Starting phenix.real_space_refine
on Thu Mar  5 17:16:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zpj_14855/03_2026/7zpj_14855.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zpj_14855/03_2026/7zpj_14855.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zpj_14855/03_2026/7zpj_14855.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zpj_14855/03_2026/7zpj_14855.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zpj_14855/03_2026/7zpj_14855.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zpj_14855/03_2026/7zpj_14855.cif"
  }
  resolution = 3.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      55      5.49       5
     S      63      5.16       5
     C    7428      2.51       5
     N    2043      2.21       5
     O    2382      1.98       5
     H   11508      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 23479
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 20612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1280, 20612
          Classifications: {'peptide': 1280}
          Link IDs: {'PTRANS': 76, 'TRANS': 1203}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "B"
      Number of atoms: 1763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 1763
          Classifications: {'RNA': 55}
          Modifications used: {'3*END': 1, 'rna3p_pur': 28, 'rna3p_pyr': 27}
          Link IDs: {'rna3p': 54}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1104
          Classifications: {'peptide': 75}
          Link IDs: {'PCIS': 1, 'TRANS': 73}
  Time building chain proxies: 3.55, per 1000 atoms: 0.15
  Number of scatterers: 23479
  At special positions: 0
  Unit cell: (98.53, 122.745, 163.66, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      63     16.00
     P      55     15.00
     O    2382      8.00
     N    2043      7.00
     C    7428      6.00
     H   11508      1.00
    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: 2.10
  Conformation dependent library (CDL) restraints added in 658.3 milliseconds
  

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2600

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 10 sheets defined
      53.6% alpha, 12.4% beta
      17 base pairs and 24 stacking pairs defined.
    Time for finding SS restraints: 3.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 58
    Processing helix  chain 'A' and resid 66 through 82
      removed outlier: 3.527A  pdb=" N   LYS A  70 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 85
      No H-bonds generated for 'chain 'A' and resid 83 through 85'
    Processing helix  chain 'A' and resid 102 through 117
    Processing helix  chain 'A' and resid 126 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 4.147A  pdb=" N   GLN A 140 " --> pdb=" O   GLU A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 162
    Processing helix  chain 'A' and resid 177 through 181
    Processing helix  chain 'A' and resid 184 through 196
      removed outlier: 4.292A  pdb=" N   GLU A 188 " --> pdb=" O   HIS A 184 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   CYS A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 231
      removed outlier: 5.037A  pdb=" N   GLU A 220 " --> pdb=" O   PRO A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 247
    Processing helix  chain 'A' and resid 265 through 284
    Processing helix  chain 'A' and resid 294 through 314
    Processing helix  chain 'A' and resid 314 through 334
      removed outlier: 3.855A  pdb=" N   LYS A 331 " --> pdb=" O   ARG A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 361
    Processing helix  chain 'A' and resid 369 through 373
    Processing helix  chain 'A' and resid 374 through 386
      removed outlier: 3.653A  pdb=" N   LYS A 386 " --> pdb=" O   GLU A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 468
    Processing helix  chain 'A' and resid 498 through 510
      removed outlier: 3.661A  pdb=" N   GLU A 502 " --> pdb=" O   PHE A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 513
      No H-bonds generated for 'chain 'A' and resid 511 through 513'
    Processing helix  chain 'A' and resid 520 through 524
    Processing helix  chain 'A' and resid 542 through 551
    Processing helix  chain 'A' and resid 565 through 592
      removed outlier: 3.981A  pdb=" N   LYS A 570 " --> pdb=" O   THR A 566 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   SER A 571 " --> pdb=" O   ASP A 567 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   GLU A 574 " --> pdb=" O   LYS A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 641
      removed outlier: 4.317A  pdb=" N   GLY A 632 " --> pdb=" O   ASN A 628 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU A 641 " --> pdb=" O   TYR A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 706
      removed outlier: 3.565A  pdb=" N   LYS A 701 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 839 through 859
    Processing helix  chain 'A' and resid 893 through 902
    Processing helix  chain 'A' and resid 967 through 976
    Processing helix  chain 'A' and resid 1044 through 1053
      removed outlier: 4.085A  pdb=" N   CYS A1053 " --> pdb=" O   ARG A1049 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1053 through 1076
    Processing helix  chain 'A' and resid 1293 through 1302
    Processing helix  chain 'A' and resid 1303 through 1307
    Processing helix  chain 'A' and resid 1313 through 1335
    Processing helix  chain 'A' and resid 1339 through 1351
    Processing helix  chain 'A' and resid 1352 through 1363
    Processing helix  chain 'A' and resid 1364 through 1368
    Processing helix  chain 'A' and resid 1552 through 1583
      removed outlier: 3.659A  pdb=" N   GLY A1571 " --> pdb=" O   LEU A1567 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   GLU A1572 " --> pdb=" O   THR A1568 " (cutoff:3.500A)
      removed outlier: 8.993A  pdb=" N   ARG A1573 " --> pdb=" O   SER A1569 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   ALA A1574 " --> pdb=" O   CYS A1570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1648 through 1657
    Processing helix  chain 'A' and resid 1660 through 1668
      removed outlier: 3.728A  pdb=" N   LYS A1666 " --> pdb=" O   THR A1662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1674 through 1682
      removed outlier: 3.787A  pdb=" N   LEU A1678 " --> pdb=" O   LYS A1674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1695 through 1716
      removed outlier: 3.616A  pdb=" N   PHE A1700 " --> pdb=" O   GLN A1696 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LEU A1701 " --> pdb=" O   ARG A1697 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA A1704 " --> pdb=" O   PHE A1700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1722 through 1735
    Processing helix  chain 'A' and resid 1735 through 1746
    Processing helix  chain 'A' and resid 1747 through 1752
      removed outlier: 4.020A  pdb=" N   TYR A1751 " --> pdb=" O   ASP A1747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1756 through 1773
      removed outlier: 3.590A  pdb=" N   LYS A1768 " --> pdb=" O   ASP A1764 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LYS A1773 " --> pdb=" O   PHE A1769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1799 through 1817
      removed outlier: 3.868A  pdb=" N   GLY A1803 " --> pdb=" O   PRO A1799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1820 through 1842
      removed outlier: 3.509A  pdb=" N   VAL A1824 " --> pdb=" O   SER A1820 " (cutoff:3.500A)
      Proline residue:  A1830  - end of helix
      Proline residue:  A1834  - end of helix
      removed outlier: 3.933A  pdb=" N   LYS A1838 " --> pdb=" O   PRO A1834 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1846 through 1855
    Processing helix  chain 'A' and resid 1890 through 1910
    Processing helix  chain 'D' and resid 292 through 304
    Processing helix  chain 'D' and resid 342 through 364
    Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 124
      removed outlier: 3.942A  pdb=" N   THR A 151 " --> pdb=" O   TYR A 124 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   THR A  96 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   MET A 150 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   PHE A  98 " --> pdb=" O   MET A 150 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   ARG A  95 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   LEU A 171 " --> pdb=" O   ARG A  95 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL A  97 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL A 173 " --> pdb=" O   VAL A  97 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASP A 175 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   THR A  60 " --> pdb=" O   GLY A 204 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   THR A 206 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   VAL A  62 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   ILE A  61 " --> pdb=" O   GLU A 235 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 251 through 256
      removed outlier: 6.166A  pdb=" N   CYS A 251 " --> pdb=" O   TYR A 560 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   MET A 562 " --> pdb=" O   CYS A 251 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ILE A 253 " --> pdb=" O   MET A 562 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   ALA A 564 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 5.671A  pdb=" N   VAL A 255 " --> pdb=" O   ALA A 564 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ILE A 445 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ASN A 477 " --> pdb=" O   ILE A 517 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 652 through 656
    Processing sheet with id=AA4, first strand: chain 'A' and resid 746 through 750
    Processing sheet with id=AA5, first strand: chain 'A' and resid 816 through 820
      removed outlier: 3.800A  pdb=" N   PHE A 816 " --> pdb=" O   ILE A 827 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   GLU A 824 " --> pdb=" O   THR A 778 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LYS A 832 " --> pdb=" O   LEU A 770 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   LEU A 770 " --> pdb=" O   LYS A 832 " (cutoff:3.500A)
      removed outlier: 5.199A  pdb=" N   SER A 834 " --> pdb=" O   CYS A 768 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   CYS A 768 " --> pdb=" O   SER A 834 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   PHE A 802 " --> pdb=" O   ILE A 773 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   THR A 889 " --> pdb=" O   VAL A 884 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 865 through 867
    Processing sheet with id=AA7, first strand: chain 'A' and resid 987 through 992
      removed outlier: 6.176A  pdb=" N   ASP A 991 " --> pdb=" O   VAL A 947 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   VAL A 947 " --> pdb=" O   ASP A 991 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1859 through 1861
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1859 through 1861
    Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 312

    581 hydrogen bonds defined for protein.
    1671 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      42 hydrogen bonds
      68 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      24 stacking parallelities
  Total time for adding SS restraints: 5.45

  Time building geometry restraints manager: 2.93 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 11467
        1.02 -     1.22: 49
        1.22 -     1.42: 5060
        1.42 -     1.62: 7181
        1.62 -     1.82: 85
  Bond restraints: 23842
  Sorted by residual:
  bond pdb=" NH1 ARG A  86 "
       pdb="HH12 ARG A  86 "
    ideal  model  delta    sigma   weight residual
    0.860  0.819  0.041 2.00e-02 2.50e+03 4.11e+00
  bond pdb=" NH1 ARG A 800 "
       pdb="HH12 ARG A 800 "
    ideal  model  delta    sigma   weight residual
    0.860  0.826  0.034 2.00e-02 2.50e+03 2.89e+00
  bond pdb=" NE2 GLN A 985 "
       pdb="HE22 GLN A 985 "
    ideal  model  delta    sigma   weight residual
    0.860  0.828  0.032 2.00e-02 2.50e+03 2.59e+00
  bond pdb=" C   ILE A 773 "
       pdb=" N   GLY A 774 "
    ideal  model  delta    sigma   weight residual
    1.330  1.319  0.011 8.80e-03 1.29e+04 1.67e+00
  bond pdb=" NH2 ARG A 640 "
       pdb="HH22 ARG A 640 "
    ideal  model  delta    sigma   weight residual
    0.860  0.835  0.025 2.00e-02 2.50e+03 1.62e+00
  ... (remaining 23837 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.58: 43165
        7.58 -    15.17: 6
       15.17 -    22.75: 0
       22.75 -    30.33: 2
       30.33 -    37.91: 4
  Bond angle restraints: 43177
  Sorted by residual:
  angle pdb=" CB  ALA A 464 "
        pdb=" CA  ALA A 464 "
        pdb=" HA  ALA A 464 "
      ideal   model   delta    sigma   weight residual
     109.00   71.09   37.91 3.00e+00 1.11e-01 1.60e+02
  angle pdb=" N   ALA A 464 "
        pdb=" CA  ALA A 464 "
        pdb=" HA  ALA A 464 "
      ideal   model   delta    sigma   weight residual
     110.00   75.34   34.66 3.00e+00 1.11e-01 1.34e+02
  angle pdb=" O3'   G B  26 "
        pdb=" C3'   G B  26 "
        pdb=" H3'   G B  26 "
      ideal   model   delta    sigma   weight residual
     109.00   76.55   32.45 3.00e+00 1.11e-01 1.17e+02
  angle pdb=" C   ALA A 464 "
        pdb=" CA  ALA A 464 "
        pdb=" HA  ALA A 464 "
      ideal   model   delta    sigma   weight residual
     109.00   77.57   31.43 3.00e+00 1.11e-01 1.10e+02
  angle pdb=" C2'   G B  26 "
        pdb=" C3'   G B  26 "
        pdb=" H3'   G B  26 "
      ideal   model   delta    sigma   weight residual
     109.00   79.64   29.36 3.00e+00 1.11e-01 9.58e+01
  ... (remaining 43172 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.91: 10952
       35.91 -    71.81: 343
       71.81 -   107.72: 23
      107.72 -   143.63: 1
      143.63 -   179.53: 9
  Dihedral angle restraints: 11328
    sinusoidal: 6674
      harmonic: 4654
  Sorted by residual:
  dihedral pdb=" O4'   U B  27 "
           pdb=" C1'   U B  27 "
           pdb=" N1    U B  27 "
           pdb=" C2    U B  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   55.37  144.63     1      1.50e+01 4.44e-03 7.75e+01
  dihedral pdb=" O4'   U B  28 "
           pdb=" C1'   U B  28 "
           pdb=" N1    U B  28 "
           pdb=" C2    U B  28 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   60.31  139.69     1      1.50e+01 4.44e-03 7.52e+01
  dihedral pdb=" CG  TRP A 316 "
           pdb=" CD2 TRP A 316 "
           pdb=" CE3 TRP A 316 "
           pdb=" HE3 TRP A 316 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   24.94  -24.94     0      5.00e+00 4.00e-02 2.49e+01
  ... (remaining 11325 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.183: 1970
       0.183 -    0.365: 12
       0.365 -    0.548: 0
       0.548 -    0.730: 0
       0.730 -    0.913: 1
  Chirality restraints: 1983
  Sorted by residual:
  chirality pdb=" C3'   G B  26 "
            pdb=" C4'   G B  26 "
            pdb=" O3'   G B  26 "
            pdb=" C2'   G B  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.56   -0.91 2.00e-01 2.50e+01 2.08e+01
  chirality pdb=" CA  ALA A 464 "
            pdb=" N   ALA A 464 "
            pdb=" C   ALA A 464 "
            pdb=" CB  ALA A 464 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.18    0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" P     U B  28 "
            pdb=" OP1   U B  28 "
            pdb=" OP2   U B  28 "
            pdb=" O5'   U B  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.71   -0.30 2.00e-01 2.50e+01 2.25e+00
  ... (remaining 1980 not shown)

  Planarity restraints: 3263
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 316 "    0.028 2.00e-02 2.50e+03   6.16e-02 1.52e+02
        pdb=" CG  TRP A 316 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 316 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 316 "   -0.023 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 316 "   -0.055 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 316 "   -0.040 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 316 "    0.120 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 316 "   -0.061 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 316 "   -0.105 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 316 "   -0.077 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 316 "   -0.015 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 316 "    0.046 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 316 "   -0.057 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 316 "    0.063 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 316 "    0.054 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 316 "    0.082 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  86 "   -0.268 9.50e-02 1.11e+02   1.16e-01 1.30e+02
        pdb=" NE  ARG A  86 "   -0.081 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  86 "    0.082 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  86 "    0.126 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  86 "    0.043 2.00e-02 2.50e+03
        pdb="HH11 ARG A  86 "    0.011 2.00e-02 2.50e+03
        pdb="HH12 ARG A  86 "   -0.125 2.00e-02 2.50e+03
        pdb="HH21 ARG A  86 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A  86 "   -0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 187 "   -0.421 9.50e-02 1.11e+02   1.51e-01 9.05e+01
        pdb=" NE  ARG A 187 "   -0.052 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 187 "    0.053 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 187 "    0.077 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 187 "    0.080 2.00e-02 2.50e+03
        pdb="HH11 ARG A 187 "    0.002 2.00e-02 2.50e+03
        pdb="HH12 ARG A 187 "   -0.062 2.00e-02 2.50e+03
        pdb="HH21 ARG A 187 "    0.003 2.00e-02 2.50e+03
        pdb="HH22 ARG A 187 "   -0.082 2.00e-02 2.50e+03
  ... (remaining 3260 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 1023
        2.18 -     2.78: 46703
        2.78 -     3.39: 65218
        3.39 -     3.99: 81336
        3.99 -     4.60: 127023
  Nonbonded interactions: 321303
  Sorted by model distance:
  nonbonded pdb="HH21 ARG A 935 "
            pdb=" O   GLU A1036 "
     model   vdw
     1.574 2.450
  nonbonded pdb=" HG1 THR A1867 "
            pdb=" OD1 ASP A1869 "
     model   vdw
     1.582 2.450
  nonbonded pdb=" O   LEU A1678 "
            pdb=" HG1 THR A1682 "
     model   vdw
     1.594 2.450
  nonbonded pdb=" O   GLU A 542 "
            pdb=" HG  SER A 545 "
     model   vdw
     1.603 2.450
  nonbonded pdb=" OE1 GLU A 866 "
            pdb=" HZ2 LYS A 868 "
     model   vdw
     1.605 2.450
  ... (remaining 321298 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             3.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.130
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.090
  Set scattering table:                    0.070
  Process input model:                     24.050
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3446
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      :  0.004   0.047  12334  Z= 0.229
  Angle     :  0.864  10.310  16970  Z= 0.501
  Chirality :  0.054   0.913   1983
  Planarity :  0.015   0.245   1955
  Dihedral  : 15.404 144.630   5027
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  2.49 %
    Favored  : 96.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.22), residues: 1333
  helix:  0.77 (0.18), residues: 672
  sheet: -0.58 (0.37), residues: 180
  loop : -0.28 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.066   0.006   ARG A 459 
 TYR   0.039   0.007   TYR A1676 
 PHE   0.055   0.004   PHE A 537 
 TRP   0.116   0.010   TRP A 316 
 HIS   0.016   0.003   HIS A1749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 (12334)
  covalent geometry    : angle       0.86424 (16970)
  hydrogen bonds       : bond        0.13178 (  621)
  hydrogen bonds       : angle       5.40087 ( 1739)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  246 is missing expected H atoms. Skipping.
Residue THR  247 is missing expected H atoms. Skipping.
Residue SER  248 is missing expected H atoms. Skipping.
Evaluate side-chains
  216 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 208
  time to evaluate  : 0.567 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
REVERT: A  269 ARG cc_start: 0.8394 (ttt180) cc_final: 0.7666 (mtm180)
REVERT: A  272 MET cc_start: 0.7855 (mtp) cc_final: 0.7155 (mtp)
REVERT: A  377 VAL cc_start: 0.8626 (t) cc_final: 0.8383 (m)
REVERT: A  379 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8277 (mmtm)
REVERT: A  503 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7179 (mt-10)
REVERT: A  710 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7581 (tp30)
REVERT: A  897 MET cc_start: 0.5371 (mtm) cc_final: 0.4778 (tmm)
REVERT: A  940 ASP cc_start: 0.2701 (OUTLIER) cc_final: 0.2307 (m-30)
REVERT: A 1368 ARG cc_start: 0.4125 (mmt90) cc_final: 0.3898 (mpt-90)
REVERT: A 1825 TRP cc_start: 0.2199 (t-100) cc_final: 0.1941 (t60)
  outliers start: 8
  outliers final: 5
  residues processed: 215
  average time/residue: 0.2806
  time to fit residues: 81.8905
Evaluate side-chains
  174 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 168
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  940 ASP
Chi-restraints excluded: chain D residue  364 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    0.0070
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0370
   overall best weight:    0.4476

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.190047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.152906 restraints weight = 67934.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.160835 restraints weight = 30896.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.165913 restraints weight = 16875.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.169061 restraints weight = 10449.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.171109 restraints weight = 7259.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.4403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3726
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12334  Z= 0.131
  Angle     :  0.584   7.311  16970  Z= 0.307
  Chirality :  0.043   0.773   1983
  Planarity :  0.005   0.094   1955
  Dihedral  : 15.813 152.507   2360
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  6.57 %
    Favored  : 92.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.23), residues: 1333
  helix:  1.49 (0.19), residues: 673
  sheet: -0.38 (0.38), residues: 182
  loop : -0.06 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 353 
 TYR   0.020   0.001   TYR A1746 
 PHE   0.050   0.002   PHE A 142 
 TRP   0.013   0.002   TRP A 316 
 HIS   0.005   0.001   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (12334)
  covalent geometry    : angle       0.58368 (16970)
  hydrogen bonds       : bond        0.05245 (  621)
  hydrogen bonds       : angle       4.58075 ( 1739)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  246 is missing expected H atoms. Skipping.
Residue THR  247 is missing expected H atoms. Skipping.
Residue SER  248 is missing expected H atoms. Skipping.
Evaluate side-chains
  187 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 179
  time to evaluate  : 0.507 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.7922 (mtp) cc_final: 0.7254 (mtp)
REVERT: A  503 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7227 (mt-10)
REVERT: A 1671 PHE cc_start: 0.4646 (m-10) cc_final: 0.4440 (m-10)
REVERT: A 1800 LYS cc_start: 0.7557 (tttp) cc_final: 0.7235 (tptp)
  outliers start: 8
  outliers final: 6
  residues processed: 185
  average time/residue: 0.2722
  time to fit residues: 69.3161
Evaluate side-chains
  172 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 166
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  748 CYS
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  958 SER
Chi-restraints excluded: chain A residue 1722 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 94 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 100 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A1548 GLN
** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.189570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.152305 restraints weight = 68083.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.160351 restraints weight = 31042.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.165403 restraints weight = 16957.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.168602 restraints weight = 10508.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.170738 restraints weight = 7284.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.4406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4160
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12334  Z= 0.153
  Angle     :  0.586   7.585  16970  Z= 0.311
  Chirality :  0.043   0.766   1983
  Planarity :  0.005   0.058   1955
  Dihedral  : 15.705 155.361   2353
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  7.15 %
    Favored  : 91.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.23), residues: 1333
  helix:  1.30 (0.19), residues: 679
  sheet: -0.96 (0.36), residues: 197
  loop :  0.13 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 459 
 TYR   0.020   0.002   TYR A1828 
 PHE   0.041   0.002   PHE A 142 
 TRP   0.009   0.002   TRP A 138 
 HIS   0.005   0.001   HIS A 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (12334)
  covalent geometry    : angle       0.58561 (16970)
  hydrogen bonds       : bond        0.04856 (  621)
  hydrogen bonds       : angle       4.56514 ( 1739)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  246 is missing expected H atoms. Skipping.
Residue THR  247 is missing expected H atoms. Skipping.
Residue SER  248 is missing expected H atoms. Skipping.
Evaluate side-chains
  193 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 179
  time to evaluate  : 0.518 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
REVERT: A  272 MET cc_start: 0.8033 (mtp) cc_final: 0.7375 (mtp)
REVERT: A  307 ARG cc_start: 0.7646 (ttt-90) cc_final: 0.7279 (ttp80)
REVERT: A  373 VAL cc_start: 0.2975 (OUTLIER) cc_final: 0.2721 (t)
REVERT: A  379 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8128 (mmtt)
REVERT: A  503 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7336 (mt-10)
REVERT: A 1036 GLU cc_start: 0.5198 (tp30) cc_final: 0.4960 (tp30)
REVERT: A 1363 LYS cc_start: 0.7324 (mmtt) cc_final: 0.6919 (mmtm)
REVERT: A 1558 CYS cc_start: 0.2135 (OUTLIER) cc_final: 0.1759 (t)
REVERT: A 1800 LYS cc_start: 0.7608 (tttp) cc_final: 0.7175 (tptp)
REVERT: A 1816 ASP cc_start: 0.2503 (OUTLIER) cc_final: 0.1231 (t70)
REVERT: A 1825 TRP cc_start: 0.2524 (t-100) cc_final: 0.0477 (t-100)
  outliers start: 14
  outliers final: 11
  residues processed: 187
  average time/residue: 0.2906
  time to fit residues: 73.8104
Evaluate side-chains
  176 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 162
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1558 CYS
Chi-restraints excluded: chain A residue 1682 THR
Chi-restraints excluded: chain A residue 1722 SER
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  352 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 132 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 133 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 35 optimal weight:    0.2980
   chunk 12 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0970
   chunk 33 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 648 HIS
A 943 HIS
A1299 GLN
A1654 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.189004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.152461 restraints weight = 68153.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.160401 restraints weight = 31026.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.165501 restraints weight = 16915.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.168714 restraints weight = 10445.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.170754 restraints weight = 7225.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.4401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4465
moved from start:          0.4976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  12334  Z= 0.162
  Angle     :  0.594   8.738  16970  Z= 0.312
  Chirality :  0.043   0.782   1983
  Planarity :  0.005   0.047   1955
  Dihedral  : 15.709 158.517   2353
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  7.81 %
    Favored  : 90.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.23), residues: 1333
  helix:  1.30 (0.20), residues: 679
  sheet: -1.00 (0.36), residues: 199
  loop :  0.16 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  86 
 TYR   0.018   0.002   TYR A1828 
 PHE   0.037   0.002   PHE A 142 
 TRP   0.007   0.002   TRP A 316 
 HIS   0.007   0.001   HIS A1325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (12334)
  covalent geometry    : angle       0.59388 (16970)
  hydrogen bonds       : bond        0.04427 (  621)
  hydrogen bonds       : angle       4.45385 ( 1739)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  246 is missing expected H atoms. Skipping.
Residue THR  247 is missing expected H atoms. Skipping.
Residue SER  248 is missing expected H atoms. Skipping.
Evaluate side-chains
  188 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 172
  time to evaluate  : 0.573 
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: symmetry clash
   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: symmetry clash
   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: 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  168 ASP cc_start: 0.7003 (m-30) cc_final: 0.6045 (p0)
REVERT: A  272 MET cc_start: 0.8067 (mtp) cc_final: 0.7467 (mtp)
REVERT: A  307 ARG cc_start: 0.7958 (ttt-90) cc_final: 0.7475 (ttp80)
REVERT: A  379 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8197 (mmtt)
REVERT: A  382 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7775 (mm-30)
REVERT: A  503 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7403 (mt-10)
REVERT: A  747 GLN cc_start: 0.7218 (tp40) cc_final: 0.6697 (tm-30)
REVERT: A 1058 LEU cc_start: 0.3999 (OUTLIER) cc_final: 0.2089 (pp)
REVERT: A 1316 GLU cc_start: 0.5577 (tt0) cc_final: 0.5104 (tm-30)
REVERT: A 1363 LYS cc_start: 0.7328 (mmtt) cc_final: 0.7033 (mmtm)
REVERT: A 1661 GLU cc_start: 0.7396 (tp30) cc_final: 0.7125 (tm-30)
REVERT: A 1816 ASP cc_start: 0.3164 (OUTLIER) cc_final: 0.2454 (t70)
REVERT: A 1831 MET cc_start: 0.4244 (mmt) cc_final: 0.3952 (tpp)
REVERT: A 1854 MET cc_start: 0.6806 (mmm) cc_final: 0.6604 (mmm)
  outliers start: 16
  outliers final: 11
  residues processed: 181
  average time/residue: 0.2678
  time to fit residues: 66.4615
Evaluate side-chains
  177 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 164
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  177 CYS
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1354 CYS
Chi-restraints excluded: chain A residue 1682 THR
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  355 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 109 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.187871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.151314 restraints weight = 68954.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.159181 restraints weight = 31834.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.164327 restraints weight = 17549.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.167540 restraints weight = 10869.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.169658 restraints weight = 7515.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.4395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4918
moved from start:          0.6511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.107  12334  Z= 0.217
  Angle     :  0.656  10.995  16970  Z= 0.353
  Chirality :  0.045   0.780   1983
  Planarity :  0.006   0.063   1955
  Dihedral  : 15.819 159.401   2353
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.73 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  :  9.73 %
    Favored  : 88.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.23), residues: 1333
  helix:  0.92 (0.20), residues: 680
  sheet: -1.20 (0.36), residues: 194
  loop : -0.24 (0.31), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 789 
 TYR   0.036   0.002   TYR A1828 
 PHE   0.025   0.002   PHE A 142 
 TRP   0.010   0.003   TRP A1380 
 HIS   0.010   0.001   HIS A1325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (12334)
  covalent geometry    : angle       0.65611 (16970)
  hydrogen bonds       : bond        0.04811 (  621)
  hydrogen bonds       : angle       4.76891 ( 1739)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  246 is missing expected H atoms. Skipping.
Residue THR  247 is missing expected H atoms. Skipping.
Residue SER  248 is missing expected H atoms. Skipping.
Evaluate side-chains
  226 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 199
  time to evaluate  : 0.620 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
REVERT: A   70 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7684 (tttp)
REVERT: A  140 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.6148 (pm20)
REVERT: A  168 ASP cc_start: 0.7455 (m-30) cc_final: 0.6658 (p0)
REVERT: A  268 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7992 (tm-30)
REVERT: A  307 ARG cc_start: 0.7851 (ttt-90) cc_final: 0.7620 (ttp80)
REVERT: A  316 TRP cc_start: 0.6403 (t60) cc_final: 0.5414 (t60)
REVERT: A  360 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7703 (mm-30)
REVERT: A  379 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8253 (mmtt)
REVERT: A  503 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7561 (mt-10)
REVERT: A  537 PHE cc_start: 0.6808 (OUTLIER) cc_final: 0.6589 (m-80)
REVERT: A  747 GLN cc_start: 0.7323 (tp40) cc_final: 0.6722 (tm-30)
REVERT: A 1316 GLU cc_start: 0.5899 (tt0) cc_final: 0.5291 (tm-30)
REVERT: A 1354 CYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6494 (m)
REVERT: A 1368 ARG cc_start: 0.7128 (mpt180) cc_final: 0.6694 (mmt180)
REVERT: A 1726 LEU cc_start: 0.3414 (OUTLIER) cc_final: 0.3081 (tp)
REVERT: A 1802 MET cc_start: 0.6279 (mmp) cc_final: 0.6018 (mmp)
REVERT: A 1816 ASP cc_start: 0.4079 (OUTLIER) cc_final: 0.3523 (t70)
REVERT: A 1854 MET cc_start: 0.6910 (mmm) cc_final: 0.6693 (mmm)
  outliers start: 27
  outliers final: 20
  residues processed: 215
  average time/residue: 0.2703
  time to fit residues: 80.5528
Evaluate side-chains
  211 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 185
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  177 CYS
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  387 TYR
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  771 TYR
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  791 LYS
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1354 CYS
Chi-restraints excluded: chain A residue 1558 CYS
Chi-restraints excluded: chain A residue 1587 LEU
Chi-restraints excluded: chain A residue 1682 THR
Chi-restraints excluded: chain A residue 1700 PHE
Chi-restraints excluded: chain A residue 1726 LEU
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  352 HIS
Chi-restraints excluded: chain D residue  355 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 52 optimal weight:    9.9990
   chunk 102 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 106 optimal weight:    0.4980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.188344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.151895 restraints weight = 69335.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.159908 restraints weight = 31826.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.165099 restraints weight = 17425.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.168319 restraints weight = 10783.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.170351 restraints weight = 7451.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.4405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5003
moved from start:          0.7318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  12334  Z= 0.147
  Angle     :  0.559   7.623  16970  Z= 0.297
  Chirality :  0.042   0.782   1983
  Planarity :  0.005   0.060   1955
  Dihedral  : 15.781 160.253   2353
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.47 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.23), residues: 1333
  helix:  1.16 (0.20), residues: 679
  sheet: -1.11 (0.36), residues: 199
  loop : -0.26 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1573 
 TYR   0.018   0.001   TYR A1828 
 PHE   0.025   0.002   PHE A 142 
 TRP   0.009   0.002   TRP A 316 
 HIS   0.005   0.001   HIS A1683 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (12334)
  covalent geometry    : angle       0.55903 (16970)
  hydrogen bonds       : bond        0.04276 (  621)
  hydrogen bonds       : angle       4.53227 ( 1739)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  246 is missing expected H atoms. Skipping.
Residue THR  247 is missing expected H atoms. Skipping.
Residue SER  248 is missing expected H atoms. Skipping.
Evaluate side-chains
  212 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 184
  time to evaluate  : 0.573 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7843 (tttp)
REVERT: A   83 HIS cc_start: 0.8465 (OUTLIER) cc_final: 0.7124 (p90)
REVERT: A  168 ASP cc_start: 0.7538 (m-30) cc_final: 0.6900 (p0)
REVERT: A  269 ARG cc_start: 0.8573 (ttt180) cc_final: 0.8169 (mtt180)
REVERT: A  272 MET cc_start: 0.8274 (mtp) cc_final: 0.7694 (mtp)
REVERT: A  307 ARG cc_start: 0.7909 (ttt-90) cc_final: 0.7657 (ttp80)
REVERT: A  503 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7573 (mt-10)
REVERT: A  537 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6602 (m-80)
REVERT: A  684 MET cc_start: 0.5866 (mpp) cc_final: 0.5562 (mpp)
REVERT: A  747 GLN cc_start: 0.7380 (tp40) cc_final: 0.6802 (tm-30)
REVERT: A  789 ARG cc_start: 0.7655 (tpp-160) cc_final: 0.7426 (tpp-160)
REVERT: A 1354 CYS cc_start: 0.7322 (t) cc_final: 0.6649 (m)
REVERT: A 1661 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7230 (tm-30)
REVERT: A 1802 MET cc_start: 0.6430 (mmp) cc_final: 0.6150 (mmp)
REVERT: A 1816 ASP cc_start: 0.3000 (OUTLIER) cc_final: 0.1836 (t70)
  outliers start: 28
  outliers final: 21
  residues processed: 202
  average time/residue: 0.2772
  time to fit residues: 77.6818
Evaluate side-chains
  198 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 174
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   83 HIS
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  177 CYS
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  387 TYR
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  771 TYR
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  791 LYS
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1580 CYS
Chi-restraints excluded: chain A residue 1587 LEU
Chi-restraints excluded: chain A residue 1682 THR
Chi-restraints excluded: chain A residue 1700 PHE
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  352 HIS
Chi-restraints excluded: chain D residue  355 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 49 optimal weight:    0.3980
   chunk 45 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 115 optimal weight:    0.0980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 301 GLN
** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.188937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.151838 restraints weight = 70031.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.159950 restraints weight = 32547.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.165148 restraints weight = 17893.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.168428 restraints weight = 11165.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.170603 restraints weight = 7781.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.4404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5102
moved from start:          0.8009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.091  12334  Z= 0.131
  Angle     :  0.561  11.860  16970  Z= 0.291
  Chirality :  0.042   0.782   1983
  Planarity :  0.005   0.054   1955
  Dihedral  : 15.696 160.429   2351
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.39 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.24), residues: 1333
  helix:  1.36 (0.20), residues: 683
  sheet: -0.97 (0.36), residues: 209
  loop : -0.26 (0.32), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 640 
 TYR   0.016   0.001   TYR A1828 
 PHE   0.020   0.001   PHE A1700 
 TRP   0.010   0.002   TRP A 316 
 HIS   0.006   0.001   HIS A 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (12334)
  covalent geometry    : angle       0.56096 (16970)
  hydrogen bonds       : bond        0.04085 (  621)
  hydrogen bonds       : angle       4.41302 ( 1739)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  246 is missing expected H atoms. Skipping.
Residue THR  247 is missing expected H atoms. Skipping.
Residue SER  248 is missing expected H atoms. Skipping.
Evaluate side-chains
  212 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 184
  time to evaluate  : 0.541 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7767 (ttpp)
REVERT: A   71 THR cc_start: 0.8325 (m) cc_final: 0.7780 (m)
REVERT: A  109 GLN cc_start: 0.7472 (tp-100) cc_final: 0.7237 (tp40)
REVERT: A  140 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.6407 (pm20)
REVERT: A  272 MET cc_start: 0.8289 (mtp) cc_final: 0.7729 (mtp)
REVERT: A  307 ARG cc_start: 0.7934 (ttt-90) cc_final: 0.7725 (ttp80)
REVERT: A  316 TRP cc_start: 0.6451 (t60) cc_final: 0.5224 (t60)
REVERT: A  360 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7702 (mm-30)
REVERT: A  503 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7557 (mt-10)
REVERT: A  537 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6622 (m-80)
REVERT: A  747 GLN cc_start: 0.7450 (tp40) cc_final: 0.6982 (tm-30)
REVERT: A  771 TYR cc_start: 0.3625 (OUTLIER) cc_final: 0.0996 (m-10)
REVERT: A  789 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7453 (tpp-160)
REVERT: A 1354 CYS cc_start: 0.7469 (t) cc_final: 0.6786 (m)
REVERT: A 1661 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7264 (tm-30)
REVERT: A 1726 LEU cc_start: 0.4042 (OUTLIER) cc_final: 0.3340 (tt)
REVERT: A 1727 THR cc_start: 0.5070 (m) cc_final: 0.3288 (t)
REVERT: A 1802 MET cc_start: 0.6675 (mmp) cc_final: 0.6421 (mmp)
REVERT: A 1816 ASP cc_start: 0.3195 (OUTLIER) cc_final: 0.2505 (t70)
  outliers start: 28
  outliers final: 19
  residues processed: 201
  average time/residue: 0.2628
  time to fit residues: 73.7887
Evaluate side-chains
  200 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 174
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  177 CYS
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  771 TYR
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  789 ARG
Chi-restraints excluded: chain A residue  791 LYS
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue  975 LYS
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1587 LEU
Chi-restraints excluded: chain A residue 1682 THR
Chi-restraints excluded: chain A residue 1687 HIS
Chi-restraints excluded: chain A residue 1700 PHE
Chi-restraints excluded: chain A residue 1726 LEU
Chi-restraints excluded: chain A residue 1800 LYS
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  352 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 96 optimal weight:    0.5980
   chunk 121 optimal weight:    0.5980
   chunk 101 optimal weight:    2.9990
   chunk 118 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 132 optimal weight:    6.9990
   chunk 90 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9990
   chunk 92 optimal weight:    0.5980
   chunk 104 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.189223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.151789 restraints weight = 70702.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.159981 restraints weight = 33234.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.165142 restraints weight = 18407.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.168446 restraints weight = 11531.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.170510 restraints weight = 8002.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.4413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5286
moved from start:          0.8779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  12334  Z= 0.134
  Angle     :  0.554   7.665  16970  Z= 0.290
  Chirality :  0.042   0.784   1983
  Planarity :  0.005   0.048   1955
  Dihedral  : 15.697 160.499   2351
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 12.72 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.24), residues: 1333
  helix:  1.36 (0.20), residues: 682
  sheet: -0.88 (0.37), residues: 199
  loop : -0.35 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 459 
 TYR   0.016   0.001   TYR A1828 
 PHE   0.018   0.002   PHE A 142 
 TRP   0.010   0.002   TRP A 316 
 HIS   0.005   0.001   HIS A 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (12334)
  covalent geometry    : angle       0.55380 (16970)
  hydrogen bonds       : bond        0.04039 (  621)
  hydrogen bonds       : angle       4.40478 ( 1739)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  246 is missing expected H atoms. Skipping.
Residue THR  247 is missing expected H atoms. Skipping.
Residue SER  248 is missing expected H atoms. Skipping.
Evaluate side-chains
  223 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 191
  time to evaluate  : 0.444 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 LYS cc_start: 0.8359 (mtpt) cc_final: 0.7867 (ttpp)
REVERT: A   71 THR cc_start: 0.8422 (m) cc_final: 0.8013 (m)
REVERT: A   83 HIS cc_start: 0.8683 (OUTLIER) cc_final: 0.7136 (p90)
REVERT: A  109 GLN cc_start: 0.7491 (tp-100) cc_final: 0.7168 (tp40)
REVERT: A  140 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6531 (pm20)
REVERT: A  266 LEU cc_start: 0.9518 (pp) cc_final: 0.8585 (pp)
REVERT: A  269 ARG cc_start: 0.8718 (ttt180) cc_final: 0.8350 (mtt180)
REVERT: A  272 MET cc_start: 0.8366 (mtp) cc_final: 0.7807 (mtp)
REVERT: A  307 ARG cc_start: 0.7970 (ttt-90) cc_final: 0.7685 (mtm110)
REVERT: A  316 TRP cc_start: 0.6605 (t60) cc_final: 0.5438 (t60)
REVERT: A  371 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8422 (tttt)
REVERT: A  379 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8261 (mttm)
REVERT: A  503 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7671 (mt-10)
REVERT: A  537 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.6665 (m-80)
REVERT: A  747 GLN cc_start: 0.7554 (tp40) cc_final: 0.6984 (tm-30)
REVERT: A  771 TYR cc_start: 0.4118 (OUTLIER) cc_final: 0.1716 (m-10)
REVERT: A 1316 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5734 (tm-30)
REVERT: A 1354 CYS cc_start: 0.7675 (t) cc_final: 0.7026 (m)
REVERT: A 1356 LEU cc_start: 0.8695 (mt) cc_final: 0.8394 (mt)
REVERT: A 1545 HIS cc_start: 0.3343 (OUTLIER) cc_final: 0.2496 (m-70)
REVERT: A 1661 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7386 (tm-30)
REVERT: A 1705 ILE cc_start: 0.6855 (mt) cc_final: 0.6449 (mm)
REVERT: A 1802 MET cc_start: 0.6758 (mmp) cc_final: 0.6457 (mmp)
REVERT: A 1816 ASP cc_start: 0.3274 (OUTLIER) cc_final: 0.2809 (t70)
  outliers start: 32
  outliers final: 23
  residues processed: 209
  average time/residue: 0.2738
  time to fit residues: 79.5951
Evaluate side-chains
  216 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 186
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 HIS
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  387 TYR
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  748 CYS
Chi-restraints excluded: chain A residue  771 TYR
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  790 ARG
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1036 GLU
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1316 GLU
Chi-restraints excluded: chain A residue 1545 HIS
Chi-restraints excluded: chain A residue 1587 LEU
Chi-restraints excluded: chain A residue 1682 THR
Chi-restraints excluded: chain A residue 1687 HIS
Chi-restraints excluded: chain A residue 1693 ASP
Chi-restraints excluded: chain A residue 1700 PHE
Chi-restraints excluded: chain A residue 1800 LYS
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  352 HIS
Chi-restraints excluded: chain D residue  355 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 131 optimal weight:    6.9990
   chunk 99 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 111 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   chunk 114 optimal weight:    0.8980
   chunk 88 optimal weight:    0.8980
   chunk 129 optimal weight:    4.9990
   chunk 43 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1299 GLN
D 356 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.187976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.150207 restraints weight = 71551.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.158364 restraints weight = 33853.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.163578 restraints weight = 18853.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.166887 restraints weight = 11886.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.169127 restraints weight = 8344.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.4389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5466
moved from start:          0.9719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  12334  Z= 0.151
  Angle     :  0.595   7.992  16970  Z= 0.315
  Chirality :  0.043   0.789   1983
  Planarity :  0.005   0.058   1955
  Dihedral  : 15.743 160.520   2351
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.72 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.24), residues: 1333
  helix:  1.22 (0.20), residues: 682
  sheet: -0.91 (0.37), residues: 199
  loop : -0.45 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  86 
 TYR   0.028   0.001   TYR A1746 
 PHE   0.018   0.002   PHE A1700 
 TRP   0.010   0.002   TRP A 316 
 HIS   0.007   0.001   HIS A1062 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (12334)
  covalent geometry    : angle       0.59450 (16970)
  hydrogen bonds       : bond        0.04198 (  621)
  hydrogen bonds       : angle       4.50622 ( 1739)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  246 is missing expected H atoms. Skipping.
Residue THR  247 is missing expected H atoms. Skipping.
Residue SER  248 is missing expected H atoms. Skipping.
Evaluate side-chains
  220 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 193
  time to evaluate  : 0.590 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
REVERT: A   70 LYS cc_start: 0.8474 (mtpt) cc_final: 0.7961 (ttpp)
REVERT: A   71 THR cc_start: 0.8409 (m) cc_final: 0.8146 (t)
REVERT: A  109 GLN cc_start: 0.7524 (tp-100) cc_final: 0.7229 (tp40)
REVERT: A  140 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6572 (pm20)
REVERT: A  272 MET cc_start: 0.8417 (mtp) cc_final: 0.7907 (mtp)
REVERT: A  307 ARG cc_start: 0.8084 (ttt-90) cc_final: 0.7820 (mtm110)
REVERT: A  316 TRP cc_start: 0.6684 (t60) cc_final: 0.5405 (t60)
REVERT: A  371 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8473 (tttt)
REVERT: A  503 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7710 (mt-10)
REVERT: A  747 GLN cc_start: 0.7604 (tp40) cc_final: 0.7093 (tm-30)
REVERT: A  771 TYR cc_start: 0.4462 (OUTLIER) cc_final: 0.2118 (m-10)
REVERT: A  897 MET cc_start: 0.5719 (mtt) cc_final: 0.5299 (ttm)
REVERT: A 1354 CYS cc_start: 0.7854 (t) cc_final: 0.7284 (m)
REVERT: A 1356 LEU cc_start: 0.8746 (mt) cc_final: 0.8488 (mt)
REVERT: A 1380 TRP cc_start: 0.4931 (t60) cc_final: 0.4187 (t60)
REVERT: A 1661 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7536 (tm-30)
REVERT: A 1802 MET cc_start: 0.6994 (mmp) cc_final: 0.6771 (mmp)
REVERT: A 1816 ASP cc_start: 0.3691 (OUTLIER) cc_final: 0.3288 (t70)
  outliers start: 27
  outliers final: 23
  residues processed: 208
  average time/residue: 0.2739
  time to fit residues: 78.3244
Evaluate side-chains
  218 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 192
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  177 CYS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  387 TYR
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  771 TYR
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  791 LYS
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue  975 LYS
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1545 HIS
Chi-restraints excluded: chain A residue 1687 HIS
Chi-restraints excluded: chain A residue 1693 ASP
Chi-restraints excluded: chain A residue 1761 HIS
Chi-restraints excluded: chain A residue 1800 LYS
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  352 HIS
Chi-restraints excluded: chain D residue  356 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 124 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 98 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 356 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4598 r_free = 0.4598 target = 0.186640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.148730 restraints weight = 70581.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.157108 restraints weight = 32887.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.162463 restraints weight = 18125.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.165763 restraints weight = 11307.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.167588 restraints weight = 7891.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.4369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5623
moved from start:          1.0382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  12334  Z= 0.182
  Angle     :  0.617  15.532  16970  Z= 0.330
  Chirality :  0.043   0.790   1983
  Planarity :  0.005   0.060   1955
  Dihedral  : 15.809 160.513   2351
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.20 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 14.21 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.23), residues: 1333
  helix:  0.97 (0.20), residues: 682
  sheet: -0.93 (0.38), residues: 199
  loop : -0.61 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 640 
 TYR   0.020   0.002   TYR A1828 
 PHE   0.018   0.002   PHE A 894 
 TRP   0.012   0.002   TRP A1380 
 HIS   0.007   0.001   HIS D 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (12334)
  covalent geometry    : angle       0.61706 (16970)
  hydrogen bonds       : bond        0.04349 (  621)
  hydrogen bonds       : angle       4.69706 ( 1739)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  246 is missing expected H atoms. Skipping.
Residue THR  247 is missing expected H atoms. Skipping.
Residue SER  248 is missing expected H atoms. Skipping.
Evaluate side-chains
  236 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 205
  time to evaluate  : 0.421 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
REVERT: A   70 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8074 (ttpp)
REVERT: A   71 THR cc_start: 0.8457 (m) cc_final: 0.8237 (t)
REVERT: A  109 GLN cc_start: 0.7601 (tp-100) cc_final: 0.7359 (tp40)
REVERT: A  140 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6673 (pm20)
REVERT: A  272 MET cc_start: 0.8434 (mtp) cc_final: 0.7935 (mtp)
REVERT: A  307 ARG cc_start: 0.8224 (ttt-90) cc_final: 0.7946 (mtp-110)
REVERT: A  360 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7933 (mm-30)
REVERT: A  371 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8520 (tttt)
REVERT: A  379 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8387 (mmtt)
REVERT: A  503 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7736 (mt-10)
REVERT: A  747 GLN cc_start: 0.7576 (tp40) cc_final: 0.7102 (tm-30)
REVERT: A  771 TYR cc_start: 0.4738 (OUTLIER) cc_final: 0.2462 (m-10)
REVERT: A  895 LYS cc_start: 0.8262 (mmmm) cc_final: 0.7992 (mmmm)
REVERT: A  896 PHE cc_start: 0.7676 (t80) cc_final: 0.7419 (t80)
REVERT: A  996 ARG cc_start: 0.6570 (mtm-85) cc_final: 0.6184 (mtm-85)
REVERT: A 1354 CYS cc_start: 0.7999 (t) cc_final: 0.7425 (m)
REVERT: A 1356 LEU cc_start: 0.8788 (mt) cc_final: 0.8495 (mt)
REVERT: A 1380 TRP cc_start: 0.5420 (t60) cc_final: 0.4608 (t60)
REVERT: A 1661 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7703 (tm-30)
REVERT: A 1802 MET cc_start: 0.7048 (mmp) cc_final: 0.6832 (mmp)
REVERT: A 1816 ASP cc_start: 0.3731 (OUTLIER) cc_final: 0.3416 (t70)
REVERT: A 1831 MET cc_start: 0.5712 (tpp) cc_final: 0.5504 (tpt)
REVERT: A 1854 MET cc_start: 0.7007 (mmm) cc_final: 0.6550 (mmm)
  outliers start: 31
  outliers final: 26
  residues processed: 226
  average time/residue: 0.2763
  time to fit residues: 85.7207
Evaluate side-chains
  229 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 199
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 HIS
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  387 TYR
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  771 TYR
Chi-restraints excluded: chain A residue  773 ILE
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  790 ARG
Chi-restraints excluded: chain A residue  791 LYS
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1036 GLU
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1545 HIS
Chi-restraints excluded: chain A residue 1687 HIS
Chi-restraints excluded: chain A residue 1693 ASP
Chi-restraints excluded: chain A residue 1722 SER
Chi-restraints excluded: chain A residue 1800 LYS
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  352 HIS
Chi-restraints excluded: chain D residue  355 LEU
Chi-restraints excluded: chain D residue  356 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 104 optimal weight:    0.0570
   chunk 110 optimal weight:    1.9990
   chunk 124 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9980
   chunk 29 optimal weight:    8.9990
   chunk 128 optimal weight:    5.9990
   chunk 133 optimal weight:   10.0000
   chunk 139 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1299 GLN
A1355 ASN
D 356 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.187732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.150041 restraints weight = 70207.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.158459 restraints weight = 32606.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.163865 restraints weight = 17966.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.167056 restraints weight = 11176.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.169364 restraints weight = 7822.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.4392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5601
moved from start:          1.0745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  12334  Z= 0.131
  Angle     :  0.570   8.314  16970  Z= 0.300
  Chirality :  0.042   0.789   1983
  Planarity :  0.005   0.059   1955
  Dihedral  : 15.765 160.796   2351
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.71 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.24), residues: 1333
  helix:  1.22 (0.20), residues: 682
  sheet: -0.78 (0.38), residues: 192
  loop : -0.52 (0.31), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 459 
 TYR   0.016   0.001   TYR A1828 
 PHE   0.041   0.002   PHE A 894 
 TRP   0.010   0.002   TRP A 316 
 HIS   0.005   0.001   HIS A 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (12334)
  covalent geometry    : angle       0.56952 (16970)
  hydrogen bonds       : bond        0.03971 (  621)
  hydrogen bonds       : angle       4.46618 ( 1739)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4066.91 seconds
wall clock time: 70 minutes 4.45 seconds (4204.45 seconds total)