Starting phenix.real_space_refine
on Tue Jul 29 08:57:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5zak_6904/07_2025/5zak_6904.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5zak_6904/07_2025/5zak_6904.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5zak_6904/07_2025/5zak_6904.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5zak_6904/07_2025/5zak_6904.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5zak_6904/07_2025/5zak_6904.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5zak_6904/07_2025/5zak_6904.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    7087      2.51       5
     N    1906      2.21       5
     O    2053      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11112
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1314, 10552
          Classifications: {'peptide': 1314}
          Link IDs: {'CIS': 21, 'PCIS': 4, 'PTRANS': 64, 'TRANS': 1224}
          Chain breaks: 8
    Chain: "B"
      Number of atoms: 560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 560
          Classifications: {'peptide': 75}
          Link IDs: {'PCIS': 2, 'TRANS': 72}
  Time building chain proxies: 6.71, per 1000 atoms: 0.60
  Number of scatterers: 11112
  At special positions: 0
  Unit cell: (109.749, 104.523, 162.011, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      66     16.00
     O    2053      8.00
     N    1906      7.00
     C    7087      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 196 " - pdb=" SG  CYS A 199 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 443 " - pdb=" SG  CYS A 531 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.75
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2666

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 8 sheets defined
      47.9% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 69 through 85
      removed outlier: 3.850A  pdb=" N   ILE A  73 " --> pdb=" O   GLY A  69 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   TYR A  83 " --> pdb=" O   LYS A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 115
      removed outlier: 4.526A  pdb=" N   THR A 115 " --> pdb=" O   SER A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 159
      removed outlier: 3.651A  pdb=" N   LEU A 156 " --> pdb=" O   CYS A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 180
    Processing helix  chain 'A' and resid 185 through 194
    Processing helix  chain 'A' and resid 218 through 231
    Processing helix  chain 'A' and resid 264 through 285
      removed outlier: 4.486A  pdb=" N   ASN A 285 " --> pdb=" O   ILE A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 314
      removed outlier: 4.314A  pdb=" N   SER A 299 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 336
      removed outlier: 3.821A  pdb=" N   ALA A 318 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   LYS A 331 " --> pdb=" O   ARG A 327 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   TYR A 332 " --> pdb=" O   GLU A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 359
    Processing helix  chain 'A' and resid 377 through 386
    Processing helix  chain 'A' and resid 451 through 461
      removed outlier: 3.642A  pdb=" N   VAL A 455 " --> pdb=" O   ARG A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 510
      removed outlier: 3.585A  pdb=" N   GLN A 501 " --> pdb=" O   GLU A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 516
      removed outlier: 3.548A  pdb=" N   ASN A 514 " --> pdb=" O   ALA A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 551
    Processing helix  chain 'A' and resid 570 through 590
      removed outlier: 4.327A  pdb=" N   ASN A 588 " --> pdb=" O   LYS A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 639
      removed outlier: 3.723A  pdb=" N   TYR A 637 " --> pdb=" O   HIS A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 704
    Processing helix  chain 'A' and resid 713 through 726
      removed outlier: 4.340A  pdb=" N   LYS A 717 " --> pdb=" O   MET A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 798
      removed outlier: 3.967A  pdb=" N   ASP A 797 " --> pdb=" O   PRO A 794 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   THR A 798 " --> pdb=" O   PRO A 795 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 794 through 798'
    Processing helix  chain 'A' and resid 839 through 855
    Processing helix  chain 'A' and resid 894 through 903
      removed outlier: 3.766A  pdb=" N   GLU A 898 " --> pdb=" O   PHE A 894 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER A 903 " --> pdb=" O   ASP A 899 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 907
      removed outlier: 4.091A  pdb=" N   ILE A 907 " --> pdb=" O   GLU A 904 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 904 through 907'
    Processing helix  chain 'A' and resid 923 through 927
    Processing helix  chain 'A' and resid 967 through 975
      removed outlier: 3.943A  pdb=" N   TYR A 971 " --> pdb=" O   THR A 967 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1002 through 1010
    Processing helix  chain 'A' and resid 1015 through 1031
      removed outlier: 3.987A  pdb=" N   GLN A1031 " --> pdb=" O   LEU A1027 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1044 through 1052
    Processing helix  chain 'A' and resid 1053 through 1072
      removed outlier: 3.776A  pdb=" N   CYS A1063 " --> pdb=" O   TYR A1059 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1294 through 1302
    Processing helix  chain 'A' and resid 1312 through 1333
      removed outlier: 4.522A  pdb=" N   SER A1321 " --> pdb=" O   MET A1317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1339 through 1352
    Processing helix  chain 'A' and resid 1352 through 1362
      removed outlier: 3.702A  pdb=" N   LYS A1362 " --> pdb=" O   ARG A1358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1363 through 1368
      Proline residue:  A1366  - end of helix
      No H-bonds generated for 'chain 'A' and resid 1363 through 1368'
    Processing helix  chain 'A' and resid 1558 through 1574
    Processing helix  chain 'A' and resid 1575 through 1587
      removed outlier: 4.730A  pdb=" N   ALA A1579 " --> pdb=" O   GLY A1575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1594 through 1599
    Processing helix  chain 'A' and resid 1656 through 1674
      removed outlier: 3.873A  pdb=" N   GLY A1665 " --> pdb=" O   HIS A1661 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLU A1667 " --> pdb=" O   ILE A1663 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   ASN A1668 " --> pdb=" O   SER A1664 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   PHE A1669 " --> pdb=" O   GLY A1665 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   LYS A1672 " --> pdb=" O   ASN A1668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1679 through 1687
      removed outlier: 4.092A  pdb=" N   LEU A1683 " --> pdb=" O   ASN A1679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1701 through 1722
      removed outlier: 4.173A  pdb=" N   ALA A1710 " --> pdb=" O   PHE A1706 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE A1711 " --> pdb=" O   LEU A1707 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ASP A1713 " --> pdb=" O   ASP A1709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1728 through 1739
    Processing helix  chain 'A' and resid 1741 through 1752
      removed outlier: 3.825A  pdb=" N   PHE A1745 " --> pdb=" O   ASN A1741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1762 through 1774
      removed outlier: 3.566A  pdb=" N   PHE A1766 " --> pdb=" O   SER A1762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1805 through 1823
      removed outlier: 4.164A  pdb=" N   GLY A1809 " --> pdb=" O   PRO A1805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1826 through 1845
      Proline residue:  A1836  - end of helix
      Proline residue:  A1840  - end of helix
    Processing helix  chain 'A' and resid 1853 through 1858
    Processing helix  chain 'A' and resid 1896 through 1911
    Processing helix  chain 'B' and resid 293 through 305
      removed outlier: 3.876A  pdb=" N   VAL B 297 " --> pdb=" O   ALA B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 362
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63
      removed outlier: 8.656A  pdb=" N   LEU A 172 " --> pdb=" O   LEU A 203 " (cutoff:3.500A)
      removed outlier: 9.417A  pdb=" N   LEU A 205 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   VAL A  97 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   PHE A  98 " --> pdb=" O   MET A 150 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 250 through 251
      removed outlier: 5.807A  pdb=" N   VAL A 534 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 474 through 475
      removed outlier: 3.705A  pdb=" N   HIS A 482 " --> pdb=" O   SER A 475 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 829 through 836
      removed outlier: 6.595A  pdb=" N   LEU A 770 " --> pdb=" O   LYS A 832 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   SER A 834 " --> pdb=" O   CYS A 768 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   CYS A 768 " --> pdb=" O   SER A 834 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   PHE A 802 " --> pdb=" O   ILE A 773 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 776 through 780
      removed outlier: 6.632A  pdb=" N   GLU A 824 " --> pdb=" O   THR A 778 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 990 through 992
      removed outlier: 4.581A  pdb=" N   ALA A 930 " --> pdb=" O   VAL A 947 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   VAL A 931 " --> pdb=" O   HIS A1041 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1882 through 1884
    Processing sheet with id=AA8, first strand: chain 'B' and resid 324 through 328

    465 hydrogen bonds defined for protein.
    1368 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.59

  Time building geometry restraints manager: 3.27 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3053
        1.33 -     1.46: 2476
        1.46 -     1.58: 5712
        1.58 -     1.70: 1
        1.70 -     1.83: 90
  Bond restraints: 11332
  Sorted by residual:
  bond pdb=" N   LYS A 862 "
       pdb=" CA  LYS A 862 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 9.60e-03 1.09e+04 1.04e+01
  bond pdb=" CA  VAL A1804 "
       pdb=" C   VAL A1804 "
    ideal  model  delta    sigma   weight residual
    1.522  1.543 -0.021 7.10e-03 1.98e+04 8.97e+00
  bond pdb=" N   LYS A1589 "
       pdb=" CA  LYS A1589 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.20e-02 6.94e+03 7.66e+00
  bond pdb=" N   LYS A 135 "
       pdb=" CA  LYS A 135 "
    ideal  model  delta    sigma   weight residual
    1.458  1.507 -0.049 1.90e-02 2.77e+03 6.67e+00
  bond pdb=" C   MET A 713 "
       pdb=" N   PRO A 714 "
    ideal  model  delta    sigma   weight residual
    1.336  1.368 -0.032 1.25e-02 6.40e+03 6.54e+00
  ... (remaining 11327 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.40: 14621
        3.40 -     6.80: 578
        6.80 -    10.19: 92
       10.19 -    13.59: 24
       13.59 -    16.99: 8
  Bond angle restraints: 15323
  Sorted by residual:
  angle pdb=" C   THR A 134 "
        pdb=" N   LYS A 135 "
        pdb=" CA  LYS A 135 "
      ideal   model   delta    sigma   weight residual
     121.70  137.95  -16.25 1.80e+00 3.09e-01 8.15e+01
  angle pdb=" C   HIS A 116 "
        pdb=" N   SER A 117 "
        pdb=" CA  SER A 117 "
      ideal   model   delta    sigma   weight residual
     121.70  136.76  -15.06 1.80e+00 3.09e-01 7.00e+01
  angle pdb=" C   LEU A 649 "
        pdb=" N   ALA A 650 "
        pdb=" CA  ALA A 650 "
      ideal   model   delta    sigma   weight residual
     121.70  135.01  -13.31 1.80e+00 3.09e-01 5.47e+01
  angle pdb=" C   ARG A 137 "
        pdb=" N   TRP A 138 "
        pdb=" CA  TRP A 138 "
      ideal   model   delta    sigma   weight residual
     121.70  134.41  -12.71 1.80e+00 3.09e-01 4.99e+01
  angle pdb=" C   GLU A1551 "
        pdb=" N   GLN A1552 "
        pdb=" CA  GLN A1552 "
      ideal   model   delta    sigma   weight residual
     121.70  134.32  -12.62 1.80e+00 3.09e-01 4.92e+01
  ... (remaining 15318 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.24: 6453
       17.24 -    34.47: 460
       34.47 -    51.71: 60
       51.71 -    68.94: 2
       68.94 -    86.18: 4
  Dihedral angle restraints: 6979
    sinusoidal: 2876
      harmonic: 4103
  Sorted by residual:
  dihedral pdb=" CA  PRO A1376 "
           pdb=" C   PRO A1376 "
           pdb=" N   PRO A1377 "
           pdb=" CA  PRO A1377 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.70  -44.30     0      5.00e+00 4.00e-02 7.85e+01
  dihedral pdb=" CA  ALA A 207 "
           pdb=" C   ALA A 207 "
           pdb=" N   SER A 208 "
           pdb=" CA  SER A 208 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -139.53  -40.47     0      5.00e+00 4.00e-02 6.55e+01
  dihedral pdb=" CA  SER A 165 "
           pdb=" C   SER A 165 "
           pdb=" N   LEU A 166 "
           pdb=" CA  LEU A 166 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.53  -38.47     0      5.00e+00 4.00e-02 5.92e+01
  ... (remaining 6976 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1201
       0.068 -    0.136: 443
       0.136 -    0.204: 80
       0.204 -    0.272: 17
       0.272 -    0.340: 6
  Chirality restraints: 1747
  Sorted by residual:
  chirality pdb=" CB  ILE A 479 "
            pdb=" CA  ILE A 479 "
            pdb=" CG1 ILE A 479 "
            pdb=" CG2 ILE A 479 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" CG  LEU A 865 "
            pdb=" CB  LEU A 865 "
            pdb=" CD1 LEU A 865 "
            pdb=" CD2 LEU A 865 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.26   -0.33 2.00e-01 2.50e+01 2.76e+00
  chirality pdb=" CB  ILE A 813 "
            pdb=" CA  ILE A 813 "
            pdb=" CG1 ILE A 813 "
            pdb=" CG2 ILE A 813 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.37e+00
  ... (remaining 1744 not shown)

  Planarity restraints: 1954
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 682 "   -0.063 5.00e-02 4.00e+02   9.57e-02 1.47e+01
        pdb=" N   PRO A 683 "    0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO A 683 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 683 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 637 "    0.036 2.00e-02 2.50e+03   2.57e-02 1.32e+01
        pdb=" CG  TYR A 637 "   -0.061 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 637 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 637 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 637 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 637 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 637 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 637 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A1664 "   -0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   SER A1664 "    0.056 2.00e-02 2.50e+03
        pdb=" O   SER A1664 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLY A1665 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1951 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 933
        2.73 -     3.27: 11569
        3.27 -     3.81: 19692
        3.81 -     4.36: 24072
        4.36 -     4.90: 37002
  Nonbonded interactions: 93268
  Sorted by model distance:
  nonbonded pdb=" O   LEU A1684 "
            pdb=" OG1 THR A1688 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   VAL A  75 "
            pdb=" OG1 THR A  78 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OG1 THR B 331 "
            pdb=" O   PRO B 333 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OD2 ASP A 283 "
            pdb=" OG  SER B 318 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   SER A1868 "
            pdb=" OH  TYR A1897 "
     model   vdw
     2.238 3.040
  ... (remaining 93263 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.590
  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:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     28.170
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6491
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.095  11334  Z= 0.420
  Angle     :  1.607  16.991  15327  Z= 0.871
  Chirality :  0.073   0.340   1747
  Planarity :  0.010   0.096   1954
  Dihedral  : 11.718  86.176   4307
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 17.87
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 17.31 %
    Favored  : 82.40 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  3.22 %
    Favored  : 96.05 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 2.86 %
    Twisted General : 0.84 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.20 (0.18), residues: 1369
  helix: -3.01 (0.15), residues: 576
  sheet: -3.81 (0.40), residues: 97
  loop : -3.86 (0.21), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.005   TRP A 133 
 HIS   0.021   0.004   HIS A 703 
 PHE   0.042   0.005   PHE A 537 
 TYR   0.061   0.005   TYR A 637 
 ARG   0.012   0.001   ARG A 640 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17211 (  465)
  hydrogen bonds       : angle       9.29059 ( 1368)
  SS BOND              : bond        0.00683 (    2)
  SS BOND              : angle       3.06336 (    4)
  covalent geometry    : bond        0.00886 (11332)
  covalent geometry    : angle       1.60674 (15323)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 266
  time to evaluate  : 1.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.7747 (tp) cc_final: 0.7479 (tp)
REVERT: A   80 GLU cc_start: 0.8731 (tt0) cc_final: 0.8280 (tp30)
REVERT: A  190 MET cc_start: 0.8634 (ttp) cc_final: 0.8380 (tmm)
REVERT: A  218 GLU cc_start: 0.9131 (pt0) cc_final: 0.8917 (pt0)
REVERT: A  224 GLN cc_start: 0.8815 (tt0) cc_final: 0.8379 (tm-30)
REVERT: A  239 ASP cc_start: 0.5620 (m-30) cc_final: 0.5401 (m-30)
REVERT: A  458 ASN cc_start: 0.6512 (t0) cc_final: 0.6217 (t0)
REVERT: A  479 ILE cc_start: 0.3082 (OUTLIER) cc_final: 0.2733 (mp)
REVERT: A  560 TYR cc_start: 0.7210 (t80) cc_final: 0.6672 (t80)
REVERT: A  580 LYS cc_start: 0.9197 (ttpt) cc_final: 0.8941 (tppt)
REVERT: A  697 ILE cc_start: 0.7652 (mt) cc_final: 0.6961 (mt)
REVERT: A 1068 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7675 (tp30)
REVERT: A 1313 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7694 (mm-30)
REVERT: A 1327 ILE cc_start: 0.8175 (mm) cc_final: 0.7849 (pt)
REVERT: A 1346 MET cc_start: 0.7857 (mmm) cc_final: 0.7622 (mmm)
REVERT: A 1358 ARG cc_start: 0.7458 (mtt180) cc_final: 0.7180 (mtt-85)
REVERT: A 1363 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8433 (mmmt)
REVERT: A 1564 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8658 (mt-10)
REVERT: A 1576 GLU cc_start: 0.8692 (tt0) cc_final: 0.8414 (mm-30)
REVERT: A 1687 PHE cc_start: 0.8364 (m-80) cc_final: 0.7820 (m-80)
REVERT: A 1692 TYR cc_start: 0.7894 (t80) cc_final: 0.7443 (t80)
REVERT: A 1705 GLU cc_start: 0.7121 (tt0) cc_final: 0.6528 (tt0)
REVERT: A 1768 VAL cc_start: 0.7740 (t) cc_final: 0.7374 (p)
REVERT: A 1772 PHE cc_start: 0.6296 (t80) cc_final: 0.5960 (t80)
REVERT: A 1782 MET cc_start: 0.4860 (mmt) cc_final: 0.4396 (mpp)
REVERT: A 1810 ASP cc_start: 0.6632 (m-30) cc_final: 0.6152 (t0)
REVERT: A 1813 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6638 (mm-30)
REVERT: A 1825 MET cc_start: 0.7483 (mtt) cc_final: 0.7110 (mtm)
REVERT: B  353 ARG cc_start: 0.8378 (ttp80) cc_final: 0.8112 (ttp80)
  outliers start: 9
  outliers final: 1
  residues processed: 273
  average time/residue: 0.3582
  time to fit residues: 129.0853
Evaluate side-chains
  156 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 154
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    0.9990
   chunk 104 optimal weight:    0.8980
   chunk 58 optimal weight:    0.1980
   chunk 35 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 125 optimal weight:    0.0980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 928 GLN
A1029 ASN
** A1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1041 HIS
A1305 ASN
** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1661 HIS
A1774 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.090610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.070556 restraints weight = 77090.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.072752 restraints weight = 54211.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.074289 restraints weight = 41545.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6516
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11334  Z= 0.172
  Angle     :  0.945  12.192  15327  Z= 0.490
  Chirality :  0.051   0.320   1747
  Planarity :  0.007   0.082   1954
  Dihedral  :  8.096  33.621   1519
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 22.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.61 %
    Favored  : 85.39 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.14 %
    Favored  : 96.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 1.43 %
    Twisted General : 0.46 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.23 (0.20), residues: 1369
  helix: -1.89 (0.18), residues: 612
  sheet: -3.24 (0.40), residues: 126
  loop : -3.69 (0.23), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 316 
 HIS   0.006   0.001   HIS A1661 
 PHE   0.020   0.002   PHE A1322 
 TYR   0.019   0.002   TYR A 972 
 ARG   0.006   0.001   ARG A 821 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05621 (  465)
  hydrogen bonds       : angle       6.80487 ( 1368)
  SS BOND              : bond        0.00219 (    2)
  SS BOND              : angle       1.92628 (    4)
  covalent geometry    : bond        0.00348 (11332)
  covalent geometry    : angle       0.94485 (15323)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 227
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 GLU cc_start: 0.8604 (tt0) cc_final: 0.8131 (tp30)
REVERT: A  133 TRP cc_start: 0.7241 (p90) cc_final: 0.6986 (p-90)
REVERT: A  190 MET cc_start: 0.8434 (ttp) cc_final: 0.8166 (tmm)
REVERT: A  224 GLN cc_start: 0.8788 (tt0) cc_final: 0.8346 (tm-30)
REVERT: A  239 ASP cc_start: 0.4983 (m-30) cc_final: 0.4576 (m-30)
REVERT: A  245 ARG cc_start: 0.6895 (mtp-110) cc_final: 0.5992 (tmt170)
REVERT: A  351 PHE cc_start: 0.9189 (t80) cc_final: 0.8974 (t80)
REVERT: A  378 ILE cc_start: 0.8479 (mm) cc_final: 0.8235 (mm)
REVERT: A  462 LYS cc_start: 0.7737 (mttt) cc_final: 0.7503 (mtmt)
REVERT: A  544 ARG cc_start: 0.7069 (ttp-110) cc_final: 0.5528 (tpp-160)
REVERT: A  560 TYR cc_start: 0.7013 (t80) cc_final: 0.5852 (t80)
REVERT: A  793 TYR cc_start: 0.7946 (m-80) cc_final: 0.7696 (m-80)
REVERT: A 1068 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7623 (tp30)
REVERT: A 1314 ARG cc_start: 0.6375 (mmm-85) cc_final: 0.6144 (mmm160)
REVERT: A 1317 MET cc_start: 0.8211 (tpp) cc_final: 0.7961 (mtm)
REVERT: A 1346 MET cc_start: 0.7597 (mmm) cc_final: 0.7324 (mmm)
REVERT: A 1564 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8405 (mt-10)
REVERT: A 1566 LEU cc_start: 0.8908 (tt) cc_final: 0.8674 (tt)
REVERT: A 1668 ASN cc_start: 0.7907 (t0) cc_final: 0.7177 (t0)
REVERT: A 1685 GLN cc_start: 0.8846 (tt0) cc_final: 0.8544 (tm-30)
REVERT: A 1692 TYR cc_start: 0.7783 (t80) cc_final: 0.7438 (t80)
REVERT: A 1748 LEU cc_start: 0.8806 (mm) cc_final: 0.8459 (tp)
REVERT: A 1768 VAL cc_start: 0.7786 (t) cc_final: 0.7286 (p)
REVERT: A 1772 PHE cc_start: 0.6259 (t80) cc_final: 0.5972 (t80)
REVERT: A 1813 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6585 (mm-30)
REVERT: A 1837 MET cc_start: 0.6388 (mtt) cc_final: 0.4643 (mtt)
REVERT: B  311 TYR cc_start: 0.7834 (m-80) cc_final: 0.7485 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 227
  average time/residue: 0.3100
  time to fit residues: 93.2420
Evaluate side-chains
  156 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 12 optimal weight:    8.9990
   chunk 127 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 119 optimal weight:    8.9990
   chunk 80 optimal weight:    9.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 101 ASN
A 116 HIS
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 491 ASN
** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1325 HIS
** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1702 GLN
A1726 GLN
A1774 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.087656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.068157 restraints weight = 80134.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.070304 restraints weight = 55796.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.071909 restraints weight = 42667.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6572
moved from start:          0.3527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11334  Z= 0.200
  Angle     :  0.967  14.712  15327  Z= 0.498
  Chirality :  0.051   0.216   1747
  Planarity :  0.007   0.094   1954
  Dihedral  :  7.729  31.966   1519
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 26.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.44 %
    Favored  : 83.56 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  7.00 %
    Favored  : 92.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.78 (0.21), residues: 1369
  helix: -1.42 (0.19), residues: 623
  sheet: -3.46 (0.41), residues: 110
  loop : -3.52 (0.23), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 138 
 HIS   0.006   0.002   HIS A 703 
 PHE   0.018   0.002   PHE A 854 
 TYR   0.020   0.002   TYR A1752 
 ARG   0.007   0.001   ARG A 640 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05654 (  465)
  hydrogen bonds       : angle       6.63850 ( 1368)
  SS BOND              : bond        0.01185 (    2)
  SS BOND              : angle       2.37758 (    4)
  covalent geometry    : bond        0.00419 (11332)
  covalent geometry    : angle       0.96656 (15323)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 1.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.7660 (tp) cc_final: 0.7288 (tp)
REVERT: A   79 LYS cc_start: 0.9414 (mtmm) cc_final: 0.9203 (mtmm)
REVERT: A   80 GLU cc_start: 0.8586 (tt0) cc_final: 0.8179 (tp30)
REVERT: A  224 GLN cc_start: 0.8737 (tt0) cc_final: 0.8277 (tm-30)
REVERT: A  263 ARG cc_start: 0.4732 (tpt90) cc_final: 0.4473 (mtp180)
REVERT: A  458 ASN cc_start: 0.6623 (t0) cc_final: 0.6130 (t0)
REVERT: A  550 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7752 (pttt)
REVERT: A  560 TYR cc_start: 0.6803 (t80) cc_final: 0.5858 (t80)
REVERT: A  697 ILE cc_start: 0.7282 (mt) cc_final: 0.6737 (mt)
REVERT: A  701 LYS cc_start: 0.7744 (mmtm) cc_final: 0.7399 (mmtm)
REVERT: A  793 TYR cc_start: 0.8243 (m-80) cc_final: 0.7931 (m-80)
REVERT: A  965 TYR cc_start: 0.9022 (m-80) cc_final: 0.8656 (m-80)
REVERT: A 1068 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7589 (tp30)
REVERT: A 1313 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7384 (mm-30)
REVERT: A 1346 MET cc_start: 0.7541 (mmm) cc_final: 0.7332 (mmm)
REVERT: A 1358 ARG cc_start: 0.7290 (mtt180) cc_final: 0.6743 (mtt-85)
REVERT: A 1564 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8424 (mt-10)
REVERT: A 1664 SER cc_start: 0.7736 (t) cc_final: 0.7475 (p)
REVERT: A 1668 ASN cc_start: 0.7698 (t0) cc_final: 0.7143 (t0)
REVERT: A 1685 GLN cc_start: 0.8821 (tt0) cc_final: 0.8561 (tm-30)
REVERT: A 1692 TYR cc_start: 0.7898 (t80) cc_final: 0.7401 (t80)
REVERT: A 1705 GLU cc_start: 0.6663 (tm-30) cc_final: 0.6445 (tm-30)
REVERT: A 1748 LEU cc_start: 0.8843 (mm) cc_final: 0.8545 (tp)
REVERT: A 1768 VAL cc_start: 0.7839 (t) cc_final: 0.7517 (p)
REVERT: A 1808 MET cc_start: 0.6463 (mmt) cc_final: 0.6096 (mmm)
REVERT: A 1837 MET cc_start: 0.7085 (mtt) cc_final: 0.5829 (mtt)
REVERT: B  311 TYR cc_start: 0.7710 (m-80) cc_final: 0.7298 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 199
  average time/residue: 0.2920
  time to fit residues: 78.3391
Evaluate side-chains
  144 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 121 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   chunk 120 optimal weight:    7.9990
   chunk 97 optimal weight:    0.9990
   chunk 43 optimal weight:    7.9990
   chunk 116 optimal weight:    1.9990
   chunk 23 optimal weight:    8.9990
   chunk 60 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 GLN
A 362 HIS
** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 850 HIS
A 943 HIS
** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1660 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.086866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.066408 restraints weight = 77447.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.068441 restraints weight = 54846.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.070008 restraints weight = 42476.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6648
moved from start:          0.3967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11334  Z= 0.219
  Angle     :  0.997  15.301  15327  Z= 0.512
  Chirality :  0.052   0.211   1747
  Planarity :  0.007   0.092   1954
  Dihedral  :  7.792  31.212   1519
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 30.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.78 %
    Favored  : 84.22 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  4.03 %
    Favored  : 95.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.72 (0.21), residues: 1369
  helix: -1.30 (0.19), residues: 620
  sheet: -3.46 (0.43), residues: 110
  loop : -3.56 (0.23), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 138 
 HIS   0.007   0.002   HIS A 703 
 PHE   0.038   0.002   PHE A1669 
 TYR   0.021   0.002   TYR A1752 
 ARG   0.007   0.001   ARG A 640 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05671 (  465)
  hydrogen bonds       : angle       6.58645 ( 1368)
  SS BOND              : bond        0.00385 (    2)
  SS BOND              : angle       2.00237 (    4)
  covalent geometry    : bond        0.00464 (11332)
  covalent geometry    : angle       0.99650 (15323)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 190
  time to evaluate  : 1.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.7624 (tp) cc_final: 0.7245 (tp)
REVERT: A   79 LYS cc_start: 0.9359 (mtmm) cc_final: 0.9123 (mtmm)
REVERT: A   80 GLU cc_start: 0.8514 (tt0) cc_final: 0.8172 (tp30)
REVERT: A  224 GLN cc_start: 0.8689 (tt0) cc_final: 0.8250 (tm-30)
REVERT: A  263 ARG cc_start: 0.4508 (tpt90) cc_final: 0.4211 (mtp180)
REVERT: A  279 ASN cc_start: 0.9558 (t0) cc_final: 0.9239 (p0)
REVERT: A  333 ILE cc_start: 0.7256 (mm) cc_final: 0.7035 (mm)
REVERT: A  335 HIS cc_start: 0.8370 (t-90) cc_final: 0.7807 (m170)
REVERT: A  351 PHE cc_start: 0.9234 (t80) cc_final: 0.9015 (t80)
REVERT: A  550 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7694 (pttt)
REVERT: A  697 ILE cc_start: 0.7412 (mt) cc_final: 0.6942 (mt)
REVERT: A  965 TYR cc_start: 0.8944 (m-80) cc_final: 0.8513 (m-80)
REVERT: A 1337 ASP cc_start: 0.8857 (p0) cc_final: 0.8598 (p0)
REVERT: A 1365 LEU cc_start: 0.9170 (mm) cc_final: 0.8935 (mm)
REVERT: A 1369 MET cc_start: 0.7697 (mpp) cc_final: 0.7464 (mpp)
REVERT: A 1564 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8210 (mt-10)
REVERT: A 1664 SER cc_start: 0.7632 (t) cc_final: 0.7356 (p)
REVERT: A 1668 ASN cc_start: 0.7699 (t0) cc_final: 0.7159 (t0)
REVERT: A 1692 TYR cc_start: 0.7789 (t80) cc_final: 0.7479 (t80)
REVERT: A 1717 THR cc_start: 0.8019 (m) cc_final: 0.7625 (m)
REVERT: A 1768 VAL cc_start: 0.7827 (t) cc_final: 0.7451 (p)
REVERT: A 1808 MET cc_start: 0.6649 (mmt) cc_final: 0.6395 (mmm)
REVERT: A 1837 MET cc_start: 0.7267 (mtt) cc_final: 0.6356 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 191
  average time/residue: 0.3342
  time to fit residues: 86.1677
Evaluate side-chains
  143 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 123 optimal weight:    6.9990
   chunk 105 optimal weight:    0.0980
   chunk 41 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   chunk 103 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 4 optimal weight:   10.0000
   chunk 136 optimal weight:    8.9990
   chunk 9 optimal weight:    4.9990
   chunk 131 optimal weight:    8.9990
   overall best weight:    1.5382

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1614 GLN
** A1689 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 = 0.4213 r_free = 0.4213 target = 0.089216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.070509 restraints weight = 76470.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.072495 restraints weight = 55303.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.073915 restraints weight = 43242.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6497
moved from start:          0.4434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11334  Z= 0.168
  Angle     :  0.916  12.739  15327  Z= 0.470
  Chirality :  0.050   0.250   1747
  Planarity :  0.006   0.092   1954
  Dihedral  :  7.382  31.674   1519
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 23.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.92 %
    Favored  : 84.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.39 (0.21), residues: 1369
  helix: -0.96 (0.20), residues: 624
  sheet: -3.15 (0.44), residues: 104
  loop : -3.51 (0.23), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 138 
 HIS   0.013   0.001   HIS A1693 
 PHE   0.019   0.002   PHE A1766 
 TYR   0.018   0.002   TYR A 972 
 ARG   0.004   0.001   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05158 (  465)
  hydrogen bonds       : angle       6.26727 ( 1368)
  SS BOND              : bond        0.00246 (    2)
  SS BOND              : angle       1.49106 (    4)
  covalent geometry    : bond        0.00350 (11332)
  covalent geometry    : angle       0.91607 (15323)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.8492 (pm20) cc_final: 0.8248 (pm20)
REVERT: A   64 LEU cc_start: 0.7769 (tp) cc_final: 0.7475 (tp)
REVERT: A   79 LYS cc_start: 0.9385 (mtmm) cc_final: 0.9164 (mtmm)
REVERT: A  120 LYS cc_start: 0.8341 (tptp) cc_final: 0.8124 (tttt)
REVERT: A  218 GLU cc_start: 0.9131 (pt0) cc_final: 0.8828 (pm20)
REVERT: A  224 GLN cc_start: 0.8689 (tt0) cc_final: 0.8204 (tm-30)
REVERT: A  263 ARG cc_start: 0.4486 (tpt90) cc_final: 0.4153 (mtp180)
REVERT: A  335 HIS cc_start: 0.8293 (t-90) cc_final: 0.7687 (m170)
REVERT: A  351 PHE cc_start: 0.9049 (t80) cc_final: 0.8827 (t80)
REVERT: A  506 ARG cc_start: 0.8250 (ttt180) cc_final: 0.7866 (mmt180)
REVERT: A  965 TYR cc_start: 0.8941 (m-80) cc_final: 0.8456 (m-80)
REVERT: A 1004 HIS cc_start: 0.7764 (t70) cc_final: 0.7313 (m90)
REVERT: A 1315 LEU cc_start: 0.7915 (mm) cc_final: 0.7654 (mm)
REVERT: A 1358 ARG cc_start: 0.7297 (mtt180) cc_final: 0.6328 (mtt-85)
REVERT: A 1365 LEU cc_start: 0.9165 (mm) cc_final: 0.8885 (mm)
REVERT: A 1564 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8510 (mt-10)
REVERT: A 1574 CYS cc_start: 0.8820 (m) cc_final: 0.8599 (p)
REVERT: A 1664 SER cc_start: 0.7654 (t) cc_final: 0.7438 (p)
REVERT: A 1668 ASN cc_start: 0.7713 (t0) cc_final: 0.6873 (t0)
REVERT: A 1682 TYR cc_start: 0.8148 (m-10) cc_final: 0.7923 (m-10)
REVERT: A 1685 GLN cc_start: 0.8815 (tt0) cc_final: 0.8547 (tm-30)
REVERT: A 1692 TYR cc_start: 0.7998 (t80) cc_final: 0.7744 (t80)
REVERT: A 1768 VAL cc_start: 0.7724 (t) cc_final: 0.7358 (p)
REVERT: A 1837 MET cc_start: 0.7086 (mtt) cc_final: 0.5826 (mtt)
REVERT: B  311 TYR cc_start: 0.7511 (m-80) cc_final: 0.7255 (m-80)
REVERT: B  348 ARG cc_start: 0.8816 (mtt180) cc_final: 0.8254 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.2723
  time to fit residues: 75.1120
Evaluate side-chains
  148 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 75 optimal weight:    7.9990
   chunk 133 optimal weight:    8.9990
   chunk 65 optimal weight:    7.9990
   chunk 114 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 82 optimal weight:   20.0000
   chunk 14 optimal weight:    0.0870
   chunk 124 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 110 optimal weight:   10.0000
   overall best weight:    1.8166

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1767 HIS
B 338 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.088731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.069226 restraints weight = 73637.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.071271 restraints weight = 53483.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.072784 restraints weight = 41879.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6510
moved from start:          0.4770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11334  Z= 0.174
  Angle     :  0.921  12.724  15327  Z= 0.473
  Chirality :  0.049   0.208   1747
  Planarity :  0.006   0.093   1954
  Dihedral  :  7.250  31.484   1519
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 24.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.78 %
    Favored  : 84.22 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.09 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.34 (0.22), residues: 1369
  helix: -0.95 (0.20), residues: 633
  sheet: -3.12 (0.41), residues: 127
  loop : -3.45 (0.24), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP A 133 
 HIS   0.008   0.001   HIS A1062 
 PHE   0.017   0.002   PHE A1772 
 TYR   0.036   0.002   TYR A 637 
 ARG   0.006   0.000   ARG A 640 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05059 (  465)
  hydrogen bonds       : angle       6.17191 ( 1368)
  SS BOND              : bond        0.00278 (    2)
  SS BOND              : angle       1.48674 (    4)
  covalent geometry    : bond        0.00367 (11332)
  covalent geometry    : angle       0.92058 (15323)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 194
  time to evaluate  : 1.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.8476 (pm20) cc_final: 0.8128 (pm20)
REVERT: A   79 LYS cc_start: 0.9377 (mtmm) cc_final: 0.9162 (mtmm)
REVERT: A  224 GLN cc_start: 0.8687 (tt0) cc_final: 0.8242 (tm-30)
REVERT: A  239 ASP cc_start: 0.5544 (m-30) cc_final: 0.5259 (m-30)
REVERT: A  263 ARG cc_start: 0.4554 (tpt90) cc_final: 0.4231 (mtp180)
REVERT: A  335 HIS cc_start: 0.8314 (t-90) cc_final: 0.7714 (m170)
REVERT: A  351 PHE cc_start: 0.9023 (t80) cc_final: 0.8812 (t80)
REVERT: A  506 ARG cc_start: 0.8208 (ttt180) cc_final: 0.7828 (mmt180)
REVERT: A  544 ARG cc_start: 0.7018 (ttp-110) cc_final: 0.5666 (tpt90)
REVERT: A  697 ILE cc_start: 0.7188 (mt) cc_final: 0.6709 (mt)
REVERT: A  701 LYS cc_start: 0.7803 (mmmt) cc_final: 0.7304 (mmtm)
REVERT: A  965 TYR cc_start: 0.8954 (m-80) cc_final: 0.8554 (m-80)
REVERT: A 1004 HIS cc_start: 0.7772 (t70) cc_final: 0.7304 (m90)
REVERT: A 1062 HIS cc_start: 0.8864 (p90) cc_final: 0.8428 (t70)
REVERT: A 1315 LEU cc_start: 0.7800 (mm) cc_final: 0.7544 (mm)
REVERT: A 1365 LEU cc_start: 0.9185 (mm) cc_final: 0.8930 (mm)
REVERT: A 1564 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8451 (mt-10)
REVERT: A 1664 SER cc_start: 0.7652 (t) cc_final: 0.7436 (p)
REVERT: A 1668 ASN cc_start: 0.7639 (t0) cc_final: 0.6907 (t0)
REVERT: A 1682 TYR cc_start: 0.8221 (m-10) cc_final: 0.8010 (m-10)
REVERT: A 1685 GLN cc_start: 0.8827 (tt0) cc_final: 0.8575 (tm-30)
REVERT: A 1768 VAL cc_start: 0.7821 (t) cc_final: 0.7428 (p)
REVERT: A 1808 MET cc_start: 0.6977 (mmt) cc_final: 0.6723 (mmm)
REVERT: A 1837 MET cc_start: 0.7070 (mtt) cc_final: 0.6682 (mtt)
REVERT: B  311 TYR cc_start: 0.7476 (m-80) cc_final: 0.7220 (m-80)
REVERT: B  348 ARG cc_start: 0.8826 (mtt180) cc_final: 0.8177 (tpt90)
REVERT: B  357 GLN cc_start: 0.8473 (mt0) cc_final: 0.8272 (mt0)
  outliers start: 1
  outliers final: 0
  residues processed: 195
  average time/residue: 0.2869
  time to fit residues: 77.0162
Evaluate side-chains
  142 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 38 optimal weight:    8.9990
   chunk 79 optimal weight:    4.9990
   chunk 47 optimal weight:    7.9990
   chunk 126 optimal weight:    0.0570
   chunk 112 optimal weight:    6.9990
   chunk 127 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   overall best weight:    2.2104

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 559 ASN
** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1693 HIS
A1767 HIS
B 338 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.088704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.069373 restraints weight = 76399.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.071455 restraints weight = 54843.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.072993 restraints weight = 42616.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6526
moved from start:          0.4985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11334  Z= 0.180
  Angle     :  0.930  13.632  15327  Z= 0.478
  Chirality :  0.050   0.192   1747
  Planarity :  0.007   0.096   1954
  Dihedral  :  7.241  33.305   1519
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 25.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.70 %
    Favored  : 84.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.25 (0.21), residues: 1369
  helix: -0.94 (0.19), residues: 633
  sheet: -2.61 (0.47), residues: 106
  loop : -3.45 (0.23), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP A 138 
 HIS   0.007   0.001   HIS A1062 
 PHE   0.025   0.002   PHE A1766 
 TYR   0.028   0.002   TYR A 637 
 ARG   0.005   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05097 (  465)
  hydrogen bonds       : angle       6.08581 ( 1368)
  SS BOND              : bond        0.00295 (    2)
  SS BOND              : angle       1.49860 (    4)
  covalent geometry    : bond        0.00381 (11332)
  covalent geometry    : angle       0.93025 (15323)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.8587 (pm20) cc_final: 0.8036 (pm20)
REVERT: A  218 GLU cc_start: 0.9155 (pt0) cc_final: 0.8792 (pm20)
REVERT: A  224 GLN cc_start: 0.8721 (tt0) cc_final: 0.8279 (tm-30)
REVERT: A  239 ASP cc_start: 0.5569 (m-30) cc_final: 0.5282 (m-30)
REVERT: A  263 ARG cc_start: 0.4552 (tpt90) cc_final: 0.4153 (mtm110)
REVERT: A  279 ASN cc_start: 0.9472 (t0) cc_final: 0.9237 (t0)
REVERT: A  335 HIS cc_start: 0.8197 (t-90) cc_final: 0.7608 (m170)
REVERT: A  351 PHE cc_start: 0.9050 (t80) cc_final: 0.8782 (t80)
REVERT: A  506 ARG cc_start: 0.8232 (ttt180) cc_final: 0.7853 (mmt180)
REVERT: A  544 ARG cc_start: 0.7107 (ttp-110) cc_final: 0.5688 (tpt90)
REVERT: A  697 ILE cc_start: 0.7049 (mt) cc_final: 0.6493 (mt)
REVERT: A  701 LYS cc_start: 0.7868 (mmmt) cc_final: 0.7392 (mmtm)
REVERT: A  715 VAL cc_start: 0.7813 (t) cc_final: 0.7495 (t)
REVERT: A  965 TYR cc_start: 0.8972 (m-80) cc_final: 0.8483 (m-80)
REVERT: A 1004 HIS cc_start: 0.7798 (t70) cc_final: 0.7311 (m90)
REVERT: A 1062 HIS cc_start: 0.8849 (p90) cc_final: 0.8401 (t70)
REVERT: A 1315 LEU cc_start: 0.7919 (mm) cc_final: 0.7685 (mm)
REVERT: A 1358 ARG cc_start: 0.7302 (mtt180) cc_final: 0.6892 (mtt-85)
REVERT: A 1365 LEU cc_start: 0.9238 (mm) cc_final: 0.8941 (mm)
REVERT: A 1564 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8376 (mt-10)
REVERT: A 1668 ASN cc_start: 0.7716 (t0) cc_final: 0.7296 (t0)
REVERT: A 1685 GLN cc_start: 0.8775 (tt0) cc_final: 0.8481 (tm-30)
REVERT: A 1692 TYR cc_start: 0.8082 (t80) cc_final: 0.7562 (t80)
REVERT: A 1837 MET cc_start: 0.7074 (mtt) cc_final: 0.6741 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2987
  time to fit residues: 74.8286
Evaluate side-chains
  139 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 128 optimal weight:   30.0000
   chunk 90 optimal weight:    0.4980
   chunk 59 optimal weight:    0.0770
   chunk 47 optimal weight:    7.9990
   chunk 114 optimal weight:    3.9990
   chunk 96 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9980
   chunk 92 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.7142

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 633 HIS
** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1031 GLN
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1767 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.089107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.069609 restraints weight = 79531.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.071749 restraints weight = 55744.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.073414 restraints weight = 42487.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6547
moved from start:          0.5239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11334  Z= 0.167
  Angle     :  0.908  13.070  15327  Z= 0.465
  Chirality :  0.049   0.196   1747
  Planarity :  0.006   0.097   1954
  Dihedral  :  7.057  33.660   1519
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 23.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.78 %
    Favored  : 84.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.12 (0.22), residues: 1369
  helix: -0.78 (0.20), residues: 631
  sheet: -2.92 (0.45), residues: 116
  loop : -3.35 (0.24), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 138 
 HIS   0.008   0.001   HIS A1062 
 PHE   0.042   0.002   PHE A1669 
 TYR   0.026   0.002   TYR A1834 
 ARG   0.005   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04907 (  465)
  hydrogen bonds       : angle       5.94702 ( 1368)
  SS BOND              : bond        0.00287 (    2)
  SS BOND              : angle       1.45257 (    4)
  covalent geometry    : bond        0.00350 (11332)
  covalent geometry    : angle       0.90765 (15323)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.8688 (pm20) cc_final: 0.8354 (pm20)
REVERT: A  218 GLU cc_start: 0.9142 (pt0) cc_final: 0.8780 (pm20)
REVERT: A  224 GLN cc_start: 0.8710 (tt0) cc_final: 0.8280 (tm-30)
REVERT: A  239 ASP cc_start: 0.5559 (m-30) cc_final: 0.5260 (m-30)
REVERT: A  263 ARG cc_start: 0.4583 (tpt90) cc_final: 0.4183 (mtm110)
REVERT: A  335 HIS cc_start: 0.8166 (t-90) cc_final: 0.7527 (m170)
REVERT: A  506 ARG cc_start: 0.8215 (ttt180) cc_final: 0.7833 (mmt180)
REVERT: A  544 ARG cc_start: 0.7095 (ttp-110) cc_final: 0.5697 (tpt90)
REVERT: A  697 ILE cc_start: 0.6841 (mt) cc_final: 0.6337 (mt)
REVERT: A  701 LYS cc_start: 0.7861 (mmmt) cc_final: 0.7417 (mmtm)
REVERT: A  965 TYR cc_start: 0.8896 (m-80) cc_final: 0.8501 (m-80)
REVERT: A 1004 HIS cc_start: 0.7787 (t70) cc_final: 0.7282 (m90)
REVERT: A 1062 HIS cc_start: 0.8824 (p90) cc_final: 0.8458 (t70)
REVERT: A 1315 LEU cc_start: 0.7546 (mm) cc_final: 0.7318 (mm)
REVERT: A 1358 ARG cc_start: 0.7342 (mtt180) cc_final: 0.6915 (mtt-85)
REVERT: A 1365 LEU cc_start: 0.9100 (mm) cc_final: 0.8899 (mm)
REVERT: A 1564 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8320 (mt-10)
REVERT: A 1668 ASN cc_start: 0.7374 (t0) cc_final: 0.6861 (t0)
REVERT: A 1685 GLN cc_start: 0.8805 (tt0) cc_final: 0.8512 (tm-30)
REVERT: A 1692 TYR cc_start: 0.7808 (t80) cc_final: 0.7468 (t80)
REVERT: A 1837 MET cc_start: 0.7093 (mtt) cc_final: 0.6328 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.3651
  time to fit residues: 90.1391
Evaluate side-chains
  138 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 120 optimal weight:    1.9990
   chunk 125 optimal weight:    7.9990
   chunk 69 optimal weight:    3.9990
   chunk 37 optimal weight:    0.4980
   chunk 17 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 112 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 119 optimal weight:    3.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 146 GLN
** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1767 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.089979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.069451 restraints weight = 76368.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.071764 restraints weight = 53382.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.073429 restraints weight = 40554.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6568
moved from start:          0.5513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11334  Z= 0.164
  Angle     :  0.913  12.994  15327  Z= 0.468
  Chirality :  0.049   0.192   1747
  Planarity :  0.006   0.088   1954
  Dihedral  :  6.924  32.934   1519
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 22.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.34 %
    Favored  : 84.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.88 (0.22), residues: 1369
  helix: -0.59 (0.20), residues: 627
  sheet: -2.42 (0.53), residues: 94
  loop : -3.28 (0.23), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP A 138 
 HIS   0.008   0.001   HIS A1062 
 PHE   0.035   0.002   PHE A 351 
 TYR   0.021   0.002   TYR A 637 
 ARG   0.003   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04861 (  465)
  hydrogen bonds       : angle       5.92189 ( 1368)
  SS BOND              : bond        0.00249 (    2)
  SS BOND              : angle       1.46237 (    4)
  covalent geometry    : bond        0.00341 (11332)
  covalent geometry    : angle       0.91281 (15323)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 1.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.7368 (tp) cc_final: 0.6982 (tp)
REVERT: A  224 GLN cc_start: 0.8680 (tt0) cc_final: 0.8284 (tm-30)
REVERT: A  263 ARG cc_start: 0.4882 (tpt90) cc_final: 0.4398 (mtm110)
REVERT: A  335 HIS cc_start: 0.8342 (t-90) cc_final: 0.7615 (m90)
REVERT: A  506 ARG cc_start: 0.8165 (ttt180) cc_final: 0.7772 (mmt180)
REVERT: A  572 PHE cc_start: 0.8623 (m-80) cc_final: 0.8407 (m-10)
REVERT: A  701 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7772 (mmtt)
REVERT: A  715 VAL cc_start: 0.7824 (t) cc_final: 0.7616 (t)
REVERT: A  965 TYR cc_start: 0.8877 (m-80) cc_final: 0.8442 (m-80)
REVERT: A 1004 HIS cc_start: 0.7830 (t70) cc_final: 0.7329 (m90)
REVERT: A 1303 LEU cc_start: 0.8417 (tp) cc_final: 0.7996 (tp)
REVERT: A 1315 LEU cc_start: 0.7761 (mm) cc_final: 0.7539 (mm)
REVERT: A 1358 ARG cc_start: 0.7436 (mtt180) cc_final: 0.6927 (mtt-85)
REVERT: A 1365 LEU cc_start: 0.9116 (mm) cc_final: 0.8899 (mm)
REVERT: A 1564 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8354 (mt-10)
REVERT: A 1668 ASN cc_start: 0.7501 (t0) cc_final: 0.6937 (t0)
REVERT: A 1837 MET cc_start: 0.6875 (mtt) cc_final: 0.6026 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.3543
  time to fit residues: 89.0035
Evaluate side-chains
  136 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 62 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 66 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9990
   chunk 88 optimal weight:    5.9990
   chunk 98 optimal weight:    0.0070
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0570
   chunk 56 optimal weight:    5.9990
   overall best weight:    1.2122

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 170 ASN
** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1693 HIS
A1767 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.089942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.070433 restraints weight = 75108.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.072524 restraints weight = 53847.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.074041 restraints weight = 41722.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6519
moved from start:          0.5764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11334  Z= 0.163
  Angle     :  0.907  12.619  15327  Z= 0.467
  Chirality :  0.049   0.209   1747
  Planarity :  0.006   0.084   1954
  Dihedral  :  6.794  31.722   1519
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 22.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.97 %
    Favored  : 85.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.82 (0.22), residues: 1369
  helix: -0.48 (0.20), residues: 627
  sheet: -2.82 (0.49), residues: 110
  loop : -3.24 (0.24), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A 138 
 HIS   0.006   0.001   HIS A 633 
 PHE   0.037   0.002   PHE A 351 
 TYR   0.024   0.002   TYR A1834 
 ARG   0.012   0.001   ARG A 636 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04853 (  465)
  hydrogen bonds       : angle       5.81864 ( 1368)
  SS BOND              : bond        0.00250 (    2)
  SS BOND              : angle       1.42063 (    4)
  covalent geometry    : bond        0.00341 (11332)
  covalent geometry    : angle       0.90680 (15323)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.7289 (tp) cc_final: 0.6957 (tp)
REVERT: A  224 GLN cc_start: 0.8674 (tt0) cc_final: 0.8292 (tm-30)
REVERT: A  263 ARG cc_start: 0.4506 (tpt90) cc_final: 0.4141 (mtm110)
REVERT: A  335 HIS cc_start: 0.8271 (t-90) cc_final: 0.7550 (m90)
REVERT: A  506 ARG cc_start: 0.8121 (ttt180) cc_final: 0.7742 (mmt180)
REVERT: A  697 ILE cc_start: 0.6846 (mt) cc_final: 0.6429 (mt)
REVERT: A  701 LYS cc_start: 0.8044 (mmmt) cc_final: 0.7689 (mmtm)
REVERT: A  965 TYR cc_start: 0.8864 (m-80) cc_final: 0.8421 (m-80)
REVERT: A 1004 HIS cc_start: 0.7837 (t70) cc_final: 0.7321 (m90)
REVERT: A 1315 LEU cc_start: 0.7890 (mm) cc_final: 0.7689 (mm)
REVERT: A 1337 ASP cc_start: 0.8956 (p0) cc_final: 0.8740 (p0)
REVERT: A 1358 ARG cc_start: 0.7376 (mtt180) cc_final: 0.6860 (mtt-85)
REVERT: A 1363 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8332 (mppt)
REVERT: A 1564 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8309 (mt-10)
REVERT: A 1668 ASN cc_start: 0.7518 (t0) cc_final: 0.6892 (t0)
REVERT: A 1692 TYR cc_start: 0.7963 (t80) cc_final: 0.7508 (t80)
REVERT: A 1837 MET cc_start: 0.7064 (mtt) cc_final: 0.6234 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.3846
  time to fit residues: 97.3980
Evaluate side-chains
  139 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 6 optimal weight:    0.3980
   chunk 36 optimal weight:    7.9990
   chunk 38 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 115 optimal weight:    1.9990
   chunk 31 optimal weight:    7.9990
   chunk 110 optimal weight:    7.9990
   chunk 58 optimal weight:    0.0970
   chunk 73 optimal weight:    3.9990
   chunk 131 optimal weight:    5.9990
   overall best weight:    2.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 GLN
** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 703 HIS
** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.088052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.069467 restraints weight = 78891.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.071436 restraints weight = 57001.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.072922 restraints weight = 44605.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6553
moved from start:          0.5753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11334  Z= 0.187
  Angle     :  0.942  12.645  15327  Z= 0.482
  Chirality :  0.050   0.216   1747
  Planarity :  0.006   0.088   1954
  Dihedral  :  6.946  30.538   1519
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 25.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.00 %
    Favored  : 84.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.22), residues: 1369
  helix: -0.57 (0.20), residues: 625
  sheet: -2.37 (0.54), residues: 93
  loop : -3.26 (0.24), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A 138 
 HIS   0.005   0.001   HIS A1062 
 PHE   0.034   0.002   PHE A 351 
 TYR   0.026   0.002   TYR A 452 
 ARG   0.008   0.001   ARG A 636 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05060 (  465)
  hydrogen bonds       : angle       5.92682 ( 1368)
  SS BOND              : bond        0.00305 (    2)
  SS BOND              : angle       1.58033 (    4)
  covalent geometry    : bond        0.00401 (11332)
  covalent geometry    : angle       0.94228 (15323)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4740.02 seconds
wall clock time: 88 minutes 6.08 seconds (5286.08 seconds total)