Starting phenix.real_space_refine
on Thu Jul  2 22:32:53 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7fap_31504/07_2026/7fap_31504.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fap_31504/07_2026/7fap_31504.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fap_31504/07_2026/7fap_31504.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fap_31504/07_2026/7fap_31504.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fap_31504/07_2026/7fap_31504.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fap_31504/07_2026/7fap_31504.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7fap_31504/07_2026/7fap_31504.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7fap_31504/07_2026/7fap_31504.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      65      5.16       5
     C    6578      2.51       5
     N    1771      2.21       5
     O    2031      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10445
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1236, 10265
          Classifications: {'peptide': 1236}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 33, 'TRANS': 1202}
          Chain breaks: 33
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 180
          Unusual residues: {'ASG': 6, 'BDP': 6}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen chiralities: 12
  Residues with excluded nonbonded symmetry interactions: 12
    residue:
      pdb=" C1  BDP B   1 " occ=0.22
      ... (11 atoms not shown)
      pdb=" O6B BDP B   1 " occ=0.22
    residue:
      pdb=" C1  ASG B   2 " occ=0.34
      ... (16 atoms not shown)
      pdb=" S   ASG B   2 " occ=0.34
    residue:
      pdb=" C1  BDP B   3 " occ=0.33
      ... (10 atoms not shown)
      pdb=" O6B BDP B   3 " occ=0.33
    residue:
      pdb=" C1  ASG B   4 " occ=0.29
      ... (16 atoms not shown)
      pdb=" S   ASG B   4 " occ=0.29
    residue:
      pdb=" C1  BDP B   5 " occ=0.44
      ... (10 atoms not shown)
      pdb=" O6B BDP B   5 " occ=0.44
    residue:
      pdb=" C1  ASG B   6 " occ=0.51
      ... (16 atoms not shown)
      pdb=" S   ASG B   6 " occ=0.51
    residue:
      pdb=" C1  BDP B   7 " occ=0.67
      ... (10 atoms not shown)
      pdb=" O6B BDP B   7 " occ=0.67
    residue:
      pdb=" C1  ASG B   8 " occ=0.62
      ... (16 atoms not shown)
      pdb=" S   ASG B   8 " occ=0.62
    residue:
      pdb=" C1  BDP B   9 " occ=0.68
      ... (10 atoms not shown)
      pdb=" O6B BDP B   9 " occ=0.68
    residue:
      pdb=" C1  ASG B  10 " occ=0.62
      ... (16 atoms not shown)
      pdb=" S   ASG B  10 " occ=0.62
    residue:
      pdb=" C1  BDP B  11 " occ=0.61
      ... (9 atoms not shown)
      pdb=" O6B BDP B  11 " occ=0.61
    residue:
      pdb=" C1  ASG B  12 " occ=0.31
      ... (16 atoms not shown)
      pdb=" S   ASG B  12 " occ=0.31
  Time building chain proxies: 1.96, per 1000 atoms: 0.19
  Number of scatterers: 10445
  At special positions: 0
  Unit cell: (105.444, 144.072, 107.532, 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      65     16.00
     O    2031      8.00
     N    1771      7.00
     C    6578      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 769 " - pdb=" SG  CYS A 901 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 855 " - pdb=" SG  CYS A 868 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 966 " - pdb=" SG  CYS A1090 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1088 " - pdb=" SG  CYS A1193 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A1578 " - pdb=" SG  CYS A1614 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1802 " - pdb=" SG  CYS A1904 " distance=2.39
    Simple disulfide: pdb=" SG  CYS A1816 " - pdb=" SG  CYS A1833 " 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
  Links applied
    BETA1-3
      " ASG B   2 " - " BDP B   3 "
      " ASG B   4 " - " BDP B   5 "
      " ASG B   6 " - " BDP B   7 "
      " ASG B   8 " - " BDP B   9 "
      " ASG B  10 " - " BDP B  11 "
      " BDP B  11 " - " ASG B  12 "
    BETA1-4
      " BDP B   1 " - " ASG B   2 "
      " BDP B   3 " - " ASG B   4 "
      " BDP B   5 " - " ASG B   6 "
      " BDP B   7 " - " ASG B   8 "
      " BDP B   9 " - " ASG B  10 "
  Time building additional restraints: 1.07
  Conformation dependent library (CDL) restraints added in 277.4 milliseconds
  

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2356

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 2 sheets defined
      63.7% alpha, 0.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 27
    Processing helix  chain 'A' and resid 74 through 78
      removed outlier: 3.534A  pdb=" N   ASP A  77 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLN A  78 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 74 through 78'
    Processing helix  chain 'A' and resid 106 through 111
      removed outlier: 3.571A  pdb=" N   LYS A 111 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 140
      removed outlier: 4.051A  pdb=" N   PHE A 123 " --> pdb=" O   ASP A 119 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   GLU A 134 " --> pdb=" O   THR A 130 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ARG A 137 " --> pdb=" O   ASN A 133 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   GLN A 140 " --> pdb=" O   GLU A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 166
      removed outlier: 3.557A  pdb=" N   VAL A 150 " --> pdb=" O   ASN A 146 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ASN A 152 " --> pdb=" O   SER A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 192
      removed outlier: 3.698A  pdb=" N   ASN A 192 " --> pdb=" O   LYS A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 217
    Processing helix  chain 'A' and resid 217 through 226
      removed outlier: 3.681A  pdb=" N   VAL A 221 " --> pdb=" O   ASN A 217 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TRP A 222 " --> pdb=" O   ARG A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 297
    Processing helix  chain 'A' and resid 319 through 332
    Processing helix  chain 'A' and resid 333 through 338
    Processing helix  chain 'A' and resid 338 through 343
      removed outlier: 3.716A  pdb=" N   LYS A 343 " --> pdb=" O   TRP A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 586
    Processing helix  chain 'A' and resid 598 through 602
      removed outlier: 4.276A  pdb=" N   GLN A 601 " --> pdb=" O   LYS A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 627
    Processing helix  chain 'A' and resid 631 through 636
      removed outlier: 3.808A  pdb=" N   ASP A 636 " --> pdb=" O   LYS A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 659
      removed outlier: 3.629A  pdb=" N   CYS A 643 " --> pdb=" O   GLY A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 683
    Processing helix  chain 'A' and resid 704 through 722
      removed outlier: 5.747A  pdb=" N   LYS A 715 " --> pdb=" O   ASN A 711 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   TYR A 716 " --> pdb=" O   THR A 712 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ILE A 717 " --> pdb=" O   ASN A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 755 through 782
      Proline residue:  A 778  - end of helix
    Processing helix  chain 'A' and resid 800 through 813
      removed outlier: 3.902A  pdb=" N   TYR A 808 " --> pdb=" O   LYS A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 847
    Processing helix  chain 'A' and resid 872 through 884
    Processing helix  chain 'A' and resid 887 through 896
    Processing helix  chain 'A' and resid 943 through 945
      No H-bonds generated for 'chain 'A' and resid 943 through 945'
    Processing helix  chain 'A' and resid 950 through 954
      removed outlier: 4.146A  pdb=" N   TYR A 953 " --> pdb=" O   GLY A 950 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 961 through 966
    Processing helix  chain 'A' and resid 1016 through 1041
      removed outlier: 3.898A  pdb=" N   GLN A1034 " --> pdb=" O   ASN A1030 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   TYR A1035 " --> pdb=" O   LYS A1031 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   GLU A1038 " --> pdb=" O   GLN A1034 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1118
      removed outlier: 3.538A  pdb=" N   ASP A1107 " --> pdb=" O   ASP A1103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1131 through 1148
      removed outlier: 3.945A  pdb=" N   PHE A1137 " --> pdb=" O   SER A1133 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   GLU A1143 " --> pdb=" O   SER A1139 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   TYR A1144 " --> pdb=" O   CYS A1140 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR A1148 " --> pdb=" O   TYR A1144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1163 through 1171
    Processing helix  chain 'A' and resid 1177 through 1199
      removed outlier: 3.856A  pdb=" N   LYS A1185 " --> pdb=" O   ILE A1181 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   CYS A1193 " --> pdb=" O   ALA A1189 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   LYS A1194 " --> pdb=" O   GLU A1190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1257 through 1261
    Processing helix  chain 'A' and resid 1295 through 1308
      removed outlier: 3.815A  pdb=" N   THR A1299 " --> pdb=" O   ILE A1295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1337 through 1353
      removed outlier: 3.953A  pdb=" N   ALA A1341 " --> pdb=" O   GLY A1337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1364 through 1375
      removed outlier: 3.704A  pdb=" N   GLN A1368 " --> pdb=" O   ILE A1364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1396 through 1420
    Processing helix  chain 'A' and resid 1450 through 1468
    Processing helix  chain 'A' and resid 1482 through 1503
      removed outlier: 3.826A  pdb=" N   LYS A1486 " --> pdb=" O   ASP A1482 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   GLN A1499 " --> pdb=" O   SER A1495 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   GLU A1500 " --> pdb=" O   GLU A1496 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LYS A1503 " --> pdb=" O   GLN A1499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1505 through 1509
    Processing helix  chain 'A' and resid 1534 through 1538
    Processing helix  chain 'A' and resid 1540 through 1547
      removed outlier: 3.512A  pdb=" N   LYS A1544 " --> pdb=" O   ASN A1540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1607 through 1612
    Processing helix  chain 'A' and resid 1617 through 1625
      removed outlier: 3.806A  pdb=" N   ILE A1621 " --> pdb=" O   GLU A1617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1634 through 1659
      removed outlier: 4.273A  pdb=" N   ALA A1657 " --> pdb=" O   LYS A1653 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ASN A1659 " --> pdb=" O   TYR A1655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1662 through 1684
      removed outlier: 4.010A  pdb=" N   HIS A1666 " --> pdb=" O   THR A1662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1692 through 1706
      removed outlier: 3.650A  pdb=" N   TYR A1697 " --> pdb=" O   GLU A1693 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   GLU A1704 " --> pdb=" O   SER A1700 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   PHE A1706 " --> pdb=" O   LEU A1702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1716 through 1726
    Processing helix  chain 'A' and resid 1746 through 1763
    Processing helix  chain 'A' and resid 1788 through 1816
    Processing helix  chain 'A' and resid 1831 through 1860
      removed outlier: 3.652A  pdb=" N   LYS A1835 " --> pdb=" O   ILE A1831 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ALA A1836 " --> pdb=" O   GLU A1832 " (cutoff:3.500A)
      Proline residue:  A1846  - end of helix
    Processing helix  chain 'A' and resid 1882 through 1889
      removed outlier: 3.945A  pdb=" N   LYS A1889 " --> pdb=" O   ASP A1885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1909 through 1914
    Processing helix  chain 'A' and resid 1953 through 1971
      removed outlier: 4.140A  pdb=" N   GLU A1957 " --> pdb=" O   MET A1953 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 569 through 570
    Processing sheet with id=AA2, first strand: chain 'A' and resid 911 through 912

    527 hydrogen bonds defined for protein.
    1539 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: 1.22

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1785
        1.31 -     1.44: 2833
        1.44 -     1.57: 5932
        1.57 -     1.70: 23
        1.70 -     1.83: 74
  Bond restraints: 10647
  Sorted by residual:
  bond pdb=" OSC ASG B   2 "
       pdb=" S   ASG B   2 "
    ideal  model  delta    sigma   weight residual
    1.457  1.654 -0.197 2.00e-02 2.50e+03 9.73e+01
  bond pdb=" OSC ASG B  12 "
       pdb=" S   ASG B  12 "
    ideal  model  delta    sigma   weight residual
    1.457  1.654 -0.197 2.00e-02 2.50e+03 9.69e+01
  bond pdb=" OSC ASG B   6 "
       pdb=" S   ASG B   6 "
    ideal  model  delta    sigma   weight residual
    1.457  1.653 -0.196 2.00e-02 2.50e+03 9.61e+01
  bond pdb=" OSC ASG B  10 "
       pdb=" S   ASG B  10 "
    ideal  model  delta    sigma   weight residual
    1.457  1.653 -0.196 2.00e-02 2.50e+03 9.60e+01
  bond pdb=" OSC ASG B   4 "
       pdb=" S   ASG B   4 "
    ideal  model  delta    sigma   weight residual
    1.457  1.652 -0.195 2.00e-02 2.50e+03 9.51e+01
  ... (remaining 10642 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 13416
        2.06 -     4.11: 714
        4.11 -     6.17: 130
        6.17 -     8.22: 35
        8.22 -    10.28: 9
  Bond angle restraints: 14304
  Sorted by residual:
  angle pdb=" N   ILE A 900 "
        pdb=" CA  ILE A 900 "
        pdb=" C   ILE A 900 "
      ideal   model   delta    sigma   weight residual
     113.47  107.50    5.97 1.01e+00 9.80e-01 3.49e+01
  angle pdb=" CA  GLY A1151 "
        pdb=" C   GLY A1151 "
        pdb=" O   GLY A1151 "
      ideal   model   delta    sigma   weight residual
     122.52  117.89    4.63 7.90e-01 1.60e+00 3.43e+01
  angle pdb=" C   SER A 871 "
        pdb=" N   ASP A 872 "
        pdb=" CA  ASP A 872 "
      ideal   model   delta    sigma   weight residual
     122.11  131.43   -9.32 1.59e+00 3.96e-01 3.43e+01
  angle pdb=" CA  GLY A1784 "
        pdb=" C   GLY A1784 "
        pdb=" O   GLY A1784 "
      ideal   model   delta    sigma   weight residual
     122.52  117.94    4.58 7.90e-01 1.60e+00 3.36e+01
  angle pdb=" N   ILE A1683 "
        pdb=" CA  ILE A1683 "
        pdb=" C   ILE A1683 "
      ideal   model   delta    sigma   weight residual
     110.72  104.97    5.75 1.01e+00 9.80e-01 3.24e+01
  ... (remaining 14299 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 5595
       17.99 -    35.97: 587
       35.97 -    53.96: 114
       53.96 -    71.95: 36
       71.95 -    89.93: 19
  Dihedral angle restraints: 6351
    sinusoidal: 2726
      harmonic: 3625
  Sorted by residual:
  dihedral pdb=" CB  CYS A1578 "
           pdb=" SG  CYS A1578 "
           pdb=" SG  CYS A1614 "
           pdb=" CB  CYS A1614 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.50  -70.50     1      1.00e+01 1.00e-02 6.40e+01
  dihedral pdb=" CB  CYS A1816 "
           pdb=" SG  CYS A1816 "
           pdb=" SG  CYS A1833 "
           pdb=" CB  CYS A1833 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -143.16   57.16     1      1.00e+01 1.00e-02 4.39e+01
  dihedral pdb=" C   THR A1695 "
           pdb=" N   THR A1695 "
           pdb=" CA  THR A1695 "
           pdb=" CB  THR A1695 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.34   11.34     0      2.50e+00 1.60e-01 2.06e+01
  ... (remaining 6348 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.179: 1450
       0.179 -    0.358: 48
       0.358 -    0.537: 3
       0.537 -    0.716: 0
       0.716 -    0.895: 1
  Chirality restraints: 1502
  Sorted by residual:
  chirality pdb=" C1  ASG B   8 "
            pdb=" O4  BDP B   7 "
            pdb=" C2  ASG B   8 "
            pdb=" O5  ASG B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.51   -0.89 2.00e-02 2.50e+03 2.00e+03
  chirality pdb=" C1  BDP B   9 "
            pdb=" O3  ASG B   8 "
            pdb=" C2  BDP B   9 "
            pdb=" O5  BDP B   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.45    0.05 2.00e-02 2.50e+03 5.35e+00
  chirality pdb=" C3  BDP B  11 "
            pdb=" C2  BDP B  11 "
            pdb=" C4  BDP B  11 "
            pdb=" O3  BDP B  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.99    0.45 2.00e-01 2.50e+01 5.09e+00
  ... (remaining 1499 not shown)

  Planarity restraints: 1799
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A1149 "   -0.024 2.00e-02 2.50e+03   4.83e-02 2.33e+01
        pdb=" C   PHE A1149 "    0.083 2.00e-02 2.50e+03
        pdb=" O   PHE A1149 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   ASN A1150 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  ASG B   8 "    0.043 2.00e-02 2.50e+03   3.60e-02 1.62e+01
        pdb=" C7  ASG B   8 "   -0.012 2.00e-02 2.50e+03
        pdb=" C8  ASG B   8 "    0.033 2.00e-02 2.50e+03
        pdb=" N2  ASG B   8 "   -0.058 2.00e-02 2.50e+03
        pdb=" O7  ASG B   8 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  64 "    0.053 5.00e-02 4.00e+02   8.07e-02 1.04e+01
        pdb=" N   PRO A  65 "   -0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO A  65 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A  65 "    0.044 5.00e-02 4.00e+02
  ... (remaining 1796 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 685
        2.74 -     3.28: 10865
        3.28 -     3.82: 17122
        3.82 -     4.36: 20686
        4.36 -     4.90: 33942
  Nonbonded interactions: 83300
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 993 "
            pdb=" OD1 ASP A1019 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   CYS A 588 "
            pdb=" OH  TYR A 653 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   ASP A1688 "
            pdb=" OD1 ASP A1688 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   GLY A1893 "
            pdb=" OG  SER A1903 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   TYR A 574 "
            pdb=" OG1 THR A 577 "
     model   vdw
     2.249 3.040
  ... (remaining 83295 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=0.22 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.240
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6904
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      :  0.012   0.361  10665  Z= 0.667
  Angle     :  1.086  18.668  14351  Z= 0.655
  Chirality :  0.073   0.895   1502
  Planarity :  0.005   0.081   1799
  Dihedral  : 15.807  89.931   3974
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.31 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  3.04 %
    Favored  : 96.16 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.24), residues: 1168
  helix:  0.30 (0.19), residues: 715
  sheet:  None (None), residues: 0
  loop : -2.32 (0.27), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1720 
 TYR   0.017   0.001   TYR A 328 
 PHE   0.018   0.002   PHE A 158 
 TRP   0.038   0.002   TRP A1501 
 HIS   0.006   0.001   HIS A1666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01145 /  0.64 (10647)
  covalent geometry    : angle       1.04775 /  0.65 (14304)
  SS BOND              : bond        0.13657 /  6.83 (    7)
  SS BOND              : angle       4.38261 /  2.85 (   14)
  hydrogen bonds       : bond        0.13727 /  8.37 (  527)
  hydrogen bonds       : angle       5.33249 /  3.76 ( 1539)
  link_BETA1-3         : bond        0.01933 /  1.04 (    6)
  link_BETA1-3         : angle       4.83270 /  2.45 (   18)
  link_BETA1-4         : bond        0.01323 /  0.67 (    5)
  link_BETA1-4         : angle       5.97453 /  4.19 (   15)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 144
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1041 MET cc_start: 0.6177 (mtm) cc_final: 0.5940 (mtp)
REVERT: A 1338 PHE cc_start: 0.5419 (t80) cc_final: 0.4725 (t80)
REVERT: A 1415 LYS cc_start: 0.7013 (tttt) cc_final: 0.6653 (tptt)
REVERT: A 1778 MET cc_start: 0.6737 (mmm) cc_final: 0.5885 (mmm)
REVERT: A 1952 LYS cc_start: 0.4018 (OUTLIER) cc_final: 0.2759 (mmmt)
  outliers start: 9
  outliers final: 1
  residues processed: 149
  average time/residue: 0.1155
  time to fit residues: 23.6493
Evaluate side-chains
  102 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  855 CYS
Chi-restraints excluded: chain A residue 1952 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 117 optimal weight:    1.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  49 ASN
A 622 HIS
A 870 GLN
A1030 ASN
A1454 GLN
A1627 ASN
** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.129876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.111632 restraints weight = 20895.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 2.04
r_work: 0.3820 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3682 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3697
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3697 r_free = 0.3697    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3696 r_free = 0.3696    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.3696
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.1512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  10665  Z= 0.209
  Angle     :  0.700  16.914  14351  Z= 0.347
  Chirality :  0.046   0.416   1502
  Planarity :  0.004   0.051   1799
  Dihedral  :  5.283  58.787   1330
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  8.93 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.24), residues: 1168
  helix:  0.33 (0.18), residues: 728
  sheet:  None (None), residues: 0
  loop : -2.05 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1792 
 TYR   0.036   0.002   TYR A1663 
 PHE   0.024   0.002   PHE A 158 
 TRP   0.015   0.002   TRP A 558 
 HIS   0.006   0.002   HIS A1666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00486 /  0.21 (10647)
  covalent geometry    : angle       0.66037 /  0.34 (14304)
  SS BOND              : bond        0.00857 /  0.42 (    7)
  SS BOND              : angle       1.53988 /  0.80 (   14)
  hydrogen bonds       : bond        0.04787 /  3.03 (  527)
  hydrogen bonds       : angle       4.37855 /  3.03 ( 1539)
  link_BETA1-3         : bond        0.02116 /  1.15 (    6)
  link_BETA1-3         : angle       5.20811 /  2.79 (   18)
  link_BETA1-4         : bond        0.00988 /  0.47 (    5)
  link_BETA1-4         : angle       4.20445 /  2.33 (   15)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A   49 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.7798 (t0)
REVERT: A  328 TYR cc_start: 0.6006 (OUTLIER) cc_final: 0.4620 (t80)
REVERT: A  813 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6907 (mt-10)
REVERT: A  874 ASP cc_start: 0.7318 (t0) cc_final: 0.7075 (t0)
REVERT: A 1179 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6803 (mp0)
REVERT: A 1415 LYS cc_start: 0.7160 (tttt) cc_final: 0.6640 (tptt)
REVERT: A 1654 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7595 (tt0)
REVERT: A 1778 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6432 (mmm)
  outliers start: 22
  outliers final: 11
  residues processed: 120
  average time/residue: 0.1099
  time to fit residues: 18.3475
Evaluate side-chains
  109 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   49 ASN
Chi-restraints excluded: chain A residue  328 TYR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1035 TYR
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1591 TYR
Chi-restraints excluded: chain A residue 1656 HIS
Chi-restraints excluded: chain A residue 1688 ASP
Chi-restraints excluded: chain A residue 1778 MET
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1915 THR
Chi-restraints excluded: chain A residue 1974 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 101 optimal weight:    0.2980
   chunk 81 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 114 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0170
   overall best weight:    0.5218

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  49 ASN
A 956 GLN
A1030 ASN
A1034 GLN
** A1538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1540 ASN
A1654 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.131729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.113318 restraints weight = 21254.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3960 rms_B_bonded: 2.01
r_work: 0.3850 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3716 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3720
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3720 r_free = 0.3720    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3720 r_free = 0.3720    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10665  Z= 0.144
  Angle     :  0.622  15.744  14351  Z= 0.303
  Chirality :  0.043   0.476   1502
  Planarity :  0.004   0.039   1799
  Dihedral  :  4.796  54.773   1325
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 10.98 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.24), residues: 1168
  helix:  0.54 (0.19), residues: 732
  sheet:  None (None), residues: 0
  loop : -1.98 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1792 
 TYR   0.026   0.001   TYR A1663 
 PHE   0.018   0.002   PHE A 158 
 TRP   0.012   0.001   TRP A 214 
 HIS   0.004   0.001   HIS A1666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 (10647)
  covalent geometry    : angle       0.58281 /  0.29 (14304)
  SS BOND              : bond        0.00362 /  0.17 (    7)
  SS BOND              : angle       1.48752 /  0.75 (   14)
  hydrogen bonds       : bond        0.04311 /  2.76 (  527)
  hydrogen bonds       : angle       4.11350 /  2.85 ( 1539)
  link_BETA1-3         : bond        0.02001 /  1.13 (    6)
  link_BETA1-3         : angle       4.85840 /  2.60 (   18)
  link_BETA1-4         : bond        0.00926 /  0.46 (    5)
  link_BETA1-4         : angle       3.91709 /  2.21 (   15)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A   49 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8425 (t0)
REVERT: A  206 TYR cc_start: 0.6715 (m-80) cc_final: 0.6502 (m-80)
REVERT: A  286 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6858 (t80)
REVERT: A  328 TYR cc_start: 0.5968 (OUTLIER) cc_final: 0.4703 (t80)
REVERT: A  874 ASP cc_start: 0.7153 (t0) cc_final: 0.6925 (t0)
REVERT: A 1179 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6901 (mp0)
REVERT: A 1415 LYS cc_start: 0.7190 (tttt) cc_final: 0.6699 (tptt)
REVERT: A 1778 MET cc_start: 0.7362 (mmm) cc_final: 0.6427 (mmm)
REVERT: A 1861 ILE cc_start: 0.8861 (pt) cc_final: 0.8591 (pt)
REVERT: A 1953 MET cc_start: 0.7744 (tmm) cc_final: 0.7531 (tmm)
REVERT: A 1974 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7379 (pt)
  outliers start: 26
  outliers final: 13
  residues processed: 118
  average time/residue: 0.0951
  time to fit residues: 16.2614
Evaluate side-chains
  114 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   49 ASN
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  328 TYR
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1006 THR
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1591 TYR
Chi-restraints excluded: chain A residue 1627 ASN
Chi-restraints excluded: chain A residue 1688 ASP
Chi-restraints excluded: chain A residue 1702 LEU
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1974 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 109 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 104 optimal weight:    0.5980
   chunk 61 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  49 ASN
** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1654 GLN
** A1799 ASN ** 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 = 0.4206 r_free = 0.4206 target = 0.129134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.110519 restraints weight = 21464.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3916 rms_B_bonded: 2.01
r_work: 0.3805 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3668 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3682
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3682 r_free = 0.3682    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3682 r_free = 0.3682    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3682
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  10665  Z= 0.205
  Angle     :  0.653  16.002  14351  Z= 0.319
  Chirality :  0.045   0.473   1502
  Planarity :  0.004   0.040   1799
  Dihedral  :  4.891  53.274   1325
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.30 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.24), residues: 1168
  helix:  0.48 (0.18), residues: 732
  sheet:  None (None), residues: 0
  loop : -1.93 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 848 
 TYR   0.030   0.002   TYR A1663 
 PHE   0.024   0.002   PHE A 158 
 TRP   0.012   0.002   TRP A 558 
 HIS   0.006   0.001   HIS A1666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00483 /  0.20 (10647)
  covalent geometry    : angle       0.61584 /  0.31 (14304)
  SS BOND              : bond        0.00471 /  0.23 (    7)
  SS BOND              : angle       1.53570 /  0.78 (   14)
  hydrogen bonds       : bond        0.04461 /  2.86 (  527)
  hydrogen bonds       : angle       4.14453 /  2.87 ( 1539)
  link_BETA1-3         : bond        0.01990 /  1.11 (    6)
  link_BETA1-3         : angle       4.85245 /  2.58 (   18)
  link_BETA1-4         : bond        0.00937 /  0.46 (    5)
  link_BETA1-4         : angle       3.93692 /  2.21 (   15)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: A  206 TYR cc_start: 0.6743 (m-80) cc_final: 0.6510 (m-80)
REVERT: A  235 LEU cc_start: 0.6182 (mt) cc_final: 0.5944 (mt)
REVERT: A  286 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7177 (t80)
REVERT: A  328 TYR cc_start: 0.6082 (OUTLIER) cc_final: 0.4837 (t80)
REVERT: A  874 ASP cc_start: 0.7230 (t0) cc_final: 0.7018 (t0)
REVERT: A 1304 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6425 (pt0)
REVERT: A 1415 LYS cc_start: 0.7222 (tttt) cc_final: 0.6745 (tptt)
REVERT: A 1778 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.6641 (mmm)
  outliers start: 32
  outliers final: 21
  residues processed: 118
  average time/residue: 0.0993
  time to fit residues: 16.9001
Evaluate side-chains
  116 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  328 TYR
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  993 TYR
Chi-restraints excluded: chain A residue 1006 THR
Chi-restraints excluded: chain A residue 1035 TYR
Chi-restraints excluded: chain A residue 1090 CYS
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1304 GLU
Chi-restraints excluded: chain A residue 1494 ILE
Chi-restraints excluded: chain A residue 1577 LEU
Chi-restraints excluded: chain A residue 1591 TYR
Chi-restraints excluded: chain A residue 1627 ASN
Chi-restraints excluded: chain A residue 1656 HIS
Chi-restraints excluded: chain A residue 1688 ASP
Chi-restraints excluded: chain A residue 1702 LEU
Chi-restraints excluded: chain A residue 1778 MET
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1915 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 116 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 3 optimal weight:    0.3980
   chunk 18 optimal weight:    0.0020
   chunk 81 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.4788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1654 GLN
** A1799 ASN ** 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 = 0.4225 r_free = 0.4225 target = 0.130499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.112288 restraints weight = 21293.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 2.05
r_work: 0.3835 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3699 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3704
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3704 r_free = 0.3704    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3704 r_free = 0.3704    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3704
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10665  Z= 0.134
  Angle     :  0.596  15.892  14351  Z= 0.287
  Chirality :  0.042   0.472   1502
  Planarity :  0.003   0.041   1799
  Dihedral  :  4.655  52.101   1325
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.09 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.24), residues: 1168
  helix:  0.75 (0.19), residues: 736
  sheet:  None (None), residues: 0
  loop : -1.86 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1792 
 TYR   0.027   0.001   TYR A1663 
 PHE   0.017   0.002   PHE A 158 
 TRP   0.013   0.001   TRP A 214 
 HIS   0.005   0.001   HIS A1666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 (10647)
  covalent geometry    : angle       0.55683 /  0.28 (14304)
  SS BOND              : bond        0.00376 /  0.18 (    7)
  SS BOND              : angle       1.44180 /  0.71 (   14)
  hydrogen bonds       : bond        0.03967 /  2.56 (  527)
  hydrogen bonds       : angle       3.93855 /  2.72 ( 1539)
  link_BETA1-3         : bond        0.02021 /  1.14 (    6)
  link_BETA1-3         : angle       4.82722 /  2.56 (   18)
  link_BETA1-4         : bond        0.00896 /  0.44 (    5)
  link_BETA1-4         : angle       3.76202 /  2.12 (   15)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  185 MET cc_start: 0.7746 (tpp) cc_final: 0.7294 (tpp)
REVERT: A  206 TYR cc_start: 0.6728 (m-80) cc_final: 0.6430 (m-80)
REVERT: A  286 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7327 (t80)
REVERT: A  328 TYR cc_start: 0.6085 (OUTLIER) cc_final: 0.4972 (t80)
REVERT: A 1304 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6339 (pt0)
REVERT: A 1415 LYS cc_start: 0.7241 (tttt) cc_final: 0.6739 (tptt)
REVERT: A 1692 ASP cc_start: 0.8193 (t0) cc_final: 0.7963 (t0)
REVERT: A 1725 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6824 (mm-30)
REVERT: A 1778 MET cc_start: 0.7446 (mmm) cc_final: 0.6622 (mmm)
REVERT: A 1861 ILE cc_start: 0.8849 (pt) cc_final: 0.8582 (pt)
REVERT: A 1952 LYS cc_start: 0.5556 (OUTLIER) cc_final: 0.2388 (mmtp)
  outliers start: 28
  outliers final: 16
  residues processed: 124
  average time/residue: 0.0991
  time to fit residues: 17.5590
Evaluate side-chains
  116 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  328 TYR
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  993 TYR
Chi-restraints excluded: chain A residue 1090 CYS
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1265 VAL
Chi-restraints excluded: chain A residue 1304 GLU
Chi-restraints excluded: chain A residue 1577 LEU
Chi-restraints excluded: chain A residue 1591 TYR
Chi-restraints excluded: chain A residue 1702 LEU
Chi-restraints excluded: chain A residue 1757 VAL
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1915 THR
Chi-restraints excluded: chain A residue 1952 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 111 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 117 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 105 optimal weight:    2.9990
   chunk 47 optimal weight:    0.1980
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.129478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.111339 restraints weight = 21498.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3925 rms_B_bonded: 2.02
r_work: 0.3821 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3689 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3703
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3703 r_free = 0.3703    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3703 r_free = 0.3703    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3703
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10665  Z= 0.158
  Angle     :  0.618  15.805  14351  Z= 0.300
  Chirality :  0.043   0.470   1502
  Planarity :  0.003   0.040   1799
  Dihedral  :  4.668  52.645   1325
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.45 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.24), residues: 1168
  helix:  0.75 (0.19), residues: 738
  sheet:  None (None), residues: 0
  loop : -1.79 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1720 
 TYR   0.030   0.001   TYR A1663 
 PHE   0.021   0.002   PHE A 158 
 TRP   0.011   0.001   TRP A 214 
 HIS   0.005   0.001   HIS A1666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.16 (10647)
  covalent geometry    : angle       0.58123 /  0.29 (14304)
  SS BOND              : bond        0.00411 /  0.20 (    7)
  SS BOND              : angle       1.47074 /  0.73 (   14)
  hydrogen bonds       : bond        0.04058 /  2.62 (  527)
  hydrogen bonds       : angle       3.93112 /  2.72 ( 1539)
  link_BETA1-3         : bond        0.01968 /  1.10 (    6)
  link_BETA1-3         : angle       4.77311 /  2.54 (   18)
  link_BETA1-4         : bond        0.00912 /  0.44 (    5)
  link_BETA1-4         : angle       3.74886 /  2.11 (   15)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: A  206 TYR cc_start: 0.6714 (m-80) cc_final: 0.6380 (m-80)
REVERT: A  286 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7396 (t80)
REVERT: A  328 TYR cc_start: 0.6082 (OUTLIER) cc_final: 0.5024 (t80)
REVERT: A 1304 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6324 (pt0)
REVERT: A 1415 LYS cc_start: 0.7303 (tttt) cc_final: 0.6819 (tptt)
REVERT: A 1692 ASP cc_start: 0.8131 (t0) cc_final: 0.7851 (t0)
REVERT: A 1725 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6810 (mm-30)
REVERT: A 1778 MET cc_start: 0.7468 (mmm) cc_final: 0.6710 (mmm)
REVERT: A 1861 ILE cc_start: 0.8861 (pt) cc_final: 0.8580 (pt)
  outliers start: 28
  outliers final: 23
  residues processed: 122
  average time/residue: 0.0946
  time to fit residues: 16.7373
Evaluate side-chains
  124 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  328 TYR
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  993 TYR
Chi-restraints excluded: chain A residue 1006 THR
Chi-restraints excluded: chain A residue 1090 CYS
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1193 CYS
Chi-restraints excluded: chain A residue 1265 VAL
Chi-restraints excluded: chain A residue 1304 GLU
Chi-restraints excluded: chain A residue 1494 ILE
Chi-restraints excluded: chain A residue 1577 LEU
Chi-restraints excluded: chain A residue 1589 LYS
Chi-restraints excluded: chain A residue 1591 TYR
Chi-restraints excluded: chain A residue 1627 ASN
Chi-restraints excluded: chain A residue 1688 ASP
Chi-restraints excluded: chain A residue 1702 LEU
Chi-restraints excluded: chain A residue 1757 VAL
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1915 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 70 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 117 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 104 optimal weight:    0.8980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1454 GLN
** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.128595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.110526 restraints weight = 21140.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 1.99
r_work: 0.3809 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3676 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3690
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3690 r_free = 0.3690    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3690 r_free = 0.3690    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3690
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10665  Z= 0.174
  Angle     :  0.628  15.791  14351  Z= 0.305
  Chirality :  0.044   0.470   1502
  Planarity :  0.003   0.040   1799
  Dihedral  :  4.696  51.386   1325
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.98 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.24), residues: 1168
  helix:  0.73 (0.18), residues: 731
  sheet:  None (None), residues: 0
  loop : -1.78 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1720 
 TYR   0.027   0.001   TYR A1663 
 PHE   0.022   0.002   PHE A 158 
 TRP   0.012   0.002   TRP A 240 
 HIS   0.006   0.001   HIS A1666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.17 (10647)
  covalent geometry    : angle       0.59147 /  0.30 (14304)
  SS BOND              : bond        0.00419 /  0.20 (    7)
  SS BOND              : angle       1.51732 /  0.75 (   14)
  hydrogen bonds       : bond        0.04128 /  2.66 (  527)
  hydrogen bonds       : angle       3.97554 /  2.75 ( 1539)
  link_BETA1-3         : bond        0.01990 /  1.11 (    6)
  link_BETA1-3         : angle       4.78990 /  2.55 (   18)
  link_BETA1-4         : bond        0.00909 /  0.44 (    5)
  link_BETA1-4         : angle       3.74465 /  2.10 (   15)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7404 (t80)
REVERT: A  328 TYR cc_start: 0.6155 (OUTLIER) cc_final: 0.5074 (t80)
REVERT: A 1304 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6369 (pt0)
REVERT: A 1415 LYS cc_start: 0.7266 (tttt) cc_final: 0.6778 (tptt)
REVERT: A 1725 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6883 (mm-30)
REVERT: A 1778 MET cc_start: 0.7445 (mmm) cc_final: 0.6649 (mmm)
  outliers start: 29
  outliers final: 24
  residues processed: 124
  average time/residue: 0.0953
  time to fit residues: 16.9580
Evaluate side-chains
  124 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  328 TYR
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  993 TYR
Chi-restraints excluded: chain A residue 1006 THR
Chi-restraints excluded: chain A residue 1090 CYS
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1193 CYS
Chi-restraints excluded: chain A residue 1265 VAL
Chi-restraints excluded: chain A residue 1304 GLU
Chi-restraints excluded: chain A residue 1494 ILE
Chi-restraints excluded: chain A residue 1589 LYS
Chi-restraints excluded: chain A residue 1591 TYR
Chi-restraints excluded: chain A residue 1656 HIS
Chi-restraints excluded: chain A residue 1688 ASP
Chi-restraints excluded: chain A residue 1702 LEU
Chi-restraints excluded: chain A residue 1757 VAL
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1915 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 26 optimal weight:    0.1980
   chunk 25 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 102 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 85 optimal weight:    0.4980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1454 GLN
** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.129521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.111542 restraints weight = 21285.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 1.99
r_work: 0.3825 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3693 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (13 function evaluations)
r_final: 0.3706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10665  Z= 0.146
  Angle     :  0.616  15.681  14351  Z= 0.298
  Chirality :  0.043   0.470   1502
  Planarity :  0.003   0.041   1799
  Dihedral  :  4.608  50.344   1325
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.25 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.24), residues: 1168
  helix:  0.85 (0.19), residues: 731
  sheet:  None (None), residues: 0
  loop : -1.73 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1720 
 TYR   0.025   0.001   TYR A1663 
 PHE   0.019   0.002   PHE A 158 
 TRP   0.031   0.002   TRP A 558 
 HIS   0.005   0.001   HIS A1666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.14 (10647)
  covalent geometry    : angle       0.57909 /  0.29 (14304)
  SS BOND              : bond        0.00387 /  0.18 (    7)
  SS BOND              : angle       1.46864 /  0.71 (   14)
  hydrogen bonds       : bond        0.03974 /  2.57 (  527)
  hydrogen bonds       : angle       3.89385 /  2.70 ( 1539)
  link_BETA1-3         : bond        0.01984 /  1.12 (    6)
  link_BETA1-3         : angle       4.77515 /  2.55 (   18)
  link_BETA1-4         : bond        0.00904 /  0.44 (    5)
  link_BETA1-4         : angle       3.65890 /  2.06 (   15)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A  286 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7394 (t80)
REVERT: A  328 TYR cc_start: 0.6220 (OUTLIER) cc_final: 0.5185 (t80)
REVERT: A 1415 LYS cc_start: 0.7247 (tttt) cc_final: 0.6743 (tptt)
REVERT: A 1725 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6853 (mm-30)
REVERT: A 1778 MET cc_start: 0.7453 (mmm) cc_final: 0.6669 (mmm)
REVERT: A 1861 ILE cc_start: 0.8862 (pt) cc_final: 0.8541 (pt)
REVERT: A 1952 LYS cc_start: 0.5469 (OUTLIER) cc_final: 0.2529 (mmtp)
  outliers start: 28
  outliers final: 23
  residues processed: 118
  average time/residue: 0.1015
  time to fit residues: 16.9595
Evaluate side-chains
  122 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  328 TYR
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  993 TYR
Chi-restraints excluded: chain A residue 1006 THR
Chi-restraints excluded: chain A residue 1090 CYS
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1193 CYS
Chi-restraints excluded: chain A residue 1265 VAL
Chi-restraints excluded: chain A residue 1494 ILE
Chi-restraints excluded: chain A residue 1577 LEU
Chi-restraints excluded: chain A residue 1589 LYS
Chi-restraints excluded: chain A residue 1591 TYR
Chi-restraints excluded: chain A residue 1656 HIS
Chi-restraints excluded: chain A residue 1688 ASP
Chi-restraints excluded: chain A residue 1702 LEU
Chi-restraints excluded: chain A residue 1757 VAL
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1915 THR
Chi-restraints excluded: chain A residue 1952 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 56 optimal weight:    0.6980
   chunk 103 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 91 optimal weight:    0.1980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 555 ASN
** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1454 GLN
A1659 ASN
** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.129781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.111905 restraints weight = 21155.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 1.98
r_work: 0.3832 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3697 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3711 r_free = 0.3711    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3711 r_free = 0.3711    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10665  Z= 0.143
  Angle     :  0.612  15.600  14351  Z= 0.297
  Chirality :  0.043   0.467   1502
  Planarity :  0.003   0.041   1799
  Dihedral  :  4.552  49.630   1325
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.98 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.24), residues: 1168
  helix:  0.92 (0.19), residues: 731
  sheet:  None (None), residues: 0
  loop : -1.69 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1720 
 TYR   0.025   0.001   TYR A1663 
 PHE   0.019   0.002   PHE A 158 
 TRP   0.022   0.001   TRP A 616 
 HIS   0.005   0.001   HIS A1666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.14 (10647)
  covalent geometry    : angle       0.57606 /  0.29 (14304)
  SS BOND              : bond        0.00381 /  0.18 (    7)
  SS BOND              : angle       1.45977 /  0.71 (   14)
  hydrogen bonds       : bond        0.03899 /  2.53 (  527)
  hydrogen bonds       : angle       3.85779 /  2.67 ( 1539)
  link_BETA1-3         : bond        0.01953 /  1.10 (    6)
  link_BETA1-3         : angle       4.75110 /  2.54 (   18)
  link_BETA1-4         : bond        0.00910 /  0.45 (    5)
  link_BETA1-4         : angle       3.57785 /  2.01 (   15)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 97
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A  286 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7405 (t80)
REVERT: A  328 TYR cc_start: 0.6217 (OUTLIER) cc_final: 0.5377 (t80)
REVERT: A 1415 LYS cc_start: 0.7236 (tttt) cc_final: 0.6739 (tptt)
REVERT: A 1692 ASP cc_start: 0.8229 (t0) cc_final: 0.8022 (t0)
REVERT: A 1725 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6811 (mm-30)
REVERT: A 1778 MET cc_start: 0.7407 (mmm) cc_final: 0.6685 (mmm)
REVERT: A 1952 LYS cc_start: 0.5502 (OUTLIER) cc_final: 0.2577 (mmtp)
  outliers start: 31
  outliers final: 28
  residues processed: 119
  average time/residue: 0.0958
  time to fit residues: 16.3502
Evaluate side-chains
  123 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 92
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  328 TYR
Chi-restraints excluded: chain A residue  555 ASN
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  993 TYR
Chi-restraints excluded: chain A residue 1006 THR
Chi-restraints excluded: chain A residue 1035 TYR
Chi-restraints excluded: chain A residue 1090 CYS
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1193 CYS
Chi-restraints excluded: chain A residue 1265 VAL
Chi-restraints excluded: chain A residue 1494 ILE
Chi-restraints excluded: chain A residue 1577 LEU
Chi-restraints excluded: chain A residue 1589 LYS
Chi-restraints excluded: chain A residue 1591 TYR
Chi-restraints excluded: chain A residue 1639 THR
Chi-restraints excluded: chain A residue 1656 HIS
Chi-restraints excluded: chain A residue 1688 ASP
Chi-restraints excluded: chain A residue 1702 LEU
Chi-restraints excluded: chain A residue 1712 ASN
Chi-restraints excluded: chain A residue 1757 VAL
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1915 THR
Chi-restraints excluded: chain A residue 1952 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 49 optimal weight:    0.2980
   chunk 94 optimal weight:    0.0970
   chunk 121 optimal weight:    0.3980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 555 ASN
** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1454 GLN
** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1852 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.129329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.111391 restraints weight = 21196.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 1.99
r_work: 0.3823 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3687 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3700
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3700 r_free = 0.3700    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3700 r_free = 0.3700    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (26 function evaluations)
r_final: 0.3700
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10665  Z= 0.158
  Angle     :  0.623  15.560  14351  Z= 0.304
  Chirality :  0.043   0.468   1502
  Planarity :  0.003   0.040   1799
  Dihedral  :  4.578  49.279   1325
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 16.07 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.24), residues: 1168
  helix:  0.89 (0.19), residues: 731
  sheet:  None (None), residues: 0
  loop : -1.66 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1720 
 TYR   0.025   0.001   TYR A1663 
 PHE   0.020   0.002   PHE A 158 
 TRP   0.020   0.002   TRP A 558 
 HIS   0.006   0.001   HIS A1666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.16 (10647)
  covalent geometry    : angle       0.58830 /  0.30 (14304)
  SS BOND              : bond        0.00394 /  0.19 (    7)
  SS BOND              : angle       1.47717 /  0.72 (   14)
  hydrogen bonds       : bond        0.03968 /  2.57 (  527)
  hydrogen bonds       : angle       3.87913 /  2.69 ( 1539)
  link_BETA1-3         : bond        0.01921 /  1.08 (    6)
  link_BETA1-3         : angle       4.74878 /  2.54 (   18)
  link_BETA1-4         : bond        0.00910 /  0.45 (    5)
  link_BETA1-4         : angle       3.57404 /  2.01 (   15)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 93
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A  286 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7413 (t80)
REVERT: A  328 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.5367 (t80)
REVERT: A 1415 LYS cc_start: 0.7239 (tttt) cc_final: 0.6734 (tptt)
REVERT: A 1778 MET cc_start: 0.7412 (mmm) cc_final: 0.6698 (mmm)
REVERT: A 1952 LYS cc_start: 0.5519 (OUTLIER) cc_final: 0.2532 (mmtp)
  outliers start: 33
  outliers final: 29
  residues processed: 117
  average time/residue: 0.0887
  time to fit residues: 15.2689
Evaluate side-chains
  123 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 91
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  328 TYR
Chi-restraints excluded: chain A residue  555 ASN
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  993 TYR
Chi-restraints excluded: chain A residue 1006 THR
Chi-restraints excluded: chain A residue 1035 TYR
Chi-restraints excluded: chain A residue 1090 CYS
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1193 CYS
Chi-restraints excluded: chain A residue 1265 VAL
Chi-restraints excluded: chain A residue 1494 ILE
Chi-restraints excluded: chain A residue 1577 LEU
Chi-restraints excluded: chain A residue 1589 LYS
Chi-restraints excluded: chain A residue 1591 TYR
Chi-restraints excluded: chain A residue 1639 THR
Chi-restraints excluded: chain A residue 1656 HIS
Chi-restraints excluded: chain A residue 1688 ASP
Chi-restraints excluded: chain A residue 1702 LEU
Chi-restraints excluded: chain A residue 1712 ASN
Chi-restraints excluded: chain A residue 1757 VAL
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1915 THR
Chi-restraints excluded: chain A residue 1952 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 99 optimal weight:    0.5980
   chunk 84 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 18 optimal weight:    0.0770
   chunk 17 optimal weight:    3.9990
   chunk 83 optimal weight:    0.6980
   chunk 116 optimal weight:    0.4980
   chunk 88 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 100 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.4538

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 555 ASN
** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1454 GLN
** A1799 ASN ** 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 = 0.4221 r_free = 0.4221 target = 0.130321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.112397 restraints weight = 21400.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 2.01
r_work: 0.3840 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3708 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3715
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3715 r_free = 0.3715    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3715 r_free = 0.3715    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3715
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10665  Z= 0.134
  Angle     :  0.608  15.448  14351  Z= 0.297
  Chirality :  0.042   0.465   1502
  Planarity :  0.003   0.041   1799
  Dihedral  :  4.534  48.371   1325
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.52 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.24), residues: 1168
  helix:  0.97 (0.19), residues: 733
  sheet:  None (None), residues: 0
  loop : -1.62 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1792 
 TYR   0.025   0.001   TYR A1663 
 PHE   0.018   0.002   PHE A 158 
 TRP   0.018   0.001   TRP A 558 
 HIS   0.005   0.001   HIS A1666 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.13 (10647)
  covalent geometry    : angle       0.57232 /  0.29 (14304)
  SS BOND              : bond        0.00364 /  0.17 (    7)
  SS BOND              : angle       1.44241 /  0.69 (   14)
  hydrogen bonds       : bond        0.03824 /  2.48 (  527)
  hydrogen bonds       : angle       3.82817 /  2.65 ( 1539)
  link_BETA1-3         : bond        0.01927 /  1.09 (    6)
  link_BETA1-3         : angle       4.73728 /  2.53 (   18)
  link_BETA1-4         : bond        0.00920 /  0.45 (    5)
  link_BETA1-4         : angle       3.51324 /  1.98 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2774.63 seconds
wall clock time: 48 minutes 28.83 seconds (2908.83 seconds total)