Starting phenix.real_space_refine
on Thu Aug  6 00:29:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/21cb_67570/08_2026/21cb_67570.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/21cb_67570/08_2026/21cb_67570.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/21cb_67570/08_2026/21cb_67570.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/21cb_67570/08_2026/21cb_67570.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/21cb_67570/08_2026/21cb_67570.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/21cb_67570/08_2026/21cb_67570.map"
  }
  resolution = 3.0
  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=   0.004 sd=   0.051
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: 5
    Type Number    sf(0)   Gaussians
     P      58      5.49       5
     S      60      5.16       5
     C    7518      2.51       5
     N    2077      2.21       5
     O    2428      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12141
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1357, 10903
          Classifications: {'peptide': 1357}
          Link IDs: {'PTRANS': 80, 'TRANS': 1276}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 1238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 1238
          Classifications: {'RNA': 58}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 31, 'rna3p_pyr': 26}
          Link IDs: {'rna2p': 1, 'rna3p': 56}
          Chain breaks: 1
  Time building chain proxies: 2.21, per 1000 atoms: 0.18
  Number of scatterers: 12141
  At special positions: 0
  Unit cell: (93.539, 99.845, 160.803, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     P      58     15.00
     O    2428      8.00
     N    2077      7.00
     C    7518      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 443 " - pdb=" SG  CYS A 531 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Conformation dependent library (CDL) restraints added in 413.1 milliseconds
  

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2602

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 10 sheets defined
      50.2% alpha, 5.9% beta
      18 base pairs and 33 stacking pairs defined.
    Time for finding SS restraints: 1.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 4.378A  pdb=" N   GLU A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 58
    Processing helix  chain 'A' and resid 69 through 81
    Processing helix  chain 'A' and resid 81 through 86
      removed outlier: 4.091A  pdb=" N   ILE A  85 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ARG A  86 " --> pdb=" O   SER A  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 81 through 86'
    Processing helix  chain 'A' and resid 88 through 92
    Processing helix  chain 'A' and resid 102 through 115
    Processing helix  chain 'A' and resid 134 through 145
    Processing helix  chain 'A' and resid 152 through 161
    Processing helix  chain 'A' and resid 165 through 169
    Processing helix  chain 'A' and resid 176 through 182
      removed outlier: 4.353A  pdb=" N   LEU A 179 " --> pdb=" O   GLU A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 196
      removed outlier: 3.663A  pdb=" N   GLU A 188 " --> pdb=" O   HIS A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 230
    Processing helix  chain 'A' and resid 268 through 283
    Processing helix  chain 'A' and resid 290 through 294
    Processing helix  chain 'A' and resid 297 through 309
      removed outlier: 3.897A  pdb=" N   ILE A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 331
    Processing helix  chain 'A' and resid 339 through 363
      removed outlier: 3.943A  pdb=" N   PHE A 363 " --> pdb=" O   CYS A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 385
    Processing helix  chain 'A' and resid 451 through 466
      removed outlier: 4.065A  pdb=" N   VAL A 455 " --> pdb=" O   ARG A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 473
      removed outlier: 4.418A  pdb=" N   TYR A 473 " --> pdb=" O   PRO A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 508
    Processing helix  chain 'A' and resid 542 through 553
    Processing helix  chain 'A' and resid 568 through 589
      removed outlier: 3.618A  pdb=" N   LYS A 589 " --> pdb=" O   ILE A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 641
      removed outlier: 3.585A  pdb=" N   THR A 629 " --> pdb=" O   VAL A 625 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   ILE A 631 " --> pdb=" O   ILE A 627 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   GLY A 632 " --> pdb=" O   ASN A 628 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ALA A 639 " --> pdb=" O   ASN A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 705
    Processing helix  chain 'A' and resid 709 through 713
      removed outlier: 3.755A  pdb=" N   MET A 713 " --> pdb=" O   ASP A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 786
    Processing helix  chain 'A' and resid 794 through 798
      removed outlier: 3.650A  pdb=" N   THR A 798 " --> pdb=" O   PRO A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 839 through 857
    Processing helix  chain 'A' and resid 894 through 903
    Processing helix  chain 'A' and resid 923 through 928
      removed outlier: 3.735A  pdb=" N   TYR A 927 " --> pdb=" O   LYS A 923 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 977
    Processing helix  chain 'A' and resid 1034 through 1036
      No H-bonds generated for 'chain 'A' and resid 1034 through 1036'
    Processing helix  chain 'A' and resid 1044 through 1076
      removed outlier: 3.900A  pdb=" N   CYS A1053 " --> pdb=" O   ARG A1049 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LEU A1054 " --> pdb=" O   LYS A1050 " (cutoff:3.500A)
      Proline residue:  A1055  - end of helix
      removed outlier: 3.689A  pdb=" N   THR A1074 " --> pdb=" O   LEU A1070 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1293 through 1302
    Processing helix  chain 'A' and resid 1303 through 1307
    Processing helix  chain 'A' and resid 1312 through 1335
      removed outlier: 3.653A  pdb=" N   LEU A1318 " --> pdb=" O   ARG A1314 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   TYR A1335 " --> pdb=" O   LEU A1331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1339 through 1351
    Processing helix  chain 'A' and resid 1352 through 1362
      removed outlier: 3.896A  pdb=" N   LYS A1362 " --> pdb=" O   ARG A1358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1364 through 1369
      removed outlier: 3.607A  pdb=" N   ARG A1368 " --> pdb=" O   GLY A1364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1375 through 1380
    Processing helix  chain 'A' and resid 1557 through 1587
      removed outlier: 8.155A  pdb=" N   GLU A1576 " --> pdb=" O   THR A1572 " (cutoff:3.500A)
      removed outlier: 9.363A  pdb=" N   ARG A1577 " --> pdb=" O   SER A1573 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ALA A1578 " --> pdb=" O   CYS A1574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1655 through 1674
      removed outlier: 4.326A  pdb=" N   LEU A1659 " --> pdb=" O   ALA A1655 " (cutoff:3.500A)
      removed outlier: 5.283A  pdb=" N   LYS A1671 " --> pdb=" O   GLU A1667 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   LYS A1672 " --> pdb=" O   ASN A1668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1679 through 1687
      removed outlier: 4.195A  pdb=" N   LEU A1683 " --> pdb=" O   ASN A1679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1701 through 1723
      removed outlier: 4.065A  pdb=" N   ALA A1710 " --> pdb=" O   PHE A1706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1730 through 1740
    Processing helix  chain 'A' and resid 1741 through 1752
    Processing helix  chain 'A' and resid 1754 through 1758
    Processing helix  chain 'A' and resid 1762 through 1779
    Processing helix  chain 'A' and resid 1805 through 1823
      removed outlier: 3.912A  pdb=" N   GLY A1809 " --> pdb=" O   PRO A1805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1827 through 1848
      Proline residue:  A1836  - end of helix
      Proline residue:  A1840  - end of helix
      removed outlier: 3.603A  pdb=" N   ASN A1848 " --> pdb=" O   LYS A1844 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1852 through 1861
    Processing helix  chain 'A' and resid 1896 through 1912
      removed outlier: 3.941A  pdb=" N   ARG A1907 " --> pdb=" O   ALA A1903 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ALA A1908 " --> pdb=" O   ALA A1904 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 100
      removed outlier: 6.788A  pdb=" N   THR A  96 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   MET A 150 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   PHE A  98 " --> pdb=" O   MET A 150 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 173
    Processing sheet with id=AA3, first strand: chain 'A' and resid 515 through 517
      removed outlier: 6.757A  pdb=" N   GLY A 444 " --> pdb=" O   LEU A 516 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL A 535 " --> pdb=" O   ILE A 445 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 654 through 657
      removed outlier: 3.729A  pdb=" N   ARG A 654 " --> pdb=" O   THR A 666 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR A 666 " --> pdb=" O   ARG A 654 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ARG A 656 " --> pdb=" O   TYR A 664 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 664 " --> pdb=" O   ARG A 656 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ILE A 679 " --> pdb=" O   LEU A 667 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 746 through 750
      removed outlier: 3.607A  pdb=" N   ILE A1554 " --> pdb=" O   GLN A 747 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 829 through 831
      removed outlier: 5.599A  pdb=" N   PHE A 802 " --> pdb=" O   ILE A 773 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 776 through 779
      removed outlier: 3.550A  pdb=" N   VAL A 776 " --> pdb=" O   THR A 826 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR A 826 " --> pdb=" O   VAL A 776 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   THR A 778 " --> pdb=" O   GLU A 824 " (cutoff:3.500A)
      removed outlier: 8.160A  pdb=" N   GLU A 824 " --> pdb=" O   THR A 778 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 865 through 867
    Processing sheet with id=AA9, first strand: chain 'A' and resid 931 through 934
      removed outlier: 4.369A  pdb=" N   VAL A 931 " --> pdb=" O   HIS A1041 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 949 through 951
      removed outlier: 3.837A  pdb=" N   ASP A 949 " --> pdb=" O   ASP A 989 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLN A1031 " --> pdb=" O   VAL A 990 " (cutoff:3.500A)

    471 hydrogen bonds defined for protein.
    1344 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      44 hydrogen bonds
      72 hydrogen bond angles
      0 basepair planarities
      18 basepair parallelities
      33 stacking parallelities
  Total time for adding SS restraints: 2.13

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3715
        1.34 -     1.46: 3029
        1.46 -     1.58: 5584
        1.58 -     1.71: 114
        1.71 -     1.83: 83
  Bond restraints: 12525
  Sorted by residual:
  bond pdb=" N   VAL A 288 "
       pdb=" CA  VAL A 288 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.19e-02 7.06e+03 9.06e+00
  bond pdb=" N   VAL A 625 "
       pdb=" CA  VAL A 625 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.76e+00
  bond pdb=" N   VAL A 373 "
       pdb=" CA  VAL A 373 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.64e+00
  bond pdb=" N   ASP A 620 "
       pdb=" CA  ASP A 620 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.23e-02 6.61e+03 8.35e+00
  bond pdb=" N   HIS A 289 "
       pdb=" CA  HIS A 289 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.21e-02 6.83e+03 7.77e+00
  ... (remaining 12520 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.91: 16908
        2.91 -     5.82: 301
        5.82 -     8.72: 32
        8.72 -    11.63: 3
       11.63 -    14.54: 2
  Bond angle restraints: 17246
  Sorted by residual:
  angle pdb=" N   ARG A1895 "
        pdb=" CA  ARG A1895 "
        pdb=" C   ARG A1895 "
      ideal   model   delta    sigma   weight residual
     114.56  108.26    6.30 1.27e+00 6.20e-01 2.46e+01
  angle pdb=" CB  MET A1808 "
        pdb=" CG  MET A1808 "
        pdb=" SD  MET A1808 "
      ideal   model   delta    sigma   weight residual
     112.70  126.39  -13.69 3.00e+00 1.11e-01 2.08e+01
  angle pdb=" CA  LYS A 862 "
        pdb=" CB  LYS A 862 "
        pdb=" CG  LYS A 862 "
      ideal   model   delta    sigma   weight residual
     114.10  122.92   -8.82 2.00e+00 2.50e-01 1.94e+01
  angle pdb=" CA  LYS A 584 "
        pdb=" CB  LYS A 584 "
        pdb=" CG  LYS A 584 "
      ideal   model   delta    sigma   weight residual
     114.10  122.84   -8.74 2.00e+00 2.50e-01 1.91e+01
  angle pdb=" C   LEU A 370 "
        pdb=" CA  LEU A 370 "
        pdb=" CB  LEU A 370 "
      ideal   model   delta    sigma   weight residual
     116.63  111.65    4.98 1.16e+00 7.43e-01 1.84e+01
  ... (remaining 17241 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 6485
       17.80 -    35.60: 813
       35.60 -    53.39: 285
       53.39 -    71.19: 120
       71.19 -    88.99: 28
  Dihedral angle restraints: 7731
    sinusoidal: 3717
      harmonic: 4014
  Sorted by residual:
  dihedral pdb=" CA  ILE A 149 "
           pdb=" C   ILE A 149 "
           pdb=" N   MET A 150 "
           pdb=" CA  MET A 150 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.69  -27.31     0      5.00e+00 4.00e-02 2.98e+01
  dihedral pdb=" CA  MET A 684 "
           pdb=" C   MET A 684 "
           pdb=" N   SER A 685 "
           pdb=" CA  SER A 685 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.84  -23.16     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  THR A 915 "
           pdb=" C   THR A 915 "
           pdb=" N   LYS A 916 "
           pdb=" CA  LYS A 916 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.00  -23.00     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 7728 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 1883
       0.107 -    0.214: 101
       0.214 -    0.321: 2
       0.321 -    0.428: 0
       0.428 -    0.535: 7
  Chirality restraints: 1993
  Sorted by residual:
  chirality pdb=" P     G B  26 "
            pdb=" OP1   G B  26 "
            pdb=" OP2   G B  26 "
            pdb=" O5'   G B  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.95   -0.54 2.00e-01 2.50e+01 7.16e+00
  chirality pdb=" P     G B  60 "
            pdb=" OP1   G B  60 "
            pdb=" OP2   G B  60 "
            pdb=" O5'   G B  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.93   -0.52 2.00e-01 2.50e+01 6.64e+00
  chirality pdb=" P     G B  58 "
            pdb=" OP1   G B  58 "
            pdb=" OP2   G B  58 "
            pdb=" O5'   G B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.91   -0.50 2.00e-01 2.50e+01 6.24e+00
  ... (remaining 1990 not shown)

  Planarity restraints: 1994
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 960 "   -0.051 5.00e-02 4.00e+02   7.64e-02 9.34e+00
        pdb=" N   PRO A 961 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO A 961 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 961 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 184 "   -0.043 5.00e-02 4.00e+02   6.47e-02 6.69e+00
        pdb=" N   PRO A 185 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 185 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 185 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A1376 "    0.039 5.00e-02 4.00e+02   5.81e-02 5.40e+00
        pdb=" N   PRO A1377 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A1377 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A1377 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1991 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 194
        2.60 -     3.17: 11093
        3.17 -     3.75: 20768
        3.75 -     4.32: 27573
        4.32 -     4.90: 43090
  Nonbonded interactions: 102718
  Sorted by model distance:
  nonbonded pdb=" O   TYR A1330 "
            pdb=" OG1 THR A1334 "
     model   vdw
     2.021 3.040
  nonbonded pdb=" OG1 THR A1074 "
            pdb=" OH  TYR A1570 "
     model   vdw
     2.034 3.040
  nonbonded pdb=" O   GLU A 391 "
            pdb=" OH  TYR A 473 "
     model   vdw
     2.035 3.040
  nonbonded pdb=" O   ARG A 739 "
            pdb=" OG  SER A 742 "
     model   vdw
     2.045 3.040
  nonbonded pdb=" O   PRO A 956 "
            pdb=" OG1 THR A 967 "
     model   vdw
     2.053 3.040
  ... (remaining 102713 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.000
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6343
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081  12526  Z= 0.274
  Angle     :  0.903  14.539  17248  Z= 0.510
  Chirality :  0.057   0.535   1993
  Planarity :  0.006   0.076   1994
  Dihedral  : 19.060  88.988   5126
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 28.78 %
    Favored  : 66.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.23), residues: 1343
  helix:  0.34 (0.22), residues: 567
  sheet: -2.89 (0.47), residues: 100
  loop : -1.92 (0.24), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 789 
 TYR   0.031   0.002   TYR A1834 
 PHE   0.017   0.001   PHE A1812 
 TRP   0.009   0.002   TRP A1831 
 HIS   0.007   0.001   HIS A1041 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00525 /  0.27 (12525)
  covalent geometry    : angle       0.90262 /  0.51 (17246)
  SS BOND              : bond        0.00569 /  0.38 (    1)
  SS BOND              : angle       2.00233 /  1.20 (    2)
  hydrogen bonds       : bond        0.15586 / 10.06 (  515)
  hydrogen bonds       : angle       6.57141 /  4.67 ( 1416)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 135
  time to evaluate  : 0.400 
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: A  390 TYR cc_start: 0.5996 (t80) cc_final: 0.5743 (t80)
REVERT: A  684 MET cc_start: 0.2799 (ppp) cc_final: 0.2339 (ppp)
REVERT: A 1861 GLU cc_start: 0.6052 (mm-30) cc_final: 0.5706 (tp30)
  outliers start: 53
  outliers final: 40
  residues processed: 187
  average time/residue: 0.4643
  time to fit residues: 95.1238
Evaluate side-chains
  163 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 123
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  257 CYS
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  291 LYS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  614 TYR
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  698 CYS
Chi-restraints excluded: chain A residue  735 SER
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  824 GLU
Chi-restraints excluded: chain A residue  826 THR
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  926 ASP
Chi-restraints excluded: chain A residue  978 LEU
Chi-restraints excluded: chain A residue 1066 THR
Chi-restraints excluded: chain A residue 1304 SER
Chi-restraints excluded: chain A residue 1320 ASP
Chi-restraints excluded: chain A residue 1334 THR
Chi-restraints excluded: chain A residue 1348 SER
Chi-restraints excluded: chain A residue 1372 SER
Chi-restraints excluded: chain A residue 1550 THR
Chi-restraints excluded: chain A residue 1569 CYS
Chi-restraints excluded: chain A residue 1762 SER
Chi-restraints excluded: chain A residue 1803 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.0070
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.6398

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1073 GLN
A1379 ASN
A1660 ASN
A1719 HIS
A1727 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4842 r_free = 0.4842 target = 0.181580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.158961 restraints weight = 32976.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.4481 rms_B_bonded: 2.11
r_work: 0.4376 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.4376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6424
moved from start:          0.1070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  12526  Z= 0.159
  Angle     :  0.709  12.086  17248  Z= 0.363
  Chirality :  0.044   0.208   1993
  Planarity :  0.006   0.061   1994
  Dihedral  : 15.678  79.523   2447
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  6.95 %
    Allowed  : 24.28 %
    Favored  : 68.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.23), residues: 1343
  helix:  0.31 (0.21), residues: 576
  sheet: -3.10 (0.42), residues: 113
  loop : -1.92 (0.24), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 688 
 TYR   0.020   0.002   TYR A 560 
 PHE   0.016   0.001   PHE A1706 
 TRP   0.022   0.003   TRP A 316 
 HIS   0.006   0.001   HIS A1041 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.16 (12525)
  covalent geometry    : angle       0.70914 /  0.36 (17246)
  SS BOND              : bond        0.00067 /  0.04 (    1)
  SS BOND              : angle       0.57569 /  0.31 (    2)
  hydrogen bonds       : bond        0.05705 /  3.79 (  515)
  hydrogen bonds       : angle       5.50044 /  3.85 ( 1416)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 141
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  711 HIS cc_start: 0.5212 (OUTLIER) cc_final: 0.4812 (m90)
REVERT: A  763 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7202 (mpt-90)
REVERT: A  775 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.5866 (mpp)
REVERT: A  859 ARG cc_start: 0.5955 (OUTLIER) cc_final: 0.5202 (mtt90)
REVERT: A 1337 ASP cc_start: 0.6783 (t0) cc_final: 0.6477 (p0)
REVERT: A 1803 GLU cc_start: 0.4433 (OUTLIER) cc_final: 0.3968 (pp20)
  outliers start: 85
  outliers final: 40
  residues processed: 217
  average time/residue: 0.4827
  time to fit residues: 114.2729
Evaluate side-chains
  176 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 131
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  257 CYS
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  291 LYS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  614 TYR
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  698 CYS
Chi-restraints excluded: chain A residue  711 HIS
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  763 ARG
Chi-restraints excluded: chain A residue  775 MET
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  813 ILE
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  859 ARG
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  978 LEU
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue 1066 THR
Chi-restraints excluded: chain A residue 1304 SER
Chi-restraints excluded: chain A residue 1307 SER
Chi-restraints excluded: chain A residue 1320 ASP
Chi-restraints excluded: chain A residue 1348 SER
Chi-restraints excluded: chain A residue 1372 SER
Chi-restraints excluded: chain A residue 1381 LEU
Chi-restraints excluded: chain A residue 1550 THR
Chi-restraints excluded: chain A residue 1569 CYS
Chi-restraints excluded: chain A residue 1762 SER
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1837 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 29 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 106 optimal weight:    0.3980
   chunk 122 optimal weight:    0.7980
   chunk 97 optimal weight:    0.6980
   chunk 89 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 488 GLN
A1660 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4835 r_free = 0.4835 target = 0.180901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.158134 restraints weight = 33159.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.4469 rms_B_bonded: 2.15
r_work: 0.4365 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.4365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6427
moved from start:          0.1425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12526  Z= 0.154
  Angle     :  0.696  12.661  17248  Z= 0.353
  Chirality :  0.043   0.206   1993
  Planarity :  0.006   0.058   1994
  Dihedral  : 15.512  78.320   2431
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  7.36 %
    Allowed  : 26.17 %
    Favored  : 66.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.22), residues: 1343
  helix:  0.30 (0.21), residues: 574
  sheet: -3.04 (0.44), residues: 100
  loop : -1.76 (0.24), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 789 
 TYR   0.020   0.002   TYR A1357 
 PHE   0.019   0.001   PHE A 922 
 TRP   0.016   0.002   TRP A 316 
 HIS   0.004   0.001   HIS A1041 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.15 (12525)
  covalent geometry    : angle       0.69632 /  0.35 (17246)
  SS BOND              : bond        0.00117 /  0.08 (    1)
  SS BOND              : angle       0.60233 /  0.33 (    2)
  hydrogen bonds       : bond        0.05302 /  3.51 (  515)
  hydrogen bonds       : angle       5.32912 /  3.74 ( 1416)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 144
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 LEU cc_start: 0.2556 (OUTLIER) cc_final: 0.2203 (mp)
REVERT: A  486 LYS cc_start: -0.3412 (OUTLIER) cc_final: -0.3773 (pttp)
REVERT: A  500 LYS cc_start: 0.8560 (mmmm) cc_final: 0.8110 (tptt)
REVERT: A  563 LEU cc_start: 0.5473 (OUTLIER) cc_final: 0.5026 (mt)
REVERT: A  649 LEU cc_start: 0.5329 (OUTLIER) cc_final: 0.5088 (tm)
REVERT: A  711 HIS cc_start: 0.5213 (OUTLIER) cc_final: 0.4845 (m90)
REVERT: A  775 MET cc_start: 0.6203 (OUTLIER) cc_final: 0.5812 (mpp)
REVERT: A 1337 ASP cc_start: 0.6836 (t0) cc_final: 0.6510 (p0)
REVERT: A 1803 GLU cc_start: 0.4454 (OUTLIER) cc_final: 0.3949 (pp20)
  outliers start: 90
  outliers final: 36
  residues processed: 219
  average time/residue: 0.5034
  time to fit residues: 120.5763
Evaluate side-chains
  173 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 130
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  153 TYR
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  291 LYS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  390 TYR
Chi-restraints excluded: chain A residue  486 LYS
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  614 TYR
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  649 LEU
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  698 CYS
Chi-restraints excluded: chain A residue  711 HIS
Chi-restraints excluded: chain A residue  775 MET
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  853 ILE
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  953 ASP
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1066 THR
Chi-restraints excluded: chain A residue 1307 SER
Chi-restraints excluded: chain A residue 1320 ASP
Chi-restraints excluded: chain A residue 1550 THR
Chi-restraints excluded: chain A residue 1569 CYS
Chi-restraints excluded: chain A residue 1593 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 120 optimal weight:    0.7980
   chunk 115 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 121 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 104 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 130 ASN
A 488 GLN
** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1660 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4832 r_free = 0.4832 target = 0.181186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.158232 restraints weight = 33262.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.4466 rms_B_bonded: 2.15
r_work: 0.4360 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.4360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6450
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12526  Z= 0.154
  Angle     :  0.694  10.164  17248  Z= 0.353
  Chirality :  0.043   0.206   1993
  Planarity :  0.005   0.058   1994
  Dihedral  : 15.364  77.525   2419
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  6.46 %
    Allowed  : 27.39 %
    Favored  : 66.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.22), residues: 1343
  helix:  0.27 (0.21), residues: 575
  sheet: -2.94 (0.46), residues: 100
  loop : -1.75 (0.24), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 688 
 TYR   0.018   0.002   TYR A1714 
 PHE   0.016   0.001   PHE A1706 
 TRP   0.020   0.002   TRP A 316 
 HIS   0.009   0.001   HIS A 184 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.15 (12525)
  covalent geometry    : angle       0.69360 /  0.35 (17246)
  SS BOND              : bond        0.00118 /  0.08 (    1)
  SS BOND              : angle       0.49099 /  0.27 (    2)
  hydrogen bonds       : bond        0.05108 /  3.37 (  515)
  hydrogen bonds       : angle       5.25226 /  3.69 ( 1416)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 135
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7257 (tm)
REVERT: A   84 GLN cc_start: 0.6021 (pp30) cc_final: 0.5454 (tm-30)
REVERT: A  205 LEU cc_start: 0.2534 (OUTLIER) cc_final: 0.2194 (mp)
REVERT: A  486 LYS cc_start: -0.3550 (OUTLIER) cc_final: -0.3831 (pttp)
REVERT: A  500 LYS cc_start: 0.8514 (mmmm) cc_final: 0.8085 (tptt)
REVERT: A  507 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7649 (pptt)
REVERT: A  636 ARG cc_start: 0.5364 (OUTLIER) cc_final: 0.5075 (mtm110)
REVERT: A  649 LEU cc_start: 0.5413 (OUTLIER) cc_final: 0.5028 (tm)
REVERT: A  775 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.6067 (mpp)
REVERT: A  865 LEU cc_start: 0.6668 (mt) cc_final: 0.6438 (mt)
REVERT: A 1337 ASP cc_start: 0.6832 (t0) cc_final: 0.6518 (p0)
REVERT: A 1381 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6958 (pt)
REVERT: A 1803 GLU cc_start: 0.4413 (OUTLIER) cc_final: 0.3920 (pp20)
  outliers start: 79
  outliers final: 36
  residues processed: 201
  average time/residue: 0.4693
  time to fit residues: 103.4401
Evaluate side-chains
  177 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 132
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  291 LYS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  486 LYS
Chi-restraints excluded: chain A residue  507 LYS
Chi-restraints excluded: chain A residue  614 TYR
Chi-restraints excluded: chain A residue  636 ARG
Chi-restraints excluded: chain A residue  649 LEU
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  698 CYS
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  775 MET
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  813 ILE
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  853 ILE
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1066 THR
Chi-restraints excluded: chain A residue 1297 ILE
Chi-restraints excluded: chain A residue 1311 ASN
Chi-restraints excluded: chain A residue 1320 ASP
Chi-restraints excluded: chain A residue 1381 LEU
Chi-restraints excluded: chain A residue 1550 THR
Chi-restraints excluded: chain A residue 1569 CYS
Chi-restraints excluded: chain A residue 1593 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 123 optimal weight:    0.7980
   chunk 39 optimal weight:   20.0000
   chunk 76 optimal weight:    0.6980
   chunk 108 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1660 ASN
A1668 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.180568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.157489 restraints weight = 33043.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.4453 rms_B_bonded: 2.13
r_work: 0.4348 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.4348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6463
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  12526  Z= 0.157
  Angle     :  0.699   8.991  17248  Z= 0.356
  Chirality :  0.044   0.302   1993
  Planarity :  0.006   0.058   1994
  Dihedral  : 15.318  76.823   2417
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  7.36 %
    Allowed  : 27.56 %
    Favored  : 65.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.22), residues: 1343
  helix:  0.28 (0.21), residues: 573
  sheet: -2.92 (0.47), residues: 100
  loop : -1.77 (0.23), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 789 
 TYR   0.024   0.002   TYR A1714 
 PHE   0.020   0.002   PHE A 498 
 TRP   0.025   0.003   TRP A 316 
 HIS   0.005   0.001   HIS A1041 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.16 (12525)
  covalent geometry    : angle       0.69871 /  0.36 (17246)
  SS BOND              : bond        0.00137 /  0.09 (    1)
  SS BOND              : angle       0.37291 /  0.21 (    2)
  hydrogen bonds       : bond        0.05020 /  3.32 (  515)
  hydrogen bonds       : angle       5.17817 /  3.64 ( 1416)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 137
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ILE cc_start: 0.5220 (mp) cc_final: 0.4749 (mp)
REVERT: A  205 LEU cc_start: 0.2180 (OUTLIER) cc_final: 0.1782 (mp)
REVERT: A  230 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8006 (mp)
REVERT: A  486 LYS cc_start: -0.3403 (OUTLIER) cc_final: -0.3683 (pttp)
REVERT: A  500 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8076 (tptt)
REVERT: A  507 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7501 (pptt)
REVERT: A  636 ARG cc_start: 0.5334 (OUTLIER) cc_final: 0.5049 (mtm110)
REVERT: A  649 LEU cc_start: 0.5496 (OUTLIER) cc_final: 0.5162 (tm)
REVERT: A  775 MET cc_start: 0.6337 (OUTLIER) cc_final: 0.6037 (mpp)
REVERT: A  836 PHE cc_start: 0.2335 (OUTLIER) cc_final: 0.1521 (p90)
REVERT: A  865 LEU cc_start: 0.6723 (mt) cc_final: 0.6439 (mt)
REVERT: A 1337 ASP cc_start: 0.6824 (t0) cc_final: 0.6574 (p0)
REVERT: A 1381 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6957 (pt)
REVERT: A 1803 GLU cc_start: 0.4413 (OUTLIER) cc_final: 0.3907 (pp20)
  outliers start: 90
  outliers final: 43
  residues processed: 215
  average time/residue: 0.4601
  time to fit residues: 108.7376
Evaluate side-chains
  192 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 138
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  153 TYR
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  291 LYS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  390 TYR
Chi-restraints excluded: chain A residue  486 LYS
Chi-restraints excluded: chain A residue  500 LYS
Chi-restraints excluded: chain A residue  507 LYS
Chi-restraints excluded: chain A residue  527 ASP
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  614 TYR
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  636 ARG
Chi-restraints excluded: chain A residue  649 LEU
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  698 CYS
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  775 MET
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  813 ILE
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  836 PHE
Chi-restraints excluded: chain A residue  853 ILE
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1066 THR
Chi-restraints excluded: chain A residue 1297 ILE
Chi-restraints excluded: chain A residue 1311 ASN
Chi-restraints excluded: chain A residue 1320 ASP
Chi-restraints excluded: chain A residue 1381 LEU
Chi-restraints excluded: chain A residue 1550 THR
Chi-restraints excluded: chain A residue 1569 CYS
Chi-restraints excluded: chain A residue 1593 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 134 optimal weight:    9.9990
   chunk 132 optimal weight:   10.0000
   chunk 131 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 129 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    1.6784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 672 ASN
** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1660 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4800 r_free = 0.4800 target = 0.178762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.155152 restraints weight = 32809.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.4411 rms_B_bonded: 2.11
r_work: 0.4307 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.4187 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.4187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6711
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  12526  Z= 0.224
  Angle     :  0.781   9.529  17248  Z= 0.396
  Chirality :  0.047   0.323   1993
  Planarity :  0.006   0.059   1994
  Dihedral  : 15.403  76.205   2417
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  7.11 %
    Allowed  : 28.95 %
    Favored  : 63.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.22), residues: 1343
  helix: -0.05 (0.21), residues: 574
  sheet: -2.87 (0.49), residues: 98
  loop : -1.80 (0.23), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 688 
 TYR   0.023   0.003   TYR A 124 
 PHE   0.020   0.002   PHE A1706 
 TRP   0.027   0.003   TRP A 316 
 HIS   0.008   0.001   HIS A 184 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00535 /  0.22 (12525)
  covalent geometry    : angle       0.78053 /  0.40 (17246)
  SS BOND              : bond        0.00222 /  0.15 (    1)
  SS BOND              : angle       0.42679 /  0.24 (    2)
  hydrogen bonds       : bond        0.05366 /  3.54 (  515)
  hydrogen bonds       : angle       5.35372 /  3.75 ( 1416)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 144
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 GLN cc_start: 0.6630 (OUTLIER) cc_final: 0.6128 (tm-30)
REVERT: A  144 LYS cc_start: 0.6314 (ptmm) cc_final: 0.5968 (pttm)
REVERT: A  205 LEU cc_start: 0.2642 (OUTLIER) cc_final: 0.2202 (mp)
REVERT: A  230 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8057 (mp)
REVERT: A  499 ARG cc_start: 0.8332 (ptp-110) cc_final: 0.8087 (ptp-110)
REVERT: A  500 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8181 (tptt)
REVERT: A  507 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7517 (pptt)
REVERT: A  636 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.5585 (mtm110)
REVERT: A  672 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7262 (p0)
REVERT: A  775 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6157 (mpp)
REVERT: A  832 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7917 (mtpt)
REVERT: A  836 PHE cc_start: 0.3195 (OUTLIER) cc_final: 0.2143 (p90)
REVERT: A  837 MET cc_start: 0.1275 (mmp) cc_final: 0.0409 (mmp)
REVERT: A  842 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6618 (tpp)
REVERT: A  865 LEU cc_start: 0.6943 (mt) cc_final: 0.6564 (mt)
REVERT: A 1337 ASP cc_start: 0.7297 (t0) cc_final: 0.6982 (p0)
REVERT: A 1381 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7008 (pt)
REVERT: A 1660 ASN cc_start: 0.4711 (m-40) cc_final: 0.4499 (m110)
REVERT: A 1803 GLU cc_start: 0.5026 (OUTLIER) cc_final: 0.4401 (pp20)
  outliers start: 87
  outliers final: 42
  residues processed: 215
  average time/residue: 0.4924
  time to fit residues: 115.3231
Evaluate side-chains
  194 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 139
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  291 LYS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  500 LYS
Chi-restraints excluded: chain A residue  507 LYS
Chi-restraints excluded: chain A residue  527 ASP
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  614 TYR
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  636 ARG
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  672 ASN
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  698 CYS
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  775 MET
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  813 ILE
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  832 LYS
Chi-restraints excluded: chain A residue  836 PHE
Chi-restraints excluded: chain A residue  842 MET
Chi-restraints excluded: chain A residue  853 ILE
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1032 ILE
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1066 THR
Chi-restraints excluded: chain A residue 1297 ILE
Chi-restraints excluded: chain A residue 1311 ASN
Chi-restraints excluded: chain A residue 1320 ASP
Chi-restraints excluded: chain A residue 1381 LEU
Chi-restraints excluded: chain A residue 1550 THR
Chi-restraints excluded: chain A residue 1569 CYS
Chi-restraints excluded: chain A residue 1593 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 128 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0670
   chunk 94 optimal weight:    0.5980
   chunk 131 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 102 optimal weight:    0.5980
   chunk 95 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.5718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 139 ASN
** A1062 HIS ** 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 = 0.4820 r_free = 0.4820 target = 0.180118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.156896 restraints weight = 32856.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.4447 rms_B_bonded: 2.12
r_work: 0.4339 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work (final): 0.4339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6492
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  12526  Z= 0.153
  Angle     :  0.739  11.498  17248  Z= 0.374
  Chirality :  0.044   0.277   1993
  Planarity :  0.006   0.059   1994
  Dihedral  : 15.372  76.243   2414
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  5.72 %
    Allowed  : 30.91 %
    Favored  : 63.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.22), residues: 1343
  helix:  0.07 (0.21), residues: 574
  sheet: -3.00 (0.45), residues: 110
  loop : -1.70 (0.24), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 688 
 TYR   0.024   0.002   TYR A1714 
 PHE   0.023   0.002   PHE A 498 
 TRP   0.030   0.003   TRP A 316 
 HIS   0.005   0.001   HIS A1041 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.15 (12525)
  covalent geometry    : angle       0.73940 /  0.37 (17246)
  SS BOND              : bond        0.00229 /  0.15 (    1)
  SS BOND              : angle       0.42261 /  0.24 (    2)
  hydrogen bonds       : bond        0.04973 /  3.27 (  515)
  hydrogen bonds       : angle       5.24081 /  3.67 ( 1416)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 135
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 LEU cc_start: 0.2320 (OUTLIER) cc_final: 0.1916 (mp)
REVERT: A  230 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7937 (mp)
REVERT: A  499 ARG cc_start: 0.8257 (ptp-110) cc_final: 0.7983 (ptp-110)
REVERT: A  500 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8089 (tptt)
REVERT: A  507 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7463 (pptt)
REVERT: A  636 ARG cc_start: 0.5434 (OUTLIER) cc_final: 0.5170 (mtm110)
REVERT: A  836 PHE cc_start: 0.2533 (OUTLIER) cc_final: 0.1649 (p90)
REVERT: A  842 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6171 (tpp)
REVERT: A  865 LEU cc_start: 0.6810 (mt) cc_final: 0.6465 (mt)
REVERT: A 1381 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6904 (OUTLIER)
  outliers start: 70
  outliers final: 42
  residues processed: 194
  average time/residue: 0.5280
  time to fit residues: 111.7507
Evaluate side-chains
  178 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 129
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  291 LYS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  390 TYR
Chi-restraints excluded: chain A residue  500 LYS
Chi-restraints excluded: chain A residue  507 LYS
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  614 TYR
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  636 ARG
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  698 CYS
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  813 ILE
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  836 PHE
Chi-restraints excluded: chain A residue  842 MET
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  853 ILE
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1066 THR
Chi-restraints excluded: chain A residue 1311 ASN
Chi-restraints excluded: chain A residue 1320 ASP
Chi-restraints excluded: chain A residue 1381 LEU
Chi-restraints excluded: chain A residue 1550 THR
Chi-restraints excluded: chain A residue 1569 CYS
Chi-restraints excluded: chain A residue 1593 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 111 optimal weight:    0.0970
   chunk 77 optimal weight:    2.9990
   chunk 113 optimal weight:    0.7980
   chunk 31 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 928 GLN
** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1660 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4811 r_free = 0.4811 target = 0.179517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.156092 restraints weight = 32718.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.4437 rms_B_bonded: 2.10
r_work: 0.4339 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.4222 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.4222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6627
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12526  Z= 0.171
  Angle     :  0.766  11.596  17248  Z= 0.386
  Chirality :  0.045   0.290   1993
  Planarity :  0.006   0.059   1994
  Dihedral  : 15.362  77.108   2411
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 15.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 31.97 %
    Favored  : 62.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.22), residues: 1343
  helix:  0.04 (0.21), residues: 573
  sheet: -3.03 (0.46), residues: 110
  loop : -1.73 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 688 
 TYR   0.025   0.002   TYR A1714 
 PHE   0.021   0.002   PHE A 894 
 TRP   0.033   0.003   TRP A 316 
 HIS   0.006   0.001   HIS A1041 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00412 /  0.17 (12525)
  covalent geometry    : angle       0.76573 /  0.39 (17246)
  SS BOND              : bond        0.00220 /  0.15 (    1)
  SS BOND              : angle       0.47338 /  0.25 (    2)
  hydrogen bonds       : bond        0.04991 /  3.29 (  515)
  hydrogen bonds       : angle       5.26952 /  3.69 ( 1416)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 134
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 LEU cc_start: 0.2546 (OUTLIER) cc_final: 0.2087 (mp)
REVERT: A  230 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7987 (mp)
REVERT: A  500 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8200 (tptt)
REVERT: A  507 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7574 (pptt)
REVERT: A  636 ARG cc_start: 0.5861 (OUTLIER) cc_final: 0.5515 (mtm110)
REVERT: A  836 PHE cc_start: 0.2893 (OUTLIER) cc_final: 0.1956 (p90)
REVERT: A  842 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6296 (tpp)
REVERT: A  865 LEU cc_start: 0.6879 (mt) cc_final: 0.6505 (mt)
REVERT: A 1381 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6916 (pt)
REVERT: A 1660 ASN cc_start: 0.4755 (m-40) cc_final: 0.4526 (m110)
REVERT: A 1709 ASP cc_start: 0.6146 (t0) cc_final: 0.5901 (t0)
  outliers start: 64
  outliers final: 38
  residues processed: 187
  average time/residue: 0.5187
  time to fit residues: 105.6361
Evaluate side-chains
  178 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 132
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  291 LYS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  500 LYS
Chi-restraints excluded: chain A residue  507 LYS
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  614 TYR
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  627 ILE
Chi-restraints excluded: chain A residue  636 ARG
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  698 CYS
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  813 ILE
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  836 PHE
Chi-restraints excluded: chain A residue  842 MET
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  853 ILE
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1066 THR
Chi-restraints excluded: chain A residue 1311 ASN
Chi-restraints excluded: chain A residue 1381 LEU
Chi-restraints excluded: chain A residue 1550 THR
Chi-restraints excluded: chain A residue 1569 CYS
Chi-restraints excluded: chain A residue 1593 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 103 optimal weight:    0.6980
   chunk 132 optimal weight:    1.9990
   chunk 110 optimal weight:    0.7980
   chunk 81 optimal weight:    0.5980
   chunk 108 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 104 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 21 optimal weight:    9.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4819 r_free = 0.4819 target = 0.179993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.156724 restraints weight = 32819.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.4449 rms_B_bonded: 2.12
r_work: 0.4350 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.4234 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.4234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6604
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12526  Z= 0.157
  Angle     :  0.771  12.690  17248  Z= 0.388
  Chirality :  0.044   0.283   1993
  Planarity :  0.006   0.060   1994
  Dihedral  : 15.318  77.904   2409
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 32.22 %
    Favored  : 62.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.22), residues: 1343
  helix:  0.13 (0.21), residues: 570
  sheet: -3.05 (0.46), residues: 110
  loop : -1.71 (0.24), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 688 
 TYR   0.029   0.002   TYR A 560 
 PHE   0.019   0.001   PHE A 920 
 TRP   0.041   0.003   TRP A 316 
 HIS   0.006   0.001   HIS A1041 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.16 (12525)
  covalent geometry    : angle       0.77104 /  0.39 (17246)
  SS BOND              : bond        0.00198 /  0.13 (    1)
  SS BOND              : angle       0.33683 /  0.18 (    2)
  hydrogen bonds       : bond        0.04890 /  3.22 (  515)
  hydrogen bonds       : angle       5.23190 /  3.66 ( 1416)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 134
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 LEU cc_start: 0.2687 (OUTLIER) cc_final: 0.2217 (mp)
REVERT: A  230 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7962 (mp)
REVERT: A  390 TYR cc_start: 0.6933 (t80) cc_final: 0.6427 (t80)
REVERT: A  507 LYS cc_start: 0.7883 (pttt) cc_final: 0.7468 (pptt)
REVERT: A  636 ARG cc_start: 0.5835 (OUTLIER) cc_final: 0.5469 (mtm110)
REVERT: A  654 ARG cc_start: 0.5617 (ppt170) cc_final: 0.5273 (pmt-80)
REVERT: A  836 PHE cc_start: 0.2874 (OUTLIER) cc_final: 0.1948 (p90)
REVERT: A  865 LEU cc_start: 0.6765 (mt) cc_final: 0.6456 (mt)
REVERT: A 1381 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6839 (pt)
REVERT: A 1660 ASN cc_start: 0.4937 (m-40) cc_final: 0.4726 (m110)
  outliers start: 59
  outliers final: 40
  residues processed: 185
  average time/residue: 0.5146
  time to fit residues: 103.6924
Evaluate side-chains
  172 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 127
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  291 LYS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  580 LYS
Chi-restraints excluded: chain A residue  614 TYR
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  627 ILE
Chi-restraints excluded: chain A residue  636 ARG
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  698 CYS
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  813 ILE
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  836 PHE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  853 ILE
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1066 THR
Chi-restraints excluded: chain A residue 1297 ILE
Chi-restraints excluded: chain A residue 1311 ASN
Chi-restraints excluded: chain A residue 1381 LEU
Chi-restraints excluded: chain A residue 1550 THR
Chi-restraints excluded: chain A residue 1569 CYS
Chi-restraints excluded: chain A residue 1593 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 64 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 100 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4798 r_free = 0.4798 target = 0.178482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.154840 restraints weight = 33064.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.4414 rms_B_bonded: 2.19
r_work: 0.4303 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.4303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6554
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  12526  Z= 0.200
  Angle     :  0.826  12.905  17248  Z= 0.416
  Chirality :  0.046   0.284   1993
  Planarity :  0.006   0.067   1994
  Dihedral  : 15.327  78.752   2409
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 17.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 33.20 %
    Favored  : 62.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.22), residues: 1343
  helix: -0.06 (0.21), residues: 575
  sheet: -3.02 (0.46), residues: 100
  loop : -1.83 (0.23), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG A 688 
 TYR   0.025   0.002   TYR A 914 
 PHE   0.033   0.002   PHE A 867 
 TRP   0.051   0.004   TRP A 316 
 HIS   0.005   0.001   HIS A 184 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00483 /  0.20 (12525)
  covalent geometry    : angle       0.82579 /  0.42 (17246)
  SS BOND              : bond        0.00252 /  0.17 (    1)
  SS BOND              : angle       0.44926 /  0.24 (    2)
  hydrogen bonds       : bond        0.05109 /  3.36 (  515)
  hydrogen bonds       : angle       5.35679 /  3.74 ( 1416)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 137
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 LEU cc_start: 0.2250 (OUTLIER) cc_final: 0.1825 (mp)
REVERT: A  230 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7956 (mp)
REVERT: A  507 LYS cc_start: 0.7800 (pttt) cc_final: 0.7382 (pptt)
REVERT: A  636 ARG cc_start: 0.5267 (OUTLIER) cc_final: 0.4958 (mtm110)
REVERT: A  654 ARG cc_start: 0.5439 (ppt170) cc_final: 0.5186 (pmt-80)
REVERT: A  812 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7656 (tm-30)
REVERT: A  836 PHE cc_start: 0.2625 (OUTLIER) cc_final: 0.1598 (p90)
REVERT: A  865 LEU cc_start: 0.6810 (mt) cc_final: 0.6400 (mp)
REVERT: A 1337 ASP cc_start: 0.7030 (t0) cc_final: 0.6694 (p0)
REVERT: A 1381 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6942 (pt)
  outliers start: 50
  outliers final: 38
  residues processed: 181
  average time/residue: 0.5338
  time to fit residues: 105.4789
Evaluate side-chains
  174 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 131
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  187 ARG
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  291 LYS
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  527 ASP
Chi-restraints excluded: chain A residue  614 TYR
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  627 ILE
Chi-restraints excluded: chain A residue  636 ARG
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  698 CYS
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  813 ILE
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  836 PHE
Chi-restraints excluded: chain A residue  853 ILE
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1066 THR
Chi-restraints excluded: chain A residue 1297 ILE
Chi-restraints excluded: chain A residue 1311 ASN
Chi-restraints excluded: chain A residue 1381 LEU
Chi-restraints excluded: chain A residue 1550 THR
Chi-restraints excluded: chain A residue 1593 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 103 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   chunk 134 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 100 optimal weight:    0.5980
   chunk 123 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0770
   overall best weight:    0.5538

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1660 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4815 r_free = 0.4815 target = 0.179662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.156568 restraints weight = 32699.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.4443 rms_B_bonded: 2.12
r_work: 0.4339 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.4223 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6613
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  12526  Z= 0.157
  Angle     :  0.810  15.898  17248  Z= 0.406
  Chirality :  0.045   0.255   1993
  Planarity :  0.006   0.059   1994
  Dihedral  : 15.207  78.255   2404
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 34.34 %
    Favored  : 62.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.22), residues: 1343
  helix: -0.00 (0.21), residues: 575
  sheet: -2.97 (0.46), residues: 100
  loop : -1.81 (0.23), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 789 
 TYR   0.028   0.002   TYR A 914 
 PHE   0.028   0.002   PHE A 867 
 TRP   0.052   0.003   TRP A 316 
 HIS   0.006   0.001   HIS A1041 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.16 (12525)
  covalent geometry    : angle       0.81006 /  0.41 (17246)
  SS BOND              : bond        0.00193 /  0.13 (    1)
  SS BOND              : angle       0.33757 /  0.18 (    2)
  hydrogen bonds       : bond        0.04883 /  3.20 (  515)
  hydrogen bonds       : angle       5.29273 /  3.70 ( 1416)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3878.46 seconds
wall clock time: 67 minutes 1.12 seconds (4021.12 seconds total)