
   chunk 116 optimal weight:   50.0000
   chunk 93 optimal weight:    0.9990
   chunk 82 optimal weight:   10.0000
   overall best weight:    0.5716

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
C  77 ASN
** D  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 ASN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 219 ASN
** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.070036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.052920 restraints weight = 80926.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.054560 restraints weight = 42529.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.055641 restraints weight = 27742.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.4279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14582  Z= 0.144
  Angle     :  0.629   9.273  20617  Z= 0.349
  Chirality :  0.039   0.174   2338
  Planarity :  0.005   0.067   1836
  Dihedral  : 28.169 136.665   3682
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.89 %
    Favored  : 96.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.25), residues: 1142
  helix:  1.09 (0.18), residues: 772
  sheet: -0.19 (0.75), residues: 49
  loop : -1.25 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP K 622 
 HIS   0.005   0.001   HIS K 499 
 PHE   0.026   0.002   PHE D  67 
 TYR   0.016   0.002   TYR C  66 
 ARG   0.011   0.001   ARG K 661 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 (  861)
  hydrogen bonds       : angle       3.86178 ( 2278)
  covalent geometry    : bond        0.00309 (14582)
  covalent geometry    : angle       0.62923 (20617)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 317
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 PHE cc_start: 0.7677 (t80) cc_final: 0.7316 (t80)
REVERT: A   86 SER cc_start: 0.8463 (m) cc_final: 0.8035 (t)
REVERT: A   94 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7080 (mt-10)
REVERT: A  109 LEU cc_start: 0.9025 (tp) cc_final: 0.8814 (tp)
REVERT: A  133 GLU cc_start: 0.6704 (pm20) cc_final: 0.6228 (pt0)
REVERT: B   27 GLN cc_start: 0.8068 (tp-100) cc_final: 0.7808 (mm-40)
REVERT: B   84 MET cc_start: 0.7187 (tpt) cc_final: 0.6917 (mmm)
REVERT: B   88 TYR cc_start: 0.7193 (m-80) cc_final: 0.6378 (m-80)
REVERT: B   91 LYS cc_start: 0.7754 (tmmt) cc_final: 0.7273 (tttt)
REVERT: B   97 LEU cc_start: 0.7608 (tp) cc_final: 0.7282 (tp)
REVERT: B   98 TYR cc_start: 0.6836 (m-10) cc_final: 0.6403 (m-10)
REVERT: C   28 MET cc_start: 0.5038 (mtm) cc_final: 0.4068 (ttp)
REVERT: C   39 ILE cc_start: 0.7950 (pt) cc_final: 0.7677 (pt)
REVERT: C   42 PHE cc_start: 0.7288 (m-10) cc_final: 0.7041 (m-80)
REVERT: C   98 ASN cc_start: 0.7957 (m-40) cc_final: 0.7463 (t0)
REVERT: D   63 LYS cc_start: 0.7466 (mptt) cc_final: 0.6815 (mmmt)
REVERT: D  110 LYS cc_start: 0.6878 (mmtt) cc_final: 0.6335 (mtpp)
REVERT: D  111 LYS cc_start: 0.7846 (tptt) cc_final: 0.7397 (tptt)
REVERT: D  130 GLU cc_start: 0.7552 (mp0) cc_final: 0.6804 (mt-10)
REVERT: E   79 LYS cc_start: 0.6789 (tmtt) cc_final: 0.6578 (mmtt)
REVERT: F   30 THR cc_start: 0.7590 (p) cc_final: 0.7177 (t)
REVERT: F   63 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7851 (mm-30)
REVERT: G   60 MET cc_start: 0.8397 (ttt) cc_final: 0.7975 (ptm)
REVERT: G   83 LYS cc_start: 0.8018 (mmmm) cc_final: 0.6922 (ptpp)
REVERT: G   90 ARG cc_start: 0.7506 (tpm170) cc_final: 0.7301 (tpm170)
REVERT: K  249 LEU cc_start: 0.8225 (mt) cc_final: 0.7830 (tp)
REVERT: K  315 MET cc_start: 0.7204 (tpp) cc_final: 0.6706 (tpp)
REVERT: K  352 LEU cc_start: 0.7690 (mt) cc_final: 0.6564 (tp)
REVERT: K  373 TRP cc_start: 0.6536 (t-100) cc_final: 0.6216 (t-100)
REVERT: K  382 ASP cc_start: 0.6702 (m-30) cc_final: 0.6414 (m-30)
REVERT: K  384 PHE cc_start: 0.8436 (m-80) cc_final: 0.7295 (m-10)
REVERT: K  468 LEU cc_start: 0.8118 (tp) cc_final: 0.7694 (tp)
REVERT: K  570 ILE cc_start: 0.7005 (mm) cc_final: 0.6644 (mp)
REVERT: K  615 CYS cc_start: 0.6271 (t) cc_final: 0.6031 (m)
REVERT: K  621 ASP cc_start: 0.7723 (t0) cc_final: 0.6880 (m-30)
REVERT: K  669 GLU cc_start: 0.9425 (tp30) cc_final: 0.9225 (tp30)
REVERT: K  755 SER cc_start: 0.6744 (p) cc_final: 0.6541 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 318
  average time/residue: 0.2813
  time to fit residues: 126.3260
Evaluate side-chains
  228 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 128 optimal weight:    8.9990
   chunk 0 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   chunk 115 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 126 optimal weight:    7.9990
   chunk 74 optimal weight:   10.0000
   chunk 106 optimal weight:    8.9990
   chunk 123 optimal weight:    5.9990
   chunk 133 optimal weight:    7.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
C 113 HIS
** D  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
** H  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 219 ASN
** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 471 HIS
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.066924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.049952 restraints weight = 83083.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.051505 restraints weight = 43606.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.052485 restraints weight = 28527.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.5378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077  14582  Z= 0.269
  Angle     :  0.776   8.893  20617  Z= 0.423
  Chirality :  0.044   0.212   2338
  Planarity :  0.006   0.050   1836
  Dihedral  : 28.677 140.460   3682
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 18.60
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.29 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  6.49 %
    Favored  : 93.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.24), residues: 1142
  helix:  0.61 (0.18), residues: 772
  sheet: -0.25 (0.71), residues: 54
  loop : -1.39 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP K 622 
 HIS   0.015   0.002   HIS B  75 
 PHE   0.029   0.003   PHE D  67 
 TYR   0.018   0.003   TYR C  48 
 ARG   0.011   0.001   ARG K 661 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05602 (  861)
  hydrogen bonds       : angle       4.29747 ( 2278)
  covalent geometry    : bond        0.00612 (14582)
  covalent geometry    : angle       0.77554 (20617)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 259
  time to evaluate  : 1.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 PHE cc_start: 0.7677 (t80) cc_final: 0.7223 (t80)
REVERT: A   86 SER cc_start: 0.8430 (m) cc_final: 0.8094 (t)
REVERT: A   94 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6878 (mt-10)
REVERT: A   97 GLU cc_start: 0.7903 (mp0) cc_final: 0.7597 (mt-10)
REVERT: A  133 GLU cc_start: 0.6365 (pm20) cc_final: 0.5888 (pt0)
REVERT: B   35 ARG cc_start: 0.8689 (ttm-80) cc_final: 0.8259 (ttt180)
REVERT: B   84 MET cc_start: 0.7348 (tpt) cc_final: 0.7135 (mmm)
REVERT: B   91 LYS cc_start: 0.7663 (tmmt) cc_final: 0.7285 (tttt)
REVERT: B   98 TYR cc_start: 0.6809 (m-10) cc_final: 0.6298 (m-10)
REVERT: C   28 MET cc_start: 0.4692 (mtm) cc_final: 0.3671 (tpt)
REVERT: C   98 ASN cc_start: 0.7892 (m-40) cc_final: 0.7297 (t0)
REVERT: D  110 LYS cc_start: 0.7012 (mmtt) cc_final: 0.6682 (mtpp)
REVERT: D  130 GLU cc_start: 0.7718 (mp0) cc_final: 0.7099 (mt-10)
REVERT: E   79 LYS cc_start: 0.6923 (tmtt) cc_final: 0.6657 (tttt)
REVERT: F   63 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8171 (mm-30)
REVERT: G   38 ARG cc_start: 0.6779 (ttt180) cc_final: 0.6236 (tpp80)
REVERT: G   60 MET cc_start: 0.8419 (ttt) cc_final: 0.8070 (tpt)
REVERT: G   73 GLU cc_start: 0.7116 (pt0) cc_final: 0.6734 (pt0)
REVERT: G   83 LYS cc_start: 0.8079 (mmmm) cc_final: 0.6998 (ptpp)
REVERT: G   90 ARG cc_start: 0.7595 (tpm170) cc_final: 0.7331 (tpm170)
REVERT: H  118 GLU cc_start: 0.8214 (mp0) cc_final: 0.7332 (mp0)
REVERT: K  249 LEU cc_start: 0.8428 (mt) cc_final: 0.7910 (tp)
REVERT: K  296 MET cc_start: 0.3526 (ptm) cc_final: 0.2573 (ppp)
REVERT: K  315 MET cc_start: 0.7311 (tpp) cc_final: 0.6803 (tpp)
REVERT: K  373 TRP cc_start: 0.6543 (t-100) cc_final: 0.6255 (t-100)
REVERT: K  382 ASP cc_start: 0.7089 (m-30) cc_final: 0.6757 (m-30)
REVERT: K  384 PHE cc_start: 0.8564 (m-80) cc_final: 0.7348 (m-10)
REVERT: K  468 LEU cc_start: 0.8223 (tp) cc_final: 0.8016 (tp)
REVERT: K  556 MET cc_start: 0.7878 (ttm) cc_final: 0.7632 (ttm)
REVERT: K  570 ILE cc_start: 0.6907 (mm) cc_final: 0.6629 (mp)
REVERT: K  621 ASP cc_start: 0.7580 (t0) cc_final: 0.6698 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 261
  average time/residue: 0.2565
  time to fit residues: 97.3712
Evaluate side-chains
  194 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 129 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 106 optimal weight:   10.0000
   chunk 101 optimal weight:    0.0670
   chunk 42 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 115 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.7718

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
** H  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 421 HIS
** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.069108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.051960 restraints weight = 83052.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.053555 restraints weight = 44312.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.054587 restraints weight = 29251.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.5520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14582  Z= 0.152
  Angle     :  0.650   8.201  20617  Z= 0.361
  Chirality :  0.039   0.227   2338
  Planarity :  0.005   0.045   1836
  Dihedral  : 28.389 136.336   3682
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.50 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.69 %
    Favored  : 96.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.24), residues: 1142
  helix:  0.99 (0.18), residues: 765
  sheet: -0.16 (0.77), residues: 49
  loop : -1.32 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP K 748 
 HIS   0.012   0.001   HIS K 243 
 PHE   0.027   0.002   PHE D  67 
 TYR   0.017   0.002   TYR B  88 
 ARG   0.009   0.001   ARG K 633 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04061 (  861)
  hydrogen bonds       : angle       3.85089 ( 2278)
  covalent geometry    : bond        0.00325 (14582)
  covalent geometry    : angle       0.64998 (20617)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 289
  time to evaluate  : 1.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8408 (tp30) cc_final: 0.8014 (tm-30)
REVERT: A   78 PHE cc_start: 0.7593 (t80) cc_final: 0.7245 (t80)
REVERT: A   86 SER cc_start: 0.8451 (m) cc_final: 0.7934 (t)
REVERT: A   94 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6641 (mt-10)
REVERT: A   97 GLU cc_start: 0.7899 (mp0) cc_final: 0.7400 (mp0)
REVERT: A  109 LEU cc_start: 0.8958 (tp) cc_final: 0.8525 (tp)
REVERT: A  118 THR cc_start: 0.8320 (m) cc_final: 0.8084 (p)
REVERT: A  133 GLU cc_start: 0.6410 (pm20) cc_final: 0.6022 (pt0)
REVERT: B   27 GLN cc_start: 0.7255 (mm-40) cc_final: 0.7043 (mm-40)
REVERT: B   35 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.8186 (ttt90)
REVERT: B   75 HIS cc_start: 0.9001 (t70) cc_final: 0.8681 (t-170)
REVERT: B   84 MET cc_start: 0.7288 (tpt) cc_final: 0.6080 (tpp)
REVERT: B   91 LYS cc_start: 0.8044 (tmmt) cc_final: 0.7725 (tttt)
REVERT: B   98 TYR cc_start: 0.6788 (m-10) cc_final: 0.6275 (m-10)
REVERT: C   28 MET cc_start: 0.4729 (mtm) cc_final: 0.4306 (mmp)
REVERT: C   72 LEU cc_start: 0.7941 (mp) cc_final: 0.7478 (tt)
REVERT: C   98 ASN cc_start: 0.7909 (m-40) cc_final: 0.7308 (t0)
REVERT: D  110 LYS cc_start: 0.6250 (mmtp) cc_final: 0.5794 (mtpp)
REVERT: D  130 GLU cc_start: 0.7266 (mp0) cc_final: 0.6472 (mt-10)
REVERT: E   79 LYS cc_start: 0.6891 (tmtt) cc_final: 0.6616 (tttt)
REVERT: F   63 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8083 (mm-30)
REVERT: F   66 ILE cc_start: 0.8675 (mm) cc_final: 0.8460 (mm)
REVERT: G   38 ARG cc_start: 0.6371 (ttt180) cc_final: 0.5742 (tpp80)
REVERT: G   59 TYR cc_start: 0.7832 (t80) cc_final: 0.7630 (t80)
REVERT: G   60 MET cc_start: 0.8508 (ttt) cc_final: 0.8182 (ptm)
REVERT: G   73 GLU cc_start: 0.7197 (pt0) cc_final: 0.6742 (pt0)
REVERT: G   83 LYS cc_start: 0.8058 (mmmm) cc_final: 0.6921 (ptpp)
REVERT: G   90 ARG cc_start: 0.7571 (tpm170) cc_final: 0.7250 (tpm170)
REVERT: H   87 MET cc_start: 0.8488 (tpp) cc_final: 0.8173 (tmm)
REVERT: H  101 GLU cc_start: 0.8133 (tp30) cc_final: 0.7822 (tp30)
REVERT: H  118 GLU cc_start: 0.8257 (mp0) cc_final: 0.7769 (mp0)
REVERT: H  125 LEU cc_start: 0.8629 (tt) cc_final: 0.8407 (tt)
REVERT: H  127 LEU cc_start: 0.7899 (mm) cc_final: 0.7581 (mp)
REVERT: K  205 TYR cc_start: 0.6950 (m-10) cc_final: 0.6570 (m-10)
REVERT: K  243 HIS cc_start: 0.6412 (t-170) cc_final: 0.6184 (t-170)
REVERT: K  249 LEU cc_start: 0.8357 (mt) cc_final: 0.7874 (tp)
REVERT: K  281 TYR cc_start: 0.7090 (t80) cc_final: 0.6734 (t80)
REVERT: K  296 MET cc_start: 0.3420 (ptm) cc_final: 0.2520 (ppp)
REVERT: K  315 MET cc_start: 0.7174 (tpp) cc_final: 0.6694 (tpp)
REVERT: K  373 TRP cc_start: 0.6587 (t-100) cc_final: 0.6290 (t-100)
REVERT: K  384 PHE cc_start: 0.8408 (m-80) cc_final: 0.6943 (m-80)
REVERT: K  537 PHE cc_start: 0.8443 (t80) cc_final: 0.8169 (t80)
REVERT: K  556 MET cc_start: 0.7720 (ttm) cc_final: 0.7487 (ttm)
REVERT: K  570 ILE cc_start: 0.7031 (mm) cc_final: 0.6790 (mp)
REVERT: K  623 ASN cc_start: 0.7491 (t0) cc_final: 0.7238 (t0)
REVERT: K  626 MET cc_start: 0.8012 (tpt) cc_final: 0.7771 (tpt)
REVERT: K  659 LEU cc_start: 0.9401 (tt) cc_final: 0.9175 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 290
  average time/residue: 0.2961
  time to fit residues: 123.2025
Evaluate side-chains
  207 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 1.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 130 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0270
   chunk 82 optimal weight:   10.0000
   chunk 122 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 76 optimal weight:   10.0000
   chunk 106 optimal weight:    5.9990
   chunk 95 optimal weight:    7.9990
   chunk 89 optimal weight:   20.0000
   chunk 19 optimal weight:   20.0000
   overall best weight:    2.6044

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 HIS
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** H  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 541 HIS
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.068018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.051322 restraints weight = 82477.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.052950 restraints weight = 43352.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.053972 restraints weight = 28112.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.5947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  14582  Z= 0.182
  Angle     :  0.666   9.162  20617  Z= 0.370
  Chirality :  0.040   0.223   2338
  Planarity :  0.005   0.045   1836
  Dihedral  : 28.493 138.411   3682
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 16.06
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.68 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.24), residues: 1142
  helix:  1.03 (0.18), residues: 766
  sheet: -0.17 (0.76), residues: 49
  loop : -1.39 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP K 748 
 HIS   0.011   0.002   HIS B  75 
 PHE   0.029   0.002   PHE D  67 
 TYR   0.021   0.002   TYR H  65 
 ARG   0.006   0.001   ARG K 531 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04518 (  861)
  hydrogen bonds       : angle       3.88195 ( 2278)
  covalent geometry    : bond        0.00409 (14582)
  covalent geometry    : angle       0.66589 (20617)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 1.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 PHE cc_start: 0.7783 (t80) cc_final: 0.7331 (t80)
REVERT: A   86 SER cc_start: 0.8458 (m) cc_final: 0.8055 (t)
REVERT: A   97 GLU cc_start: 0.8008 (mp0) cc_final: 0.7430 (mp0)
REVERT: A  133 GLU cc_start: 0.6351 (pm20) cc_final: 0.6092 (pt0)
REVERT: B   27 GLN cc_start: 0.7238 (mm-40) cc_final: 0.7006 (mm-40)
REVERT: B   84 MET cc_start: 0.7369 (tpt) cc_final: 0.6781 (tpp)
REVERT: B   91 LYS cc_start: 0.7960 (tmmt) cc_final: 0.7531 (tttt)
REVERT: B   98 TYR cc_start: 0.6743 (m-10) cc_final: 0.6109 (m-10)
REVERT: C   98 ASN cc_start: 0.8021 (m-40) cc_final: 0.7490 (t0)
REVERT: D  130 GLU cc_start: 0.7148 (mp0) cc_final: 0.6470 (mt-10)
REVERT: E   79 LYS cc_start: 0.6967 (tmtt) cc_final: 0.6612 (tttt)
REVERT: F   66 ILE cc_start: 0.8643 (mm) cc_final: 0.8415 (mm)
REVERT: G   38 ARG cc_start: 0.6858 (ttt180) cc_final: 0.6208 (tpp80)
REVERT: G   59 TYR cc_start: 0.7753 (t80) cc_final: 0.7450 (t80)
REVERT: G   60 MET cc_start: 0.8481 (ttt) cc_final: 0.8200 (ptm)
REVERT: G   73 GLU cc_start: 0.7237 (pt0) cc_final: 0.6772 (pt0)
REVERT: G   83 LYS cc_start: 0.8076 (mmmm) cc_final: 0.6881 (ptpp)
REVERT: G   90 ARG cc_start: 0.7492 (tpm170) cc_final: 0.7250 (tpm170)
REVERT: H   87 MET cc_start: 0.8527 (tpp) cc_final: 0.8197 (tmm)
REVERT: H   94 ILE cc_start: 0.8496 (mm) cc_final: 0.8266 (mm)
REVERT: H   95 PHE cc_start: 0.8001 (t80) cc_final: 0.7741 (t80)
REVERT: H  118 GLU cc_start: 0.8244 (mp0) cc_final: 0.7474 (mp0)
REVERT: H  127 LEU cc_start: 0.7806 (mm) cc_final: 0.7473 (mp)
REVERT: K  205 TYR cc_start: 0.7004 (m-10) cc_final: 0.6577 (m-10)
REVERT: K  243 HIS cc_start: 0.6235 (t-170) cc_final: 0.6015 (t-170)
REVERT: K  249 LEU cc_start: 0.8321 (mt) cc_final: 0.7806 (tp)
REVERT: K  281 TYR cc_start: 0.7191 (t80) cc_final: 0.6835 (t80)
REVERT: K  296 MET cc_start: 0.3479 (ptm) cc_final: 0.2678 (ppp)
REVERT: K  315 MET cc_start: 0.7510 (tpp) cc_final: 0.6831 (tpp)
REVERT: K  333 ASP cc_start: 0.7455 (t0) cc_final: 0.7027 (t0)
REVERT: K  334 GLU cc_start: 0.7378 (pt0) cc_final: 0.7076 (mp0)
REVERT: K  373 TRP cc_start: 0.6558 (t-100) cc_final: 0.6314 (t-100)
REVERT: K  384 PHE cc_start: 0.8369 (m-80) cc_final: 0.6975 (m-80)
REVERT: K  409 GLU cc_start: 0.3734 (mm-30) cc_final: 0.3515 (pm20)
REVERT: K  468 LEU cc_start: 0.8253 (mt) cc_final: 0.7948 (mt)
REVERT: K  556 MET cc_start: 0.7689 (ttm) cc_final: 0.7486 (ttm)
REVERT: K  570 ILE cc_start: 0.7191 (mm) cc_final: 0.6960 (mp)
REVERT: K  623 ASN cc_start: 0.7570 (t0) cc_final: 0.7247 (t0)
REVERT: K  626 MET cc_start: 0.8048 (tpt) cc_final: 0.7844 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.2447
  time to fit residues: 93.7677
Evaluate side-chains
  195 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 85 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 134 optimal weight:    6.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 HIS
E  93 GLN
F  25 ASN
** H  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 421 HIS
K 471 HIS
** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 541 HIS
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.067834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.051491 restraints weight = 82865.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.053061 restraints weight = 43101.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.054072 restraints weight = 28039.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7047
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      :  0.004   0.047  14582  Z= 0.178
  Angle     :  0.684   8.548  20617  Z= 0.378
  Chirality :  0.040   0.193   2338
  Planarity :  0.005   0.050   1836
  Dihedral  : 28.508 137.753   3682
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.85 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.24), residues: 1142
  helix:  1.02 (0.18), residues: 765
  sheet: -0.69 (0.73), residues: 51
  loop : -1.53 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP K 748 
 HIS   0.010   0.002   HIS K 387 
 PHE   0.038   0.002   PHE D  67 
 TYR   0.017   0.002   TYR F  72 
 ARG   0.007   0.001   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04583 (  861)
  hydrogen bonds       : angle       3.89520 ( 2278)
  covalent geometry    : bond        0.00399 (14582)
  covalent geometry    : angle       0.68369 (20617)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 1.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8337 (tp30) cc_final: 0.7888 (tm-30)
REVERT: A   78 PHE cc_start: 0.7690 (t80) cc_final: 0.7288 (t80)
REVERT: A   86 SER cc_start: 0.8358 (m) cc_final: 0.7512 (t)
REVERT: A   94 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6861 (mt-10)
REVERT: A   97 GLU cc_start: 0.8105 (mp0) cc_final: 0.7405 (mp0)
REVERT: A  133 GLU cc_start: 0.6298 (pm20) cc_final: 0.5719 (pt0)
REVERT: B   24 ASP cc_start: 0.5461 (t0) cc_final: 0.5167 (t0)
REVERT: B   27 GLN cc_start: 0.7215 (mm-40) cc_final: 0.7000 (mm-40)
REVERT: B   75 HIS cc_start: 0.8637 (t70) cc_final: 0.8070 (t-170)
REVERT: B   84 MET cc_start: 0.7234 (tpt) cc_final: 0.6956 (tpp)
REVERT: B   91 LYS cc_start: 0.7903 (tmmt) cc_final: 0.7527 (tttt)
REVERT: B   98 TYR cc_start: 0.6825 (m-10) cc_final: 0.6356 (m-10)
REVERT: C   72 LEU cc_start: 0.7984 (mp) cc_final: 0.7591 (tp)
REVERT: D  130 GLU cc_start: 0.7188 (mp0) cc_final: 0.6534 (mt-10)
REVERT: E   79 LYS cc_start: 0.6991 (tmtt) cc_final: 0.6652 (tttt)
REVERT: F   66 ILE cc_start: 0.8696 (mm) cc_final: 0.8475 (mm)
REVERT: G   38 ARG cc_start: 0.6539 (ttt180) cc_final: 0.6073 (tpp80)
REVERT: G   59 TYR cc_start: 0.7820 (t80) cc_final: 0.7558 (t80)
REVERT: G   60 MET cc_start: 0.8512 (ttt) cc_final: 0.8259 (tpt)
REVERT: G   73 GLU cc_start: 0.7243 (pt0) cc_final: 0.6921 (pt0)
REVERT: G   83 LYS cc_start: 0.7926 (mmmm) cc_final: 0.6805 (ptpp)
REVERT: G   90 ARG cc_start: 0.7443 (tpm170) cc_final: 0.7202 (tpm170)
REVERT: H   87 MET cc_start: 0.8554 (tpp) cc_final: 0.8211 (tmm)
REVERT: H   91 ILE cc_start: 0.8434 (tp) cc_final: 0.8203 (tp)
REVERT: H   94 ILE cc_start: 0.8506 (mm) cc_final: 0.8290 (mm)
REVERT: H  118 GLU cc_start: 0.8284 (mp0) cc_final: 0.7481 (mp0)
REVERT: H  127 LEU cc_start: 0.7943 (mm) cc_final: 0.7600 (mp)
REVERT: K  205 TYR cc_start: 0.7057 (m-10) cc_final: 0.6632 (m-10)
REVERT: K  249 LEU cc_start: 0.8337 (mt) cc_final: 0.7807 (tp)
REVERT: K  315 MET cc_start: 0.7364 (tpp) cc_final: 0.6561 (tpp)
REVERT: K  333 ASP cc_start: 0.7705 (t0) cc_final: 0.7227 (t0)
REVERT: K  373 TRP cc_start: 0.6593 (t-100) cc_final: 0.6376 (t-100)
REVERT: K  384 PHE cc_start: 0.8341 (m-80) cc_final: 0.6953 (m-80)
REVERT: K  409 GLU cc_start: 0.3994 (mm-30) cc_final: 0.3740 (pm20)
REVERT: K  468 LEU cc_start: 0.8183 (mt) cc_final: 0.7536 (tt)
REVERT: K  556 MET cc_start: 0.7627 (ttm) cc_final: 0.7402 (ttm)
REVERT: K  570 ILE cc_start: 0.7241 (mm) cc_final: 0.6971 (mp)
REVERT: K  623 ASN cc_start: 0.7487 (t0) cc_final: 0.7147 (t0)
REVERT: K  626 MET cc_start: 0.7991 (tpt) cc_final: 0.7750 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.2593
  time to fit residues: 97.6192
Evaluate side-chains
  193 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 89 optimal weight:    7.9990
   chunk 112 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 85 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 HIS
F  25 ASN
** G  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 190 GLN
** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 421 HIS
K 471 HIS
K 541 HIS
K 675 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.068009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.050530 restraints weight = 77816.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.051876 restraints weight = 44813.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.052752 restraints weight = 31278.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.7019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  14582  Z= 0.248
  Angle     :  0.784  11.306  20617  Z= 0.430
  Chirality :  0.045   0.237   2338
  Planarity :  0.006   0.064   1836
  Dihedral  : 28.914 139.594   3682
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 19.32
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.90 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.24), residues: 1142
  helix:  0.59 (0.18), residues: 759
  sheet: -1.15 (0.63), residues: 59
  loop : -1.70 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.004   TRP K 748 
 HIS   0.014   0.002   HIS K 387 
 PHE   0.040   0.003   PHE D  67 
 TYR   0.021   0.002   TYR B  88 
 ARG   0.006   0.001   ARG G  51 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05790 (  861)
  hydrogen bonds       : angle       4.26456 ( 2278)
  covalent geometry    : bond        0.00560 (14582)
  covalent geometry    : angle       0.78445 (20617)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 1.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 PHE cc_start: 0.7602 (t80) cc_final: 0.7316 (t80)
REVERT: A   86 SER cc_start: 0.8202 (m) cc_final: 0.7923 (t)
REVERT: A  133 GLU cc_start: 0.5791 (pm20) cc_final: 0.5565 (pt0)
REVERT: B   27 GLN cc_start: 0.7273 (mm-40) cc_final: 0.7039 (mm-40)
REVERT: B   75 HIS cc_start: 0.8690 (t70) cc_final: 0.8189 (t-170)
REVERT: B   84 MET cc_start: 0.7338 (tpt) cc_final: 0.7041 (tpp)
REVERT: B   91 LYS cc_start: 0.8010 (tmmt) cc_final: 0.7623 (tttt)
REVERT: B   98 TYR cc_start: 0.7016 (m-10) cc_final: 0.6720 (m-10)
REVERT: D  130 GLU cc_start: 0.7377 (mp0) cc_final: 0.6844 (mt-10)
REVERT: E   83 ARG cc_start: 0.7221 (tpp-160) cc_final: 0.6850 (tpp-160)
REVERT: G   38 ARG cc_start: 0.6624 (ttt180) cc_final: 0.6242 (tpp80)
REVERT: G   59 TYR cc_start: 0.7615 (t80) cc_final: 0.7214 (t80)
REVERT: G   60 MET cc_start: 0.8447 (ttt) cc_final: 0.8078 (tpt)
REVERT: G   77 ASN cc_start: 0.7983 (t0) cc_final: 0.7772 (t0)
REVERT: G   83 LYS cc_start: 0.8040 (mmmm) cc_final: 0.6905 (ptpp)
REVERT: G   90 ARG cc_start: 0.7273 (tpm170) cc_final: 0.7058 (tpm170)
REVERT: G   99 ASP cc_start: 0.7142 (t0) cc_final: 0.6773 (t0)
REVERT: H   87 MET cc_start: 0.8384 (tpp) cc_final: 0.7931 (tmm)
REVERT: H  118 GLU cc_start: 0.8207 (mp0) cc_final: 0.7494 (mp0)
REVERT: H  127 LEU cc_start: 0.8107 (mm) cc_final: 0.7765 (mp)
REVERT: K  205 TYR cc_start: 0.7070 (m-10) cc_final: 0.6645 (m-10)
REVERT: K  315 MET cc_start: 0.7379 (tpp) cc_final: 0.6718 (tpp)
REVERT: K  373 TRP cc_start: 0.6567 (t-100) cc_final: 0.6345 (t-100)
REVERT: K  384 PHE cc_start: 0.8219 (m-80) cc_final: 0.6812 (m-80)
REVERT: K  409 GLU cc_start: 0.4243 (mm-30) cc_final: 0.3582 (pm20)
REVERT: K  468 LEU cc_start: 0.8127 (mt) cc_final: 0.7412 (tp)
REVERT: K  599 SER cc_start: 0.8623 (m) cc_final: 0.8256 (m)
REVERT: K  623 ASN cc_start: 0.7561 (t0) cc_final: 0.7187 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 250
  average time/residue: 0.2561
  time to fit residues: 93.5543
Evaluate side-chains
  186 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 11 optimal weight:    0.2980
   chunk 6 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   chunk 83 optimal weight:   10.0000
   chunk 109 optimal weight:    0.9990
   chunk 110 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 HIS
F  25 ASN
** H  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 243 HIS
K 324 HIS
** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.068352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.052208 restraints weight = 81686.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.053718 restraints weight = 44453.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.054707 restraints weight = 29490.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.7118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14582  Z= 0.162
  Angle     :  0.688  10.818  20617  Z= 0.379
  Chirality :  0.040   0.188   2338
  Planarity :  0.005   0.068   1836
  Dihedral  : 28.539 136.159   3682
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.20 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.24), residues: 1142
  helix:  0.97 (0.18), residues: 759
  sheet: -1.11 (0.65), residues: 55
  loop : -1.66 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP K 748 
 HIS   0.010   0.001   HIS K 387 
 PHE   0.030   0.002   PHE A  67 
 TYR   0.016   0.002   TYR H  65 
 ARG   0.012   0.001   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04459 (  861)
  hydrogen bonds       : angle       3.87785 ( 2278)
  covalent geometry    : bond        0.00351 (14582)
  covalent geometry    : angle       0.68796 (20617)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 1.211 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8062 (tp30) cc_final: 0.7638 (tm-30)
REVERT: A   78 PHE cc_start: 0.7549 (t80) cc_final: 0.7227 (t80)
REVERT: A   86 SER cc_start: 0.8053 (m) cc_final: 0.7668 (t)
REVERT: A  133 GLU cc_start: 0.5849 (pm20) cc_final: 0.5620 (pt0)
REVERT: B   75 HIS cc_start: 0.8706 (t70) cc_final: 0.8149 (t-170)
REVERT: B   84 MET cc_start: 0.7439 (tpt) cc_final: 0.7233 (tpp)
REVERT: B   91 LYS cc_start: 0.7993 (tmmt) cc_final: 0.7650 (tttt)
REVERT: B   98 TYR cc_start: 0.7116 (m-10) cc_final: 0.6792 (m-10)
REVERT: C   72 LEU cc_start: 0.7890 (mp) cc_final: 0.7473 (tp)
REVERT: D  130 GLU cc_start: 0.6879 (mp0) cc_final: 0.6353 (mt-10)
REVERT: E   79 LYS cc_start: 0.7004 (tttm) cc_final: 0.6717 (mmtt)
REVERT: E   83 ARG cc_start: 0.7043 (tpp-160) cc_final: 0.6637 (tpp-160)
REVERT: E  110 CYS cc_start: 0.7549 (t) cc_final: 0.7326 (t)
REVERT: F   66 ILE cc_start: 0.8708 (mm) cc_final: 0.8499 (mm)
REVERT: G   38 ARG cc_start: 0.6396 (ttt180) cc_final: 0.5966 (tpp80)
REVERT: G   59 TYR cc_start: 0.7684 (t80) cc_final: 0.7455 (t80)
REVERT: G   60 MET cc_start: 0.8319 (ttt) cc_final: 0.8091 (tpt)
REVERT: G   83 LYS cc_start: 0.7845 (mmmm) cc_final: 0.6720 (ptpp)
REVERT: G   90 ARG cc_start: 0.7440 (tpm170) cc_final: 0.7188 (tpm170)
REVERT: G   99 ASP cc_start: 0.6897 (t0) cc_final: 0.6517 (t0)
REVERT: H   66 ILE cc_start: 0.9063 (pt) cc_final: 0.8590 (pt)
REVERT: H   94 ILE cc_start: 0.8512 (mm) cc_final: 0.8267 (mm)
REVERT: H  104 LYS cc_start: 0.5036 (tttt) cc_final: 0.4800 (tttt)
REVERT: H  118 GLU cc_start: 0.8249 (mp0) cc_final: 0.7474 (mp0)
REVERT: H  127 LEU cc_start: 0.7989 (mm) cc_final: 0.7696 (mp)
REVERT: K  205 TYR cc_start: 0.7087 (m-10) cc_final: 0.6648 (m-10)
REVERT: K  249 LEU cc_start: 0.7934 (mt) cc_final: 0.7730 (tp)
REVERT: K  315 MET cc_start: 0.7109 (tpp) cc_final: 0.6216 (tpp)
REVERT: K  366 GLN cc_start: 0.6206 (mp10) cc_final: 0.5925 (mt0)
REVERT: K  373 TRP cc_start: 0.6630 (t-100) cc_final: 0.6369 (t-100)
REVERT: K  384 PHE cc_start: 0.8263 (m-80) cc_final: 0.6819 (m-80)
REVERT: K  409 GLU cc_start: 0.4157 (mm-30) cc_final: 0.3695 (pm20)
REVERT: K  468 LEU cc_start: 0.8019 (mt) cc_final: 0.7398 (tp)
REVERT: K  623 ASN cc_start: 0.7415 (t0) cc_final: 0.6987 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 263
  average time/residue: 0.2643
  time to fit residues: 102.6864
Evaluate side-chains
  191 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 125 optimal weight:   20.0000
   chunk 120 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 98 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 107 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 81 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 HIS
F  25 ASN
** G  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 243 HIS
** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 471 HIS
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.068271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.051928 restraints weight = 81186.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.053506 restraints weight = 43230.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.054503 restraints weight = 28355.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
moved from start:          0.7267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  14582  Z= 0.168
  Angle     :  0.701  11.674  20617  Z= 0.385
  Chirality :  0.040   0.185   2338
  Planarity :  0.005   0.055   1836
  Dihedral  : 28.475 137.203   3682
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 16.29
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.38 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.25), residues: 1142
  helix:  1.01 (0.19), residues: 757
  sheet: -1.09 (0.70), residues: 51
  loop : -1.70 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP K 393 
 HIS   0.011   0.002   HIS K 387 
 PHE   0.037   0.002   PHE C  42 
 TYR   0.018   0.002   TYR C  66 
 ARG   0.012   0.001   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04513 (  861)
  hydrogen bonds       : angle       3.97795 ( 2278)
  covalent geometry    : bond        0.00373 (14582)
  covalent geometry    : angle       0.70104 (20617)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 PHE cc_start: 0.7668 (t80) cc_final: 0.7276 (t80)
REVERT: A   86 SER cc_start: 0.7995 (m) cc_final: 0.7668 (t)
REVERT: A   94 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6826 (mt-10)
REVERT: A   97 GLU cc_start: 0.8003 (mp0) cc_final: 0.7462 (mp0)
REVERT: A  133 GLU cc_start: 0.5933 (pm20) cc_final: 0.5729 (pt0)
REVERT: B   75 HIS cc_start: 0.8822 (t70) cc_final: 0.8236 (t-170)
REVERT: B   91 LYS cc_start: 0.8028 (tmmt) cc_final: 0.7659 (tttt)
REVERT: C   72 LEU cc_start: 0.7953 (mp) cc_final: 0.7533 (tp)
REVERT: D  130 GLU cc_start: 0.7003 (mp0) cc_final: 0.6450 (mt-10)
REVERT: E   79 LYS cc_start: 0.6970 (tttm) cc_final: 0.6614 (mmtt)
REVERT: E   83 ARG cc_start: 0.7140 (tpp-160) cc_final: 0.6808 (tpp-160)
REVERT: G   38 ARG cc_start: 0.6493 (ttt180) cc_final: 0.6136 (tpp80)
REVERT: G   60 MET cc_start: 0.8471 (ttt) cc_final: 0.8222 (ptm)
REVERT: G   73 GLU cc_start: 0.7662 (pt0) cc_final: 0.7446 (pt0)
REVERT: G   83 LYS cc_start: 0.7841 (mmmm) cc_final: 0.6743 (ptpp)
REVERT: G   99 ASP cc_start: 0.6830 (t0) cc_final: 0.6455 (t0)
REVERT: H   94 ILE cc_start: 0.8419 (mm) cc_final: 0.8180 (mm)
REVERT: H   95 PHE cc_start: 0.7962 (t80) cc_final: 0.7759 (t80)
REVERT: H  118 GLU cc_start: 0.8294 (mp0) cc_final: 0.7490 (mp0)
REVERT: H  127 LEU cc_start: 0.7959 (mm) cc_final: 0.7648 (mp)
REVERT: K  205 TYR cc_start: 0.7012 (m-10) cc_final: 0.6611 (m-10)
REVERT: K  243 HIS cc_start: 0.6539 (t70) cc_final: 0.6184 (t-170)
REVERT: K  373 TRP cc_start: 0.6586 (t-100) cc_final: 0.6287 (t-100)
REVERT: K  384 PHE cc_start: 0.8366 (m-80) cc_final: 0.6893 (m-80)
REVERT: K  409 GLU cc_start: 0.4145 (mm-30) cc_final: 0.3693 (pm20)
REVERT: K  468 LEU cc_start: 0.8171 (mt) cc_final: 0.7589 (tp)
REVERT: K  623 ASN cc_start: 0.7451 (t0) cc_final: 0.7097 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.2387
  time to fit residues: 82.9248
Evaluate side-chains
  185 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   chunk 80 optimal weight:   10.0000
   chunk 122 optimal weight:    8.9990
   chunk 108 optimal weight:    9.9990
   chunk 96 optimal weight:    8.9990
   chunk 114 optimal weight:    6.9990
   chunk 11 optimal weight:    0.3980
   chunk 113 optimal weight:    0.5980
   chunk 127 optimal weight:    9.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 HIS
D  92 ASN
F  25 ASN
** G  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.067662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.051350 restraints weight = 83310.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.052840 restraints weight = 45164.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.053814 restraints weight = 30018.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.7561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  14582  Z= 0.202
  Angle     :  0.733  12.074  20617  Z= 0.400
  Chirality :  0.042   0.174   2338
  Planarity :  0.005   0.072   1836
  Dihedral  : 28.621 138.593   3682
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 18.48
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.73 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.24), residues: 1142
  helix:  0.82 (0.19), residues: 757
  sheet: -1.50 (0.64), residues: 57
  loop : -1.76 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP K 622 
 HIS   0.013   0.002   HIS K 387 
 PHE   0.034   0.002   PHE A  67 
 TYR   0.035   0.002   TYR H 108 
 ARG   0.012   0.001   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04980 (  861)
  hydrogen bonds       : angle       4.08846 ( 2278)
  covalent geometry    : bond        0.00458 (14582)
  covalent geometry    : angle       0.73295 (20617)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4292.16 seconds
wall clock time: 75 minutes 22.26 seconds (4522.26 seconds total)