Starting phenix.real_space_refine
on Thu May 15 21:11:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j90_36083/05_2025/8j90_36083.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j90_36083/05_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_36083/05_2025/8j90_36083.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j90_36083/05_2025/8j90_36083.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j90_36083/05_2025/8j90_36083.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j90_36083/05_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-5687/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: 8.09, per 1000 atoms: 0.58
  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: 3.58
  Conformation dependent library (CDL) restraints added in 1.3 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: 5.89
  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: 7.11

  Time building geometry restraints manager: 4.17 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:             0.520
  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:          0.560
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     37.760
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.390
-------------------------------------------------------------------------------
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  : 1.156 
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: 0.3452
  time to fit residues: 225.8095
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  : 1.208 
-------------------------------------------------------------------------------
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 = 0.3477 r_free = 0.3477 target = 0.069865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.051524 restraints weight = 80702.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.053010 restraints weight = 45627.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.053947 restraints weight = 31437.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
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  : 1.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 PHE cc_start: 0.7636 (t80) cc_final: 0.7303 (t80)
REVERT: A   86 SER cc_start: 0.8438 (m) cc_final: 0.8077 (t)
REVERT: A  118 THR cc_start: 0.8749 (m) cc_final: 0.8259 (m)
REVERT: A  133 GLU cc_start: 0.6580 (pm20) cc_final: 0.5757 (pt0)
REVERT: B   64 ASN cc_start: 0.7310 (t0) cc_final: 0.7081 (t0)
REVERT: B   88 TYR cc_start: 0.7025 (m-80) cc_final: 0.5955 (m-80)
REVERT: B   91 LYS cc_start: 0.7850 (tmmt) cc_final: 0.7279 (tttt)
REVERT: B   98 TYR cc_start: 0.6944 (m-10) cc_final: 0.6280 (m-10)
REVERT: C   28 MET cc_start: 0.5056 (mtm) cc_final: 0.4082 (ttp)
REVERT: C   42 PHE cc_start: 0.7321 (m-10) cc_final: 0.7091 (m-80)
REVERT: C   98 ASN cc_start: 0.7814 (m-40) cc_final: 0.7292 (t0)
REVERT: D   63 LYS cc_start: 0.7331 (mptt) cc_final: 0.6606 (mmmt)
REVERT: D  110 LYS cc_start: 0.6906 (mmtt) cc_final: 0.6320 (mtpp)
REVERT: D  111 LYS cc_start: 0.8166 (tptt) cc_final: 0.7529 (tptt)
REVERT: D  130 GLU cc_start: 0.7756 (mp0) cc_final: 0.7088 (mt-10)
REVERT: E   79 LYS cc_start: 0.6914 (tmtt) cc_final: 0.6521 (mmtt)
REVERT: F   21 VAL cc_start: 0.6297 (t) cc_final: 0.4471 (m)
REVERT: G   47 ARG cc_start: 0.7953 (mmm-85) cc_final: 0.7582 (mmm-85)
REVERT: G   83 LYS cc_start: 0.8034 (mmmm) cc_final: 0.6903 (ptpp)
REVERT: H  125 LEU cc_start: 0.8652 (tt) cc_final: 0.8420 (tt)
REVERT: K  224 ILE cc_start: 0.8519 (mp) cc_final: 0.8119 (mm)
REVERT: K  229 MET cc_start: 0.5010 (ptt) cc_final: 0.4644 (ptt)
REVERT: K  249 LEU cc_start: 0.8276 (mt) cc_final: 0.7868 (tp)
REVERT: K  281 TYR cc_start: 0.7262 (t80) cc_final: 0.6228 (t80)
REVERT: K  282 HIS cc_start: 0.5249 (m90) cc_final: 0.4933 (m-70)
REVERT: K  315 MET cc_start: 0.7133 (tpp) cc_final: 0.6894 (tpp)
REVERT: K  321 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6768 (mm)
REVERT: K  373 TRP cc_start: 0.6600 (t-100) cc_final: 0.6115 (t-100)
REVERT: K  382 ASP cc_start: 0.6716 (m-30) cc_final: 0.6392 (m-30)
REVERT: K  384 PHE cc_start: 0.8384 (m-80) cc_final: 0.7944 (m-80)
REVERT: K  468 LEU cc_start: 0.8141 (tp) cc_final: 0.7729 (tt)
REVERT: K  553 LEU cc_start: 0.7442 (mp) cc_final: 0.7041 (mp)
REVERT: K  557 ASP cc_start: 0.7978 (t0) cc_final: 0.7497 (t70)
REVERT: K  570 ILE cc_start: 0.6714 (mm) cc_final: 0.6495 (mp)
REVERT: K  621 ASP cc_start: 0.7460 (t0) cc_final: 0.7070 (m-30)
REVERT: K  623 ASN cc_start: 0.7950 (t0) cc_final: 0.7587 (t0)
REVERT: K  748 TRP cc_start: 0.5594 (p-90) cc_final: 0.5389 (p-90)
REVERT: K  755 SER cc_start: 0.7221 (p) cc_final: 0.6993 (t)
  outliers start: 10
  outliers final: 1
  residues processed: 322
  average time/residue: 0.2640
  time to fit residues: 119.3656
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  : 1.137 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 37 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0370
   chunk 134 optimal weight:   10.0000
   chunk 116 optimal weight:   40.0000
   chunk 93 optimal weight:    0.9990
   chunk 82 optimal weight:   10.0000
   overall best weight:    0.7862

-------------------------------------------------------------------------------
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 = 0.3476 r_free = 0.3476 target = 0.069683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.052781 restraints weight = 80232.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.054366 restraints weight = 42779.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.055384 restraints weight = 28168.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6973
moved from start:          0.4317

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= 0.148
  Angle     :  0.631   9.595  20617  Z= 0.351
  Chirality :  0.039   0.175   2338
  Planarity :  0.005   0.069   1836
  Dihedral  : 28.181 136.924   3682
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.29 %
    Favored  : 95.61 %
  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:  0.55 (0.25), residues: 1142
  helix:  1.09 (0.18), residues: 772
  sheet: -0.18 (0.75), residues: 49
  loop : -1.26 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP K 622 
 HIS   0.006   0.001   HIS K 499 
 PHE   0.028   0.002   PHE D  67 
 TYR   0.016   0.002   TYR C  48 
 ARG   0.011   0.001   ARG K 661 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04009 (  861)
  hydrogen bonds       : angle       3.86493 ( 2278)
  covalent geometry    : bond        0.00315 (14582)
  covalent geometry    : angle       0.63080 (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
  317 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 316
  time to evaluate  : 1.134 
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: 0.7607 (t80) cc_final: 0.7289 (t80)
REVERT: A   86 SER cc_start: 0.8507 (m) cc_final: 0.8074 (t)
REVERT: A  109 LEU cc_start: 0.8957 (tp) cc_final: 0.8697 (tp)
REVERT: A  133 GLU cc_start: 0.6583 (pm20) cc_final: 0.6049 (pt0)
REVERT: B   88 TYR cc_start: 0.7169 (m-80) cc_final: 0.6189 (m-80)
REVERT: B   91 LYS cc_start: 0.7748 (tmmt) cc_final: 0.7239 (tttt)
REVERT: B   97 LEU cc_start: 0.7683 (tp) cc_final: 0.7327 (tp)
REVERT: B   98 TYR cc_start: 0.6831 (m-10) cc_final: 0.6401 (m-10)
REVERT: C   28 MET cc_start: 0.4988 (mtm) cc_final: 0.3998 (ttp)
REVERT: C   39 ILE cc_start: 0.8001 (pt) cc_final: 0.7640 (pt)
REVERT: C   42 PHE cc_start: 0.7176 (m-10) cc_final: 0.6933 (m-80)
REVERT: C   72 LEU cc_start: 0.7961 (mp) cc_final: 0.7514 (tt)
REVERT: C   98 ASN cc_start: 0.7966 (m-40) cc_final: 0.7415 (t0)
REVERT: D  110 LYS cc_start: 0.6916 (mmtt) cc_final: 0.6324 (mtpp)
REVERT: D  111 LYS cc_start: 0.7909 (tptt) cc_final: 0.7453 (tptt)
REVERT: D  130 GLU cc_start: 0.7424 (mp0) cc_final: 0.6762 (mt-10)
REVERT: E   79 LYS cc_start: 0.6860 (tmtt) cc_final: 0.6649 (mmtt)
REVERT: F   63 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7755 (mm-30)
REVERT: G   60 MET cc_start: 0.8307 (ttt) cc_final: 0.7927 (ptm)
REVERT: G   73 GLU cc_start: 0.7214 (pt0) cc_final: 0.7013 (pt0)
REVERT: G   83 LYS cc_start: 0.8012 (mmmm) cc_final: 0.6855 (ptpp)
REVERT: K  249 LEU cc_start: 0.8097 (mt) cc_final: 0.7716 (tp)
REVERT: K  315 MET cc_start: 0.7136 (tpp) cc_final: 0.6774 (tpp)
REVERT: K  373 TRP cc_start: 0.6583 (t-100) cc_final: 0.6235 (t-100)
REVERT: K  382 ASP cc_start: 0.6751 (m-30) cc_final: 0.6437 (m-30)
REVERT: K  384 PHE cc_start: 0.8318 (m-80) cc_final: 0.7181 (m-10)
REVERT: K  468 LEU cc_start: 0.8039 (tp) cc_final: 0.7580 (tp)
REVERT: K  570 ILE cc_start: 0.7049 (mm) cc_final: 0.6689 (mp)
REVERT: K  615 CYS cc_start: 0.6241 (t) cc_final: 0.6010 (m)
REVERT: K  616 ILE cc_start: 0.7583 (tp) cc_final: 0.7367 (tp)
REVERT: K  621 ASP cc_start: 0.7620 (t0) cc_final: 0.6821 (m-30)
REVERT: K  669 GLU cc_start: 0.9393 (tp30) cc_final: 0.9189 (tp30)
REVERT: K  755 SER cc_start: 0.6758 (p) cc_final: 0.6547 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 317
  average time/residue: 0.2637
  time to fit residues: 117.8733
Evaluate side-chains
  222 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   chunk 115 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0370
   chunk 40 optimal weight:    5.9990
   chunk 126 optimal weight:   10.0000
   chunk 74 optimal weight:   10.0000
   chunk 106 optimal weight:    5.9990
   chunk 123 optimal weight:    8.9990
   chunk 133 optimal weight:    5.9990
   overall best weight:    3.6066

-------------------------------------------------------------------------------
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
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 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 = 0.3423 r_free = 0.3423 target = 0.067696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.050623 restraints weight = 82054.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.052181 restraints weight = 43050.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.053198 restraints weight = 28229.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.5325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  14582  Z= 0.217
  Angle     :  0.722  10.476  20617  Z= 0.396
  Chirality :  0.042   0.275   2338
  Planarity :  0.005   0.049   1836
  Dihedral  : 28.535 139.400   3682
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 16.91
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.12 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  6.39 %
    Favored  : 93.51 %
  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:  0.21 (0.24), residues: 1142
  helix:  0.79 (0.18), residues: 772
  sheet: -0.25 (0.71), residues: 54
  loop : -1.26 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP K 748 
 HIS   0.015   0.002   HIS B  75 
 PHE   0.026   0.002   PHE D  67 
 TYR   0.018   0.002   TYR C  48 
 ARG   0.007   0.001   ARG E 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05067 (  861)
  hydrogen bonds       : angle       4.14752 ( 2278)
  covalent geometry    : bond        0.00489 (14582)
  covalent geometry    : angle       0.72202 (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
  275 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 274
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 PHE cc_start: 0.7738 (t80) cc_final: 0.7297 (t80)
REVERT: A   86 SER cc_start: 0.8429 (m) cc_final: 0.8078 (t)
REVERT: A  133 GLU cc_start: 0.6513 (pm20) cc_final: 0.6026 (pt0)
REVERT: B   27 GLN cc_start: 0.7334 (mm-40) cc_final: 0.7081 (mm-40)
REVERT: B   35 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8254 (ttm-80)
REVERT: B   91 LYS cc_start: 0.7687 (tmmt) cc_final: 0.7272 (tttt)
REVERT: B   98 TYR cc_start: 0.6802 (m-10) cc_final: 0.6300 (m-10)
REVERT: C   28 MET cc_start: 0.4657 (mtm) cc_final: 0.3682 (tpt)
REVERT: C   98 ASN cc_start: 0.7981 (m-40) cc_final: 0.7355 (t0)
REVERT: D  110 LYS cc_start: 0.7021 (mmtt) cc_final: 0.6681 (mtpp)
REVERT: D  130 GLU cc_start: 0.7648 (mp0) cc_final: 0.6968 (mt-10)
REVERT: E   79 LYS cc_start: 0.6925 (tmtt) cc_final: 0.6662 (tttt)
REVERT: F   63 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8165 (mm-30)
REVERT: G   38 ARG cc_start: 0.6681 (ttt180) cc_final: 0.6134 (tpp80)
REVERT: G   59 TYR cc_start: 0.7881 (t80) cc_final: 0.7602 (t80)
REVERT: G   83 LYS cc_start: 0.8099 (mmmm) cc_final: 0.7031 (ptpp)
REVERT: H  118 GLU cc_start: 0.8266 (mp0) cc_final: 0.7381 (mp0)
REVERT: K  224 ILE cc_start: 0.8321 (mp) cc_final: 0.8017 (mm)
REVERT: K  243 HIS cc_start: 0.6426 (t-170) cc_final: 0.6069 (t-170)
REVERT: K  249 LEU cc_start: 0.8360 (mt) cc_final: 0.7858 (tp)
REVERT: K  256 ILE cc_start: 0.8816 (mp) cc_final: 0.8568 (mp)
REVERT: K  296 MET cc_start: 0.3533 (ptm) cc_final: 0.2537 (ppp)
REVERT: K  315 MET cc_start: 0.7303 (tpp) cc_final: 0.6823 (tpp)
REVERT: K  382 ASP cc_start: 0.7092 (m-30) cc_final: 0.6778 (m-30)
REVERT: K  384 PHE cc_start: 0.8564 (m-80) cc_final: 0.7385 (m-10)
REVERT: K  468 LEU cc_start: 0.8272 (tp) cc_final: 0.7736 (tt)
REVERT: K  556 MET cc_start: 0.7905 (ttm) cc_final: 0.7678 (ttm)
REVERT: K  570 ILE cc_start: 0.7022 (mm) cc_final: 0.6745 (mp)
REVERT: K  621 ASP cc_start: 0.7480 (t0) cc_final: 0.6890 (m-30)
REVERT: K  646 TYR cc_start: 0.5739 (OUTLIER) cc_final: 0.5297 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 274
  average time/residue: 0.2595
  time to fit residues: 102.3556
Evaluate side-chains
  198 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 197
  time to evaluate  : 1.273 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 106 optimal weight:    7.9990
   chunk 101 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 76 optimal weight:   10.0000
   chunk 115 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 92 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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  88 ASN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 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 = 0.3419 r_free = 0.3419 target = 0.067493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.050550 restraints weight = 84353.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.052103 restraints weight = 45165.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.053087 restraints weight = 29832.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.5951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  14582  Z= 0.200
  Angle     :  0.702   8.342  20617  Z= 0.388
  Chirality :  0.041   0.200   2338
  Planarity :  0.005   0.077   1836
  Dihedral  : 28.656 138.178   3682
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.85 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.99 %
    Favored  : 94.91 %
  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:  0.07 (0.24), residues: 1142
  helix:  0.75 (0.18), residues: 772
  sheet: -0.08 (0.80), residues: 44
  loop : -1.53 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.004   TRP K 373 
 HIS   0.012   0.002   HIS B  75 
 PHE   0.028   0.003   PHE C  42 
 TYR   0.023   0.002   TYR B  88 
 ARG   0.006   0.001   ARG K 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04771 (  861)
  hydrogen bonds       : angle       4.04950 ( 2278)
  covalent geometry    : bond        0.00449 (14582)
  covalent geometry    : angle       0.70228 (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
  261 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 260
  time to evaluate  : 1.136 
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: 0.7532 (t80) cc_final: 0.7039 (t80)
REVERT: A   86 SER cc_start: 0.8412 (m) cc_final: 0.8056 (t)
REVERT: A   92 LEU cc_start: 0.8513 (mt) cc_final: 0.8270 (mp)
REVERT: A  109 LEU cc_start: 0.8826 (tp) cc_final: 0.8513 (tp)
REVERT: A  133 GLU cc_start: 0.6342 (pm20) cc_final: 0.6015 (pt0)
REVERT: B   75 HIS cc_start: 0.8636 (t70) cc_final: 0.8055 (t-170)
REVERT: B   91 LYS cc_start: 0.7966 (tmmt) cc_final: 0.7612 (tttt)
REVERT: B   98 TYR cc_start: 0.6800 (m-10) cc_final: 0.6406 (m-10)
REVERT: C   72 LEU cc_start: 0.8099 (mp) cc_final: 0.7690 (tp)
REVERT: C   98 ASN cc_start: 0.8077 (m-40) cc_final: 0.7406 (t0)
REVERT: D   67 PHE cc_start: 0.6344 (m-80) cc_final: 0.6040 (m-80)
REVERT: D  130 GLU cc_start: 0.7385 (mp0) cc_final: 0.6662 (mt-10)
REVERT: E   79 LYS cc_start: 0.6976 (tmtt) cc_final: 0.6739 (tttt)
REVERT: F   63 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8147 (mm-30)
REVERT: G   38 ARG cc_start: 0.6607 (ttt180) cc_final: 0.6096 (tpp80)
REVERT: G   77 ASN cc_start: 0.8187 (t0) cc_final: 0.7984 (t0)
REVERT: G   83 LYS cc_start: 0.8167 (mmmm) cc_final: 0.7086 (ptpp)
REVERT: G   99 ASP cc_start: 0.6819 (t0) cc_final: 0.6350 (t0)
REVERT: H   87 MET cc_start: 0.8485 (tpp) cc_final: 0.8105 (tmm)
REVERT: H   91 ILE cc_start: 0.8444 (tp) cc_final: 0.8186 (tp)
REVERT: H  118 GLU cc_start: 0.8279 (mp0) cc_final: 0.7465 (mp0)
REVERT: H  127 LEU cc_start: 0.7987 (mm) cc_final: 0.7669 (mp)
REVERT: K  205 TYR cc_start: 0.7065 (m-10) cc_final: 0.6728 (m-10)
REVERT: K  249 LEU cc_start: 0.8406 (mt) cc_final: 0.7878 (tp)
REVERT: K  296 MET cc_start: 0.3630 (ptm) cc_final: 0.2976 (ppp)
REVERT: K  315 MET cc_start: 0.7350 (tpp) cc_final: 0.6796 (tpp)
REVERT: K  384 PHE cc_start: 0.8388 (m-80) cc_final: 0.7477 (m-80)
REVERT: K  409 GLU cc_start: 0.3716 (mm-30) cc_final: 0.3421 (pm20)
REVERT: K  553 LEU cc_start: 0.6768 (mt) cc_final: 0.6492 (mt)
REVERT: K  556 MET cc_start: 0.7996 (ttm) cc_final: 0.7717 (ttm)
REVERT: K  570 ILE cc_start: 0.7017 (mm) cc_final: 0.6757 (mp)
  outliers start: 1
  outliers final: 1
  residues processed: 261
  average time/residue: 0.2525
  time to fit residues: 96.0202
Evaluate side-chains
  196 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 1.267 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   chunk 122 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 76 optimal weight:   10.0000
   chunk 106 optimal weight:   10.0000
   chunk 95 optimal weight:    8.9990
   chunk 89 optimal weight:   10.0000
   chunk 19 optimal weight:    0.0980
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 HIS
** D  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** H  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 243 HIS
K 247 ASN
** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 324 HIS
** 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**
K 675 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.067893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.051302 restraints weight = 82766.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.052920 restraints weight = 43121.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.053907 restraints weight = 27980.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.6249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  14582  Z= 0.178
  Angle     :  0.674   9.868  20617  Z= 0.376
  Chirality :  0.040   0.177   2338
  Planarity :  0.005   0.052   1836
  Dihedral  : 28.613 138.024   3682
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.68 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  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:  0.27 (0.24), residues: 1142
  helix:  0.94 (0.18), residues: 766
  sheet: -0.43 (0.73), residues: 49
  loop : -1.44 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP K 373 
 HIS   0.010   0.001   HIS K 387 
 PHE   0.028   0.002   PHE D  67 
 TYR   0.025   0.002   TYR B  88 
 ARG   0.009   0.001   ARG K 633 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04679 (  861)
  hydrogen bonds       : angle       3.95162 ( 2278)
  covalent geometry    : bond        0.00400 (14582)
  covalent geometry    : angle       0.67390 (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
  264 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 1.155 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 PHE cc_start: 0.7513 (t80) cc_final: 0.7066 (t80)
REVERT: A   86 SER cc_start: 0.8375 (m) cc_final: 0.8076 (t)
REVERT: A   97 GLU cc_start: 0.7977 (mp0) cc_final: 0.7328 (mp0)
REVERT: A  133 GLU cc_start: 0.6329 (pm20) cc_final: 0.6004 (pt0)
REVERT: B   75 HIS cc_start: 0.8723 (t70) cc_final: 0.8380 (t-90)
REVERT: B   91 LYS cc_start: 0.7948 (tmmt) cc_final: 0.7622 (tttt)
REVERT: B   98 TYR cc_start: 0.6825 (m-10) cc_final: 0.6155 (m-10)
REVERT: C   98 ASN cc_start: 0.8068 (m-40) cc_final: 0.7507 (t0)
REVERT: D  130 GLU cc_start: 0.7191 (mp0) cc_final: 0.6520 (mt-10)
REVERT: E   79 LYS cc_start: 0.7131 (tmtt) cc_final: 0.6703 (tttt)
REVERT: E  128 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.7795 (mmm-85)
REVERT: E  133 GLU cc_start: 0.6710 (pm20) cc_final: 0.5408 (pt0)
REVERT: G   38 ARG cc_start: 0.6565 (ttt180) cc_final: 0.6085 (tpp80)
REVERT: G   59 TYR cc_start: 0.7790 (t80) cc_final: 0.7520 (t80)
REVERT: G   83 LYS cc_start: 0.8012 (mmmm) cc_final: 0.6968 (ptpp)
REVERT: G   99 ASP cc_start: 0.6824 (t0) cc_final: 0.6548 (t0)
REVERT: H   87 MET cc_start: 0.8480 (tpp) cc_final: 0.8178 (tmm)
REVERT: H   91 ILE cc_start: 0.8416 (tp) cc_final: 0.8196 (tp)
REVERT: H   94 ILE cc_start: 0.8486 (mm) cc_final: 0.8230 (mm)
REVERT: H  118 GLU cc_start: 0.8254 (mp0) cc_final: 0.7465 (mp0)
REVERT: H  127 LEU cc_start: 0.8063 (mm) cc_final: 0.7783 (mp)
REVERT: K  205 TYR cc_start: 0.7031 (m-10) cc_final: 0.6663 (m-10)
REVERT: K  249 LEU cc_start: 0.8329 (mt) cc_final: 0.7813 (tp)
REVERT: K  296 MET cc_start: 0.3470 (ptm) cc_final: 0.2918 (ppp)
REVERT: K  315 MET cc_start: 0.7396 (tpp) cc_final: 0.6559 (tpp)
REVERT: K  373 TRP cc_start: 0.6646 (t-100) cc_final: 0.6109 (t-100)
REVERT: K  384 PHE cc_start: 0.8337 (m-80) cc_final: 0.7387 (m-80)
REVERT: K  409 GLU cc_start: 0.4007 (mm-30) cc_final: 0.3576 (pm20)
REVERT: K  556 MET cc_start: 0.7827 (ttm) cc_final: 0.7580 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 264
  average time/residue: 0.2514
  time to fit residues: 94.9811
Evaluate side-chains
  194 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 103 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 85 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 134 optimal weight:    0.3980
   chunk 89 optimal weight:   10.0000
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 HIS
** D  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
F  25 ASN
** H  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 243 HIS
K 247 ASN
** K 366 GLN ** 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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.068881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.051837 restraints weight = 84182.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.053450 restraints weight = 44609.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.054485 restraints weight = 29289.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.6460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14582  Z= 0.152
  Angle     :  0.663   9.329  20617  Z= 0.368
  Chirality :  0.039   0.224   2338
  Planarity :  0.004   0.043   1836
  Dihedral  : 28.480 136.790   3682
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.59 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  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:  0.42 (0.24), residues: 1142
  helix:  1.11 (0.18), residues: 765
  sheet: -0.68 (0.72), residues: 51
  loop : -1.49 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP K 373 
 HIS   0.008   0.001   HIS B  75 
 PHE   0.024   0.002   PHE K 526 
 TYR   0.020   0.002   TYR H  65 
 ARG   0.009   0.001   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04252 (  861)
  hydrogen bonds       : angle       3.80963 ( 2278)
  covalent geometry    : bond        0.00330 (14582)
  covalent geometry    : angle       0.66256 (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
  260 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 SER cc_start: 0.8310 (m) cc_final: 0.7982 (t)
REVERT: A   97 GLU cc_start: 0.7907 (mp0) cc_final: 0.7181 (mp0)
REVERT: A  133 GLU cc_start: 0.6211 (pm20) cc_final: 0.5885 (pt0)
REVERT: B   75 HIS cc_start: 0.8764 (t70) cc_final: 0.8454 (t-90)
REVERT: B   84 MET cc_start: 0.7003 (tpp) cc_final: 0.5965 (tpp)
REVERT: B   91 LYS cc_start: 0.7919 (tmmt) cc_final: 0.7590 (tttt)
REVERT: B   98 TYR cc_start: 0.6882 (m-10) cc_final: 0.6420 (m-10)
REVERT: C   72 LEU cc_start: 0.8032 (mp) cc_final: 0.7634 (tt)
REVERT: C   98 ASN cc_start: 0.8106 (m-40) cc_final: 0.7521 (t0)
REVERT: D  130 GLU cc_start: 0.7065 (mp0) cc_final: 0.6407 (mt-10)
REVERT: E   83 ARG cc_start: 0.7252 (tpp-160) cc_final: 0.6912 (tpp-160)
REVERT: E  128 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.7659 (mmm-85)
REVERT: E  133 GLU cc_start: 0.6750 (pm20) cc_final: 0.5638 (pt0)
REVERT: G   38 ARG cc_start: 0.6422 (ttt180) cc_final: 0.5844 (tpp80)
REVERT: G   59 TYR cc_start: 0.7727 (t80) cc_final: 0.7518 (t80)
REVERT: G   60 MET cc_start: 0.7754 (ptm) cc_final: 0.7449 (ptm)
REVERT: G   83 LYS cc_start: 0.7924 (mmmm) cc_final: 0.6804 (ptpp)
REVERT: G   90 ARG cc_start: 0.7573 (tpm170) cc_final: 0.7281 (tpm170)
REVERT: G   99 ASP cc_start: 0.6741 (t0) cc_final: 0.6254 (t0)
REVERT: H   87 MET cc_start: 0.8470 (tpp) cc_final: 0.8220 (tmm)
REVERT: H  118 GLU cc_start: 0.8284 (mp0) cc_final: 0.7491 (mp0)
REVERT: H  127 LEU cc_start: 0.8116 (mm) cc_final: 0.7832 (mp)
REVERT: K  205 TYR cc_start: 0.7058 (m-10) cc_final: 0.6649 (m-10)
REVERT: K  224 ILE cc_start: 0.8243 (mp) cc_final: 0.7903 (mm)
REVERT: K  249 LEU cc_start: 0.8324 (mt) cc_final: 0.7805 (tp)
REVERT: K  315 MET cc_start: 0.7336 (tpp) cc_final: 0.6797 (tpp)
REVERT: K  373 TRP cc_start: 0.6623 (t-100) cc_final: 0.6067 (t-100)
REVERT: K  384 PHE cc_start: 0.8409 (m-80) cc_final: 0.7480 (m-80)
REVERT: K  409 GLU cc_start: 0.4032 (mm-30) cc_final: 0.3821 (pm20)
REVERT: K  623 ASN cc_start: 0.7368 (t0) cc_final: 0.7074 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.2550
  time to fit residues: 97.6362
Evaluate side-chains
  197 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 72 optimal weight:   10.0000
   chunk 89 optimal weight:   10.0000
   chunk 112 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 85 optimal weight:    9.9990
   chunk 50 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    3.9188

-------------------------------------------------------------------------------
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 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.068955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.051092 restraints weight = 79521.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.052474 restraints weight = 46848.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.053374 restraints weight = 32870.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.6934

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= 0.225
  Angle     :  0.763  11.756  20617  Z= 0.418
  Chirality :  0.043   0.300   2338
  Planarity :  0.005   0.049   1836
  Dihedral  : 28.767 139.295   3682
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 18.17
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.55 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.24), residues: 1142
  helix:  0.80 (0.18), residues: 766
  sheet: -1.19 (0.62), residues: 60
  loop : -1.65 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP K 373 
 HIS   0.016   0.002   HIS K 243 
 PHE   0.037   0.003   PHE A  67 
 TYR   0.029   0.002   TYR H  65 
 ARG   0.013   0.001   ARG K 531 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05409 (  861)
  hydrogen bonds       : angle       4.20403 ( 2278)
  covalent geometry    : bond        0.00509 (14582)
  covalent geometry    : angle       0.76256 (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
  253 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 SER cc_start: 0.8495 (m) cc_final: 0.8243 (t)
REVERT: A   92 LEU cc_start: 0.8550 (mt) cc_final: 0.8290 (mp)
REVERT: A  133 GLU cc_start: 0.5977 (pm20) cc_final: 0.5504 (pt0)
REVERT: B   75 HIS cc_start: 0.8829 (t70) cc_final: 0.8371 (t-90)
REVERT: B   91 LYS cc_start: 0.8036 (tmmt) cc_final: 0.7710 (tttt)
REVERT: B   98 TYR cc_start: 0.6787 (m-10) cc_final: 0.6466 (m-10)
REVERT: C   98 ASN cc_start: 0.8064 (m-40) cc_final: 0.7457 (t0)
REVERT: D   67 PHE cc_start: 0.6609 (m-80) cc_final: 0.6286 (m-80)
REVERT: D  130 GLU cc_start: 0.7086 (mp0) cc_final: 0.6515 (mt-10)
REVERT: E   79 LYS cc_start: 0.6817 (tttt) cc_final: 0.6487 (tptm)
REVERT: E   83 ARG cc_start: 0.7366 (tpp-160) cc_final: 0.6828 (tpp-160)
REVERT: E  128 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7783 (mmm-85)
REVERT: E  133 GLU cc_start: 0.6664 (pm20) cc_final: 0.5563 (pt0)
REVERT: G   38 ARG cc_start: 0.6510 (ttt180) cc_final: 0.6173 (tpp80)
REVERT: G   59 TYR cc_start: 0.7602 (t80) cc_final: 0.7204 (t80)
REVERT: G   60 MET cc_start: 0.7860 (ptm) cc_final: 0.7649 (ptm)
REVERT: G   83 LYS cc_start: 0.7955 (mmmm) cc_final: 0.6786 (ptpp)
REVERT: G   90 ARG cc_start: 0.7408 (tpm170) cc_final: 0.7076 (tpm170)
REVERT: G   99 ASP cc_start: 0.6776 (t0) cc_final: 0.6366 (t0)
REVERT: H   87 MET cc_start: 0.8479 (tpp) cc_final: 0.8074 (tmm)
REVERT: H   91 ILE cc_start: 0.8433 (tp) cc_final: 0.8223 (tp)
REVERT: H  118 GLU cc_start: 0.8231 (mp0) cc_final: 0.7505 (mp0)
REVERT: H  127 LEU cc_start: 0.8022 (mm) cc_final: 0.7749 (mp)
REVERT: K  205 TYR cc_start: 0.7082 (m-10) cc_final: 0.6659 (m-10)
REVERT: K  214 ILE cc_start: 0.7786 (mm) cc_final: 0.7529 (mm)
REVERT: K  373 TRP cc_start: 0.6622 (t-100) cc_final: 0.6331 (t-100)
REVERT: K  384 PHE cc_start: 0.8384 (m-80) cc_final: 0.6976 (m-80)
REVERT: K  409 GLU cc_start: 0.4187 (mm-30) cc_final: 0.3562 (pm20)
REVERT: K  623 ASN cc_start: 0.7460 (t0) cc_final: 0.7204 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 253
  average time/residue: 0.2376
  time to fit residues: 88.7442
Evaluate side-chains
  183 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 83 optimal weight:   10.0000
   chunk 109 optimal weight:    4.9990
   chunk 110 optimal weight:   20.0000
   chunk 30 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 247 ASN
K 471 HIS
** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.068757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.052109 restraints weight = 83031.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.053714 restraints weight = 44914.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.054705 restraints weight = 29685.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.7081

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= 0.161
  Angle     :  0.694  11.433  20617  Z= 0.384
  Chirality :  0.040   0.174   2338
  Planarity :  0.005   0.044   1836
  Dihedral  : 28.480 136.387   3682
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 15.76
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.77 %
    Favored  : 96.06 %
  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:  0.20 (0.24), residues: 1142
  helix:  0.99 (0.18), residues: 768
  sheet: -1.00 (0.71), residues: 51
  loop : -1.70 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP K 748 
 HIS   0.009   0.001   HIS K 387 
 PHE   0.036   0.002   PHE D  67 
 TYR   0.027   0.002   TYR K 311 
 ARG   0.011   0.001   ARG K 531 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04403 (  861)
  hydrogen bonds       : angle       3.96392 ( 2278)
  covalent geometry    : bond        0.00354 (14582)
  covalent geometry    : angle       0.69409 (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
  264 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 1.318 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8577 (t80) cc_final: 0.8336 (t80)
REVERT: A   86 SER cc_start: 0.8457 (m) cc_final: 0.8176 (t)
REVERT: A   92 LEU cc_start: 0.8446 (mt) cc_final: 0.8229 (mp)
REVERT: A  109 LEU cc_start: 0.8849 (tp) cc_final: 0.8532 (tp)
REVERT: A  133 GLU cc_start: 0.5873 (pm20) cc_final: 0.5548 (pt0)
REVERT: B   75 HIS cc_start: 0.8986 (t70) cc_final: 0.8729 (t-90)
REVERT: B   84 MET cc_start: 0.7136 (tpp) cc_final: 0.6086 (tpp)
REVERT: B   91 LYS cc_start: 0.7915 (tmmt) cc_final: 0.7563 (tttt)
REVERT: B   98 TYR cc_start: 0.6857 (m-10) cc_final: 0.6435 (m-10)
REVERT: C   72 LEU cc_start: 0.7893 (mp) cc_final: 0.7501 (tp)
REVERT: D  130 GLU cc_start: 0.6860 (mp0) cc_final: 0.6332 (mt-10)
REVERT: E   79 LYS cc_start: 0.6851 (tttt) cc_final: 0.6515 (tptm)
REVERT: E   83 ARG cc_start: 0.7285 (tpp-160) cc_final: 0.6768 (tpp-160)
REVERT: E  128 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7596 (mmm-85)
REVERT: E  133 GLU cc_start: 0.6688 (pm20) cc_final: 0.5739 (pt0)
REVERT: G   38 ARG cc_start: 0.6387 (ttt180) cc_final: 0.6080 (tpp80)
REVERT: G   59 TYR cc_start: 0.7589 (t80) cc_final: 0.7387 (t80)
REVERT: G   60 MET cc_start: 0.7730 (ptm) cc_final: 0.7429 (ptm)
REVERT: G   73 GLU cc_start: 0.6750 (pt0) cc_final: 0.6449 (pt0)
REVERT: G   83 LYS cc_start: 0.7829 (mmmm) cc_final: 0.6681 (ptpp)
REVERT: G   90 ARG cc_start: 0.7323 (tpm170) cc_final: 0.7000 (tpm170)
REVERT: G   99 ASP cc_start: 0.6808 (t0) cc_final: 0.6414 (t0)
REVERT: H   87 MET cc_start: 0.8451 (tpp) cc_final: 0.8194 (tmm)
REVERT: H   94 ILE cc_start: 0.8581 (mm) cc_final: 0.8307 (mm)
REVERT: H  118 GLU cc_start: 0.8279 (mp0) cc_final: 0.7563 (mp0)
REVERT: H  127 LEU cc_start: 0.7947 (mm) cc_final: 0.7696 (mp)
REVERT: K  205 TYR cc_start: 0.6987 (m-10) cc_final: 0.6627 (m-10)
REVERT: K  249 LEU cc_start: 0.8056 (mt) cc_final: 0.7800 (tp)
REVERT: K  320 ARG cc_start: 0.7219 (mtm180) cc_final: 0.6964 (mtp85)
REVERT: K  373 TRP cc_start: 0.6586 (t-100) cc_final: 0.6206 (t-100)
REVERT: K  384 PHE cc_start: 0.8348 (m-80) cc_final: 0.6847 (m-80)
REVERT: K  409 GLU cc_start: 0.4120 (mm-30) cc_final: 0.3777 (pm20)
REVERT: K  596 PHE cc_start: 0.7867 (t80) cc_final: 0.7611 (t80)
REVERT: K  623 ASN cc_start: 0.7336 (t0) cc_final: 0.7000 (t0)
REVERT: K  744 LYS cc_start: 0.6899 (ptpp) cc_final: 0.6252 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 264
  average time/residue: 0.2532
  time to fit residues: 97.7399
Evaluate side-chains
  192 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.276 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 120 optimal weight:    0.8980
   chunk 85 optimal weight:    0.5980
   chunk 98 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 107 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 81 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 54 optimal weight:    9.9990
   overall best weight:    2.2584

-------------------------------------------------------------------------------
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 247 ASN
K 625 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.068666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.052075 restraints weight = 84707.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.053673 restraints weight = 45669.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.054672 restraints weight = 30097.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.7265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  14582  Z= 0.175
  Angle     :  0.704  12.045  20617  Z= 0.387
  Chirality :  0.041   0.196   2338
  Planarity :  0.005   0.044   1836
  Dihedral  : 28.458 137.454   3682
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.47 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  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:  0.11 (0.24), residues: 1142
  helix:  0.94 (0.18), residues: 761
  sheet: -1.23 (0.69), residues: 51
  loop : -1.70 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP K 748 
 HIS   0.011   0.002   HIS K 387 
 PHE   0.034   0.002   PHE C  42 
 TYR   0.032   0.002   TYR H  65 
 ARG   0.010   0.001   ARG K 531 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04566 (  861)
  hydrogen bonds       : angle       3.99400 ( 2278)
  covalent geometry    : bond        0.00395 (14582)
  covalent geometry    : angle       0.70386 (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
  242 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 1.294 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8656 (t80) cc_final: 0.8421 (t80)
REVERT: A   86 SER cc_start: 0.8369 (m) cc_final: 0.8107 (t)
REVERT: A  133 GLU cc_start: 0.5803 (pm20) cc_final: 0.5491 (pt0)
REVERT: B   75 HIS cc_start: 0.8933 (t70) cc_final: 0.8476 (t-90)
REVERT: B   84 MET cc_start: 0.6887 (tpp) cc_final: 0.6140 (tpp)
REVERT: B   91 LYS cc_start: 0.7985 (tmmt) cc_final: 0.7631 (tttt)
REVERT: B   98 TYR cc_start: 0.7071 (m-10) cc_final: 0.6585 (m-10)
REVERT: C   72 LEU cc_start: 0.7888 (mp) cc_final: 0.7483 (tp)
REVERT: D  130 GLU cc_start: 0.7016 (mp0) cc_final: 0.6423 (mt-10)
REVERT: E   79 LYS cc_start: 0.6841 (tttt) cc_final: 0.6293 (mmtt)
REVERT: E   83 ARG cc_start: 0.7361 (tpp-160) cc_final: 0.6798 (tpp-160)
REVERT: E  133 GLU cc_start: 0.6685 (pm20) cc_final: 0.5808 (pt0)
REVERT: G   38 ARG cc_start: 0.6439 (ttt180) cc_final: 0.6060 (tpp80)
REVERT: G   83 LYS cc_start: 0.7853 (mmmm) cc_final: 0.6733 (ptpp)
REVERT: G   90 ARG cc_start: 0.7186 (tpm170) cc_final: 0.6923 (tpm170)
REVERT: G   99 ASP cc_start: 0.6753 (t0) cc_final: 0.6383 (t0)
REVERT: H   87 MET cc_start: 0.8551 (tpp) cc_final: 0.8027 (tmm)
REVERT: H   91 ILE cc_start: 0.8383 (tp) cc_final: 0.8151 (tp)
REVERT: H   94 ILE cc_start: 0.8494 (mm) cc_final: 0.8200 (mm)
REVERT: H  118 GLU cc_start: 0.8326 (mp0) cc_final: 0.7561 (mp0)
REVERT: H  127 LEU cc_start: 0.7922 (mm) cc_final: 0.7590 (mp)
REVERT: K  205 TYR cc_start: 0.7140 (m-10) cc_final: 0.6772 (m-10)
REVERT: K  315 MET cc_start: 0.7463 (tpp) cc_final: 0.6716 (tpp)
REVERT: K  320 ARG cc_start: 0.7349 (mtm180) cc_final: 0.6753 (mtt90)
REVERT: K  373 TRP cc_start: 0.6578 (t-100) cc_final: 0.6217 (t-100)
REVERT: K  380 LEU cc_start: 0.7474 (mp) cc_final: 0.6856 (mt)
REVERT: K  384 PHE cc_start: 0.8420 (m-80) cc_final: 0.6945 (m-80)
REVERT: K  409 GLU cc_start: 0.4079 (mm-30) cc_final: 0.3497 (pm20)
REVERT: K  623 ASN cc_start: 0.7348 (t0) cc_final: 0.7035 (t0)
REVERT: K  744 LYS cc_start: 0.6917 (ptpp) cc_final: 0.6368 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.2395
  time to fit residues: 85.8446
Evaluate side-chains
  189 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 36 optimal weight:    0.9980
   chunk 80 optimal weight:   10.0000
   chunk 122 optimal weight:    4.9990
   chunk 108 optimal weight:    8.9990
   chunk 96 optimal weight:   10.0000
   chunk 114 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 127 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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 471 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 = 0.3419 r_free = 0.3419 target = 0.067972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.051311 restraints weight = 85321.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.052874 restraints weight = 45765.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.053840 restraints weight = 30169.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.7515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  14582  Z= 0.199
  Angle     :  0.734  12.908  20617  Z= 0.401
  Chirality :  0.042   0.227   2338
  Planarity :  0.005   0.066   1836
  Dihedral  : 28.582 138.456   3682
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.55 %
    Favored  : 95.27 %
  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: -0.15 (0.24), residues: 1142
  helix:  0.77 (0.18), residues: 760
  sheet: -1.74 (0.61), residues: 57
  loop : -1.77 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.004   TRP K 748 
 HIS   0.012   0.002   HIS K 387 
 PHE   0.038   0.002   PHE D  67 
 TYR   0.033   0.002   TYR H  65 
 ARG   0.009   0.001   ARG K 531 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05047 (  861)
  hydrogen bonds       : angle       4.12366 ( 2278)
  covalent geometry    : bond        0.00452 (14582)
  covalent geometry    : angle       0.73394 (20617)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3997.87 seconds
wall clock time: 70 minutes 54.34 seconds (4254.34 seconds total)