Starting phenix.real_space_refine
on Wed Mar  4 03:57:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fap_31504/03_2026/7fap_31504.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fap_31504/03_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_31504/03_2026/7fap_31504.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fap_31504/03_2026/7fap_31504.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fap_31504/03_2026/7fap_31504.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fap_31504/03_2026/7fap_31504.map"
  }
  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-5986/lib/python3.9/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 dihedrals: 37
          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: 2.47, per 1000 atoms: 0.24
  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: 0.86
  Conformation dependent library (CDL) restraints added in 391.0 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: 0.32
  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: 1.55

  Time building geometry restraints manager: 1.15 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 -    25.89: 6073
       25.89 -    51.78: 374
       51.78 -    77.67: 101
       77.67 -   103.56: 44
      103.56 -   129.45: 22
  Dihedral angle restraints: 6614
    sinusoidal: 2989
      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 6611 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:             2.100
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     10.450
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6621
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  : 20.810 129.454   4237
  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
  covalent geometry    : bond        0.01145 (10647)
  covalent geometry    : angle       1.04775 (14304)
  SS BOND              : bond        0.13657 (    7)
  SS BOND              : angle       4.38261 (   14)
  hydrogen bonds       : bond        0.13727 (  527)
  hydrogen bonds       : angle       5.33249 ( 1539)
  link_BETA1-3         : bond        0.01933 (    6)
  link_BETA1-3         : angle       4.83270 (   18)
  link_BETA1-4         : bond        0.01323 (    5)
  link_BETA1-4         : angle       5.97453 (   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  : 0.404 
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: 0.1185
  time to fit residues: 24.1574
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  : 0.581 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
** 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

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.129961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.111775 restraints weight = 20866.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 2.03
r_work: 0.3825 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3686 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3686
-------------------------------------------------------------------------------
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 = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3699 r_free = 0.3699    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3699
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.1478

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= 0.207
  Angle     :  0.725  15.404  14351  Z= 0.352
  Chirality :  0.046   0.384   1502
  Planarity :  0.004   0.052   1799
  Dihedral  : 19.978 118.460   1593
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  8.66 %
    Favored  : 89.20 %
  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:  0.34 (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   0.016   0.002   TRP A1501 
 HIS   0.006   0.001   HIS A1666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 (10647)
  covalent geometry    : angle       0.68180 (14304)
  SS BOND              : bond        0.00608 (    7)
  SS BOND              : angle       1.56330 (   14)
  hydrogen bonds       : bond        0.04946 (  527)
  hydrogen bonds       : angle       4.38739 ( 1539)
  link_BETA1-3         : bond        0.02007 (    6)
  link_BETA1-3         : angle       5.75678 (   18)
  link_BETA1-4         : bond        0.01086 (    5)
  link_BETA1-4         : angle       4.18491 (   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: 24
    poor density    : 106
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A   49 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.7814 (t0)
REVERT: A  286 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.6852 (t80)
REVERT: A  328 TYR cc_start: 0.6010 (OUTLIER) cc_final: 0.4631 (t80)
REVERT: A  813 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6877 (mt-10)
REVERT: A  874 ASP cc_start: 0.7302 (t0) cc_final: 0.7071 (t0)
REVERT: A 1179 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6815 (mp0)
REVERT: A 1415 LYS cc_start: 0.7160 (tttt) cc_final: 0.6638 (tptt)
REVERT: A 1778 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6440 (mmm)
  outliers start: 24
  outliers final: 12
  residues processed: 119
  average time/residue: 0.1188
  time to fit residues: 19.9384
Evaluate side-chains
  111 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
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  286 PHE
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 1654 GLN
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:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 101 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 114 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  49 ASN
** A1538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1540 ASN
A1654 GLN
** A1656 HIS ** 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 = 0.4199 r_free = 0.4199 target = 0.128608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.109778 restraints weight = 21400.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 2.02
r_work: 0.3790 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3652 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3668
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3668 r_free = 0.3668    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3668 r_free = 0.3668    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3668
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.2007

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= 0.232
  Angle     :  0.724  14.010  14351  Z= 0.350
  Chirality :  0.047   0.454   1502
  Planarity :  0.004   0.044   1799
  Dihedral  : 18.420 117.052   1588
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 11.79 %
    Favored  : 85.62 %
  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: -0.99 (0.23), residues: 1168
  helix:  0.16 (0.18), residues: 737
  sheet:  None (None), residues: 0
  loop : -2.07 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1720 
 TYR   0.026   0.002   TYR A1663 
 PHE   0.025   0.002   PHE A 158 
 TRP   0.013   0.002   TRP A 558 
 HIS   0.006   0.001   HIS A1666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 (10647)
  covalent geometry    : angle       0.68708 (14304)
  SS BOND              : bond        0.00501 (    7)
  SS BOND              : angle       1.64357 (   14)
  hydrogen bonds       : bond        0.04847 (  527)
  hydrogen bonds       : angle       4.32730 ( 1539)
  link_BETA1-3         : bond        0.01629 (    6)
  link_BETA1-3         : angle       5.24139 (   18)
  link_BETA1-4         : bond        0.01118 (    5)
  link_BETA1-4         : angle       3.92218 (   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
  125 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 96
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A  206 TYR cc_start: 0.6785 (m-80) cc_final: 0.6566 (m-80)
REVERT: A  286 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7006 (t80)
REVERT: A  328 TYR cc_start: 0.5978 (OUTLIER) cc_final: 0.4721 (t80)
REVERT: A  874 ASP cc_start: 0.7263 (t0) cc_final: 0.6938 (t0)
REVERT: A 1304 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6104 (pt0)
REVERT: A 1415 LYS cc_start: 0.7145 (tttt) cc_final: 0.6666 (tptt)
REVERT: A 1778 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6651 (mmm)
  outliers start: 29
  outliers final: 20
  residues processed: 114
  average time/residue: 0.1097
  time to fit residues: 18.0085
Evaluate side-chains
  113 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
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  668 THR
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 1030 ASN
Chi-restraints excluded: chain A residue 1035 TYR
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1304 GLU
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
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:    8.9990
   chunk 11 optimal weight:    5.9990
   chunk 109 optimal weight:    0.1980
   chunk 86 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 95 optimal weight:    4.9990
   chunk 104 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
A 956 GLN
A1654 GLN
** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1866 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.129543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.111016 restraints weight = 21480.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3924 rms_B_bonded: 2.01
r_work: 0.3815 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3679 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3687
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3687 r_free = 0.3687    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 = 0.3687 r_free = 0.3687    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3687
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
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      :  0.004   0.049  10665  Z= 0.165
  Angle     :  0.654  13.465  14351  Z= 0.313
  Chirality :  0.044   0.417   1502
  Planarity :  0.004   0.041   1799
  Dihedral  : 17.006 113.101   1588
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 13.57 %
    Favored  : 83.12 %
  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: -0.65 (0.24), residues: 1168
  helix:  0.45 (0.18), residues: 732
  sheet:  None (None), residues: 0
  loop : -1.96 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 241 
 TYR   0.031   0.001   TYR A1663 
 PHE   0.020   0.002   PHE A 158 
 TRP   0.012   0.002   TRP A1094 
 HIS   0.005   0.001   HIS A1666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (10647)
  covalent geometry    : angle       0.61827 (14304)
  SS BOND              : bond        0.00415 (    7)
  SS BOND              : angle       1.54588 (   14)
  hydrogen bonds       : bond        0.04332 (  527)
  hydrogen bonds       : angle       4.11681 ( 1539)
  link_BETA1-3         : bond        0.01594 (    6)
  link_BETA1-3         : angle       5.03353 (   18)
  link_BETA1-4         : bond        0.00928 (    5)
  link_BETA1-4         : angle       3.42611 (   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
  138 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 101
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A  206 TYR cc_start: 0.6750 (m-80) cc_final: 0.6521 (m-80)
REVERT: A  286 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7261 (t80)
REVERT: A  328 TYR cc_start: 0.6108 (OUTLIER) cc_final: 0.4902 (t80)
REVERT: A  874 ASP cc_start: 0.7229 (t0) cc_final: 0.6996 (t0)
REVERT: A 1030 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8309 (t0)
REVERT: A 1304 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.5974 (pt0)
REVERT: A 1415 LYS cc_start: 0.7151 (tttt) cc_final: 0.6684 (tptt)
REVERT: A 1692 ASP cc_start: 0.8260 (t0) cc_final: 0.8009 (t0)
REVERT: A 1778 MET cc_start: 0.7505 (mmm) cc_final: 0.6684 (mmm)
REVERT: A 1861 ILE cc_start: 0.8931 (pt) cc_final: 0.8647 (pt)
REVERT: A 1952 LYS cc_start: 0.5568 (OUTLIER) cc_final: 0.2589 (mmtp)
REVERT: A 1953 MET cc_start: 0.7912 (tmm) cc_final: 0.7640 (tmm)
  outliers start: 37
  outliers final: 21
  residues processed: 125
  average time/residue: 0.1009
  time to fit residues: 18.0961
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  : 0.420 
-------------------------------------------------------------------------------
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 1030 ASN
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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 116 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 101 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0470
   chunk 81 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.129706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.111451 restraints weight = 21304.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3930 rms_B_bonded: 2.06
r_work: 0.3823 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3684 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3684
-------------------------------------------------------------------------------
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 = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3697 r_free = 0.3697    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3697
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10665  Z= 0.141
  Angle     :  0.626  13.422  14351  Z= 0.297
  Chirality :  0.043   0.405   1502
  Planarity :  0.003   0.041   1799
  Dihedral  : 15.826 110.338   1588
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.09 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.24), residues: 1168
  helix:  0.74 (0.19), residues: 734
  sheet:  None (None), residues: 0
  loop : -1.81 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 241 
 TYR   0.023   0.001   TYR A1663 
 PHE   0.019   0.002   PHE A 158 
 TRP   0.015   0.001   TRP A 616 
 HIS   0.005   0.001   HIS A1658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10647)
  covalent geometry    : angle       0.59098 (14304)
  SS BOND              : bond        0.00388 (    7)
  SS BOND              : angle       1.47233 (   14)
  hydrogen bonds       : bond        0.03970 (  527)
  hydrogen bonds       : angle       3.94911 ( 1539)
  link_BETA1-3         : bond        0.01602 (    6)
  link_BETA1-3         : angle       4.93769 (   18)
  link_BETA1-4         : bond        0.00793 (    5)
  link_BETA1-4         : angle       3.26570 (   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
  136 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 103
  time to evaluate  : 0.413 
Fit side-chains
REVERT: A  206 TYR cc_start: 0.6740 (m-80) cc_final: 0.6441 (m-80)
REVERT: A  286 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7402 (t80)
REVERT: A  328 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.4999 (t80)
REVERT: A 1304 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6222 (pt0)
REVERT: A 1415 LYS cc_start: 0.7266 (tttt) cc_final: 0.6762 (tptt)
REVERT: A 1654 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7683 (tm-30)
REVERT: A 1692 ASP cc_start: 0.8180 (t0) cc_final: 0.7898 (t0)
REVERT: A 1725 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6830 (mm-30)
REVERT: A 1778 MET cc_start: 0.7501 (mmm) cc_final: 0.6673 (mmm)
REVERT: A 1861 ILE cc_start: 0.8858 (pt) cc_final: 0.8573 (pt)
  outliers start: 33
  outliers final: 18
  residues processed: 126
  average time/residue: 0.0954
  time to fit residues: 17.4318
Evaluate side-chains
  116 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
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  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 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 1591 TYR
Chi-restraints excluded: chain A residue 1627 ASN
Chi-restraints excluded: chain A residue 1654 GLN
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 1974 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 117 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 105 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1583 ASN
** 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 = 0.4192 r_free = 0.4192 target = 0.128349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.110232 restraints weight = 21450.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3908 rms_B_bonded: 2.00
r_work: 0.3803 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3667 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3681
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3681 r_free = 0.3681    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3681 r_free = 0.3681    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3681
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10665  Z= 0.178
  Angle     :  0.670  13.624  14351  Z= 0.315
  Chirality :  0.045   0.408   1502
  Planarity :  0.004   0.040   1799
  Dihedral  : 15.094 108.492   1588
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 15.45 %
    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: -0.37 (0.24), residues: 1168
  helix:  0.65 (0.18), residues: 737
  sheet:  None (None), residues: 0
  loop : -1.81 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1720 
 TYR   0.029   0.002   TYR A1663 
 PHE   0.023   0.002   PHE A 158 
 TRP   0.013   0.002   TRP A 616 
 HIS   0.008   0.001   HIS A1658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (10647)
  covalent geometry    : angle       0.63424 (14304)
  SS BOND              : bond        0.00427 (    7)
  SS BOND              : angle       1.49607 (   14)
  hydrogen bonds       : bond        0.04124 (  527)
  hydrogen bonds       : angle       3.99352 ( 1539)
  link_BETA1-3         : bond        0.01789 (    6)
  link_BETA1-3         : angle       5.10645 (   18)
  link_BETA1-4         : bond        0.00988 (    5)
  link_BETA1-4         : angle       3.45196 (   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
  132 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 97
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A  185 MET cc_start: 0.7851 (tpp) cc_final: 0.7418 (tpp)
REVERT: A  206 TYR cc_start: 0.6776 (m-80) cc_final: 0.6441 (m-80)
REVERT: A  286 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7442 (t80)
REVERT: A  328 TYR cc_start: 0.6103 (OUTLIER) cc_final: 0.5056 (t80)
REVERT: A 1304 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6228 (pt0)
REVERT: A 1415 LYS cc_start: 0.7273 (tttt) cc_final: 0.6791 (tptt)
REVERT: A 1692 ASP cc_start: 0.8204 (t0) cc_final: 0.7904 (t0)
REVERT: A 1725 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6809 (mm-30)
REVERT: A 1778 MET cc_start: 0.7519 (mmm) cc_final: 0.6789 (mmm)
REVERT: A 1952 LYS cc_start: 0.5587 (OUTLIER) cc_final: 0.2736 (mmtp)
  outliers start: 35
  outliers final: 26
  residues processed: 120
  average time/residue: 0.1048
  time to fit residues: 18.0894
Evaluate side-chains
  125 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
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  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 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 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
Chi-restraints excluded: chain A residue 1974 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 117 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 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 = 0.4161 r_free = 0.4161 target = 0.126151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.108155 restraints weight = 21082.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 1.95
r_work: 0.3772 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3633 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  10665  Z= 0.233
  Angle     :  0.717  13.535  14351  Z= 0.343
  Chirality :  0.047   0.405   1502
  Planarity :  0.004   0.041   1799
  Dihedral  : 14.514 105.892   1588
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.43 %
    Favored  : 80.27 %
  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:  0.48 (0.18), residues: 729
  sheet:  None (None), residues: 0
  loop : -1.85 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1720 
 TYR   0.026   0.002   TYR A1663 
 PHE   0.027   0.002   PHE A 158 
 TRP   0.019   0.002   TRP A 240 
 HIS   0.006   0.001   HIS A1666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 (10647)
  covalent geometry    : angle       0.68391 (14304)
  SS BOND              : bond        0.00497 (    7)
  SS BOND              : angle       1.60572 (   14)
  hydrogen bonds       : bond        0.04541 (  527)
  hydrogen bonds       : angle       4.18676 ( 1539)
  link_BETA1-3         : bond        0.01661 (    6)
  link_BETA1-3         : angle       5.01195 (   18)
  link_BETA1-4         : bond        0.00909 (    5)
  link_BETA1-4         : angle       3.59974 (   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
  134 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 97
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A  206 TYR cc_start: 0.6943 (m-80) cc_final: 0.6598 (m-80)
REVERT: A  276 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6775 (mt)
REVERT: A  286 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7482 (t80)
REVERT: A  328 TYR cc_start: 0.6119 (OUTLIER) cc_final: 0.5038 (t80)
REVERT: A 1304 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6092 (pt0)
REVERT: A 1415 LYS cc_start: 0.7274 (tttt) cc_final: 0.6791 (tptt)
REVERT: A 1692 ASP cc_start: 0.8217 (t0) cc_final: 0.7974 (t0)
REVERT: A 1778 MET cc_start: 0.7563 (mmm) cc_final: 0.6854 (mmm)
REVERT: A 1952 LYS cc_start: 0.5502 (OUTLIER) cc_final: 0.2396 (mmtp)
  outliers start: 37
  outliers final: 26
  residues processed: 124
  average time/residue: 0.1019
  time to fit residues: 18.0338
Evaluate side-chains
  119 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 88
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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  276 LEU
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 1012 SER
Chi-restraints excluded: chain A residue 1035 TYR
Chi-restraints excluded: chain A residue 1090 CYS
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 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 1757 VAL
Chi-restraints excluded: chain A residue 1774 PHE
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
Chi-restraints excluded: chain A residue 1974 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 26 optimal weight:    0.0010
   chunk 25 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 555 ASN
** 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 = 0.4193 r_free = 0.4193 target = 0.128459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.110546 restraints weight = 21344.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3915 rms_B_bonded: 1.99
r_work: 0.3811 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3676 rms_B_bonded: 4.70 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 = 0.32   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 |
|-----------------------------------------------------------------------------|
r_final: 0.3690
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.2760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  10665  Z= 0.159
  Angle     :  0.655  13.302  14351  Z= 0.312
  Chirality :  0.044   0.400   1502
  Planarity :  0.004   0.042   1799
  Dihedral  : 13.754 104.865   1588
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 17.05 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.30 (0.24), residues: 1168
  helix:  0.70 (0.19), residues: 730
  sheet:  None (None), residues: 0
  loop : -1.74 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1720 
 TYR   0.024   0.001   TYR A1663 
 PHE   0.018   0.002   PHE A 158 
 TRP   0.014   0.002   TRP A 214 
 HIS   0.005   0.001   HIS A1666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (10647)
  covalent geometry    : angle       0.61820 (14304)
  SS BOND              : bond        0.00404 (    7)
  SS BOND              : angle       1.48638 (   14)
  hydrogen bonds       : bond        0.04077 (  527)
  hydrogen bonds       : angle       3.99710 ( 1539)
  link_BETA1-3         : bond        0.01610 (    6)
  link_BETA1-3         : angle       4.95586 (   18)
  link_BETA1-4         : bond        0.00980 (    5)
  link_BETA1-4         : angle       3.74290 (   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
  132 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 98
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A  151 CYS cc_start: 0.7308 (m) cc_final: 0.6635 (m)
REVERT: A  206 TYR cc_start: 0.6936 (m-80) cc_final: 0.6571 (m-80)
REVERT: A  286 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7465 (t80)
REVERT: A  328 TYR cc_start: 0.6178 (OUTLIER) cc_final: 0.5279 (t80)
REVERT: A 1304 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6361 (pt0)
REVERT: A 1415 LYS cc_start: 0.7273 (tttt) cc_final: 0.6801 (tptt)
REVERT: A 1692 ASP cc_start: 0.8194 (t0) cc_final: 0.7943 (t0)
REVERT: A 1725 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6914 (mm-30)
REVERT: A 1778 MET cc_start: 0.7466 (mmm) cc_final: 0.6775 (mmm)
REVERT: A 1952 LYS cc_start: 0.5620 (OUTLIER) cc_final: 0.2693 (mmtp)
  outliers start: 34
  outliers final: 24
  residues processed: 122
  average time/residue: 0.1043
  time to fit residues: 18.4581
Evaluate side-chains
  121 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
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  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 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 1591 TYR
Chi-restraints excluded: chain A residue 1627 ASN
Chi-restraints excluded: chain A residue 1688 ASP
Chi-restraints excluded: chain A residue 1689 LEU
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 1916 VAL
Chi-restraints excluded: chain A residue 1952 LYS
Chi-restraints excluded: chain A residue 1974 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 57 optimal weight:    0.0670
   chunk 14 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0370
   chunk 51 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0870
   chunk 103 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.2974

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

Flipped N/Q/H residues before XYZ refinement:
** 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
A1852 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.129906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.112242 restraints weight = 21146.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 1.97
r_work: 0.3842 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3708 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3722
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3722 r_free = 0.3722    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3722 r_free = 0.3722    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3722
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  10665  Z= 0.128
  Angle     :  0.633  13.151  14351  Z= 0.302
  Chirality :  0.042   0.391   1502
  Planarity :  0.003   0.043   1799
  Dihedral  : 13.340 104.328   1588
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 18.39 %
    Favored  : 79.29 %
  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: -0.03 (0.24), residues: 1168
  helix:  0.93 (0.19), residues: 730
  sheet:  None (None), residues: 0
  loop : -1.65 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 241 
 TYR   0.025   0.001   TYR A1663 
 PHE   0.017   0.002   PHE A 158 
 TRP   0.015   0.001   TRP A 214 
 HIS   0.005   0.001   HIS A1666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (10647)
  covalent geometry    : angle       0.59709 (14304)
  SS BOND              : bond        0.00362 (    7)
  SS BOND              : angle       1.42060 (   14)
  hydrogen bonds       : bond        0.03821 (  527)
  hydrogen bonds       : angle       3.87207 ( 1539)
  link_BETA1-3         : bond        0.01545 (    6)
  link_BETA1-3         : angle       4.89473 (   18)
  link_BETA1-4         : bond        0.00951 (    5)
  link_BETA1-4         : angle       3.56377 (   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
  124 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  151 CYS cc_start: 0.7222 (m) cc_final: 0.6556 (m)
REVERT: A  206 TYR cc_start: 0.6745 (m-80) cc_final: 0.6408 (m-80)
REVERT: A  286 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7441 (t80)
REVERT: A  328 TYR cc_start: 0.6201 (OUTLIER) cc_final: 0.5365 (t80)
REVERT: A 1304 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6363 (pt0)
REVERT: A 1415 LYS cc_start: 0.7225 (tttt) cc_final: 0.6741 (tptt)
REVERT: A 1692 ASP cc_start: 0.8007 (t0) cc_final: 0.7754 (t0)
REVERT: A 1725 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6737 (mm-30)
REVERT: A 1778 MET cc_start: 0.7417 (mmm) cc_final: 0.6794 (mmm)
REVERT: A 1861 ILE cc_start: 0.8853 (pt) cc_final: 0.8554 (pt)
REVERT: A 1952 LYS cc_start: 0.5577 (OUTLIER) cc_final: 0.2450 (mmtp)
  outliers start: 26
  outliers final: 18
  residues processed: 115
  average time/residue: 0.1057
  time to fit residues: 17.5046
Evaluate side-chains
  116 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
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  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 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 1591 TYR
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 1916 VAL
Chi-restraints excluded: chain A residue 1952 LYS
Chi-restraints excluded: chain A residue 1974 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0670
   chunk 5 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 95 optimal weight:    0.0050
   chunk 49 optimal weight:    6.9990
   chunk 94 optimal weight:    0.2980
   chunk 121 optimal weight:    3.9990
   overall best weight:    0.3732

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

Flipped N/Q/H residues before XYZ refinement:
** 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
A1852 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.130372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.112750 restraints weight = 21156.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 1.97
r_work: 0.3849 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3714 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3730
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3730 r_free = 0.3730    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3730 r_free = 0.3730    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3730
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.2863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  10665  Z= 0.126
  Angle     :  0.619  12.928  14351  Z= 0.295
  Chirality :  0.042   0.384   1502
  Planarity :  0.004   0.045   1799
  Dihedral  : 12.667 102.563   1588
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 18.48 %
    Favored  : 79.29 %
  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:  0.12 (0.24), residues: 1168
  helix:  1.04 (0.19), residues: 732
  sheet:  None (None), residues: 0
  loop : -1.61 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 241 
 TYR   0.025   0.001   TYR A1663 
 PHE   0.018   0.001   PHE A 158 
 TRP   0.024   0.001   TRP A 616 
 HIS   0.005   0.001   HIS A1666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (10647)
  covalent geometry    : angle       0.58351 (14304)
  SS BOND              : bond        0.00350 (    7)
  SS BOND              : angle       1.44790 (   14)
  hydrogen bonds       : bond        0.03649 (  527)
  hydrogen bonds       : angle       3.77587 ( 1539)
  link_BETA1-3         : bond        0.01544 (    6)
  link_BETA1-3         : angle       4.81857 (   18)
  link_BETA1-4         : bond        0.00888 (    5)
  link_BETA1-4         : angle       3.47001 (   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
  122 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  151 CYS cc_start: 0.7253 (m) cc_final: 0.6567 (m)
REVERT: A  206 TYR cc_start: 0.6732 (m-80) cc_final: 0.6370 (m-80)
REVERT: A  286 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7433 (t80)
REVERT: A  328 TYR cc_start: 0.6241 (OUTLIER) cc_final: 0.5469 (t80)
REVERT: A 1304 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6454 (pt0)
REVERT: A 1415 LYS cc_start: 0.7254 (tttt) cc_final: 0.6763 (tptt)
REVERT: A 1692 ASP cc_start: 0.7941 (t0) cc_final: 0.7681 (t0)
REVERT: A 1778 MET cc_start: 0.7342 (mmm) cc_final: 0.6747 (mmm)
REVERT: A 1952 LYS cc_start: 0.5575 (OUTLIER) cc_final: 0.2678 (mmtp)
  outliers start: 25
  outliers final: 19
  residues processed: 114
  average time/residue: 0.1023
  time to fit residues: 16.5533
Evaluate side-chains
  112 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
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  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 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 1591 TYR
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 1916 VAL
Chi-restraints excluded: chain A residue 1952 LYS
Chi-restraints excluded: chain A residue 1974 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0270
   chunk 15 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 116 optimal weight:    0.0040
   chunk 88 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 100 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.4850

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 555 ASN
A 665 ASN
** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1454 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.130198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.112577 restraints weight = 21323.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3949 rms_B_bonded: 1.98
r_work: 0.3844 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3711 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3725 r_free = 0.3725    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3725 r_free = 0.3725    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.096  10665  Z= 0.167
  Angle     :  0.886  59.163  14351  Z= 0.505
  Chirality :  0.042   0.386   1502
  Planarity :  0.004   0.054   1799
  Dihedral  : 12.686 102.543   1588
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 18.48 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.13 (0.24), residues: 1168
  helix:  1.05 (0.19), residues: 732
  sheet:  None (None), residues: 0
  loop : -1.61 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1792 
 TYR   0.024   0.001   TYR A1663 
 PHE   0.018   0.001   PHE A 158 
 TRP   0.020   0.001   TRP A 616 
 HIS   0.005   0.001   HIS A1666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (10647)
  covalent geometry    : angle       0.86284 (14304)
  SS BOND              : bond        0.00354 (    7)
  SS BOND              : angle       1.43919 (   14)
  hydrogen bonds       : bond        0.03657 (  527)
  hydrogen bonds       : angle       3.77546 ( 1539)
  link_BETA1-3         : bond        0.01582 (    6)
  link_BETA1-3         : angle       4.83244 (   18)
  link_BETA1-4         : bond        0.00917 (    5)
  link_BETA1-4         : angle       3.45028 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2826.46 seconds
wall clock time: 49 minutes 10.59 seconds (2950.59 seconds total)