Starting phenix.real_space_refine
on Mon Jul 28 20:15:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fap_31504/07_2025/7fap_31504.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fap_31504/07_2025/7fap_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fap_31504/07_2025/7fap_31504.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fap_31504/07_2025/7fap_31504.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fap_31504/07_2025/7fap_31504.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fap_31504/07_2025/7fap_31504.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.35, per 1000 atoms: 0.61
  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: 2.78
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 0.94
  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: 3.34

  Time building geometry restraints manager: 3.17 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:             1.970
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.020
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.590
-------------------------------------------------------------------------------
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 : 10.64
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.038   0.002   TRP A1501 
 HIS   0.006   0.001   HIS A1666 
 PHE   0.018   0.002   PHE A 158 
 TYR   0.017   0.001   TYR A 328 
 ARG   0.005   0.000   ARG A1720 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.01323 (    5)
  link_BETA1-4         : angle       5.97453 (   15)
  hydrogen bonds       : bond        0.13727 (  527)
  hydrogen bonds       : angle       5.33249 ( 1539)
  SS BOND              : bond        0.13657 (    7)
  SS BOND              : angle       4.38261 (   14)
  link_BETA1-3         : bond        0.01933 (    6)
  link_BETA1-3         : angle       4.83270 (   18)
  covalent geometry    : bond        0.01145 (10647)
  covalent geometry    : angle       1.04775 (14304)

*********************** 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  : 1.136 
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: 0.2615
  time to fit residues: 53.1634
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  : 1.151 
-------------------------------------------------------------------------------
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 103 optimal weight:    2.9990
   chunk 93 optimal weight:    0.3980
   chunk 51 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 96 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 111 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  49 ASN
A 622 HIS
A 870 GLN
A1030 ASN
A1454 GLN
A1627 ASN
** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.131834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.113744 restraints weight = 20849.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3964 rms_B_bonded: 2.03
r_work: 0.3856 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3719 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3734
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3734 r_free = 0.3734    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3733 r_free = 0.3733    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10665  Z= 0.165
  Angle     :  0.695  15.540  14351  Z= 0.334
  Chirality :  0.045   0.409   1502
  Planarity :  0.004   0.051   1799
  Dihedral  : 19.768 117.586   1593
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  :  8.39 %
    Favored  : 89.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.24), residues: 1168
  helix:  0.49 (0.19), residues: 730
  sheet:  None (None), residues: 0
  loop : -2.02 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A1501 
 HIS   0.005   0.001   HIS A1666 
 PHE   0.022   0.002   PHE A1535 
 TYR   0.036   0.002   TYR A1663 
 ARG   0.006   0.001   ARG A1792 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.01152 (    5)
  link_BETA1-4         : angle       4.16651 (   15)
  hydrogen bonds       : bond        0.04560 (  527)
  hydrogen bonds       : angle       4.26823 ( 1539)
  SS BOND              : bond        0.00619 (    7)
  SS BOND              : angle       1.48751 (   14)
  link_BETA1-3         : bond        0.02052 (    6)
  link_BETA1-3         : angle       5.77977 (   18)
  covalent geometry    : bond        0.00367 (10647)
  covalent geometry    : angle       0.64987 (14304)

*********************** 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
  129 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 1.231 
Fit side-chains
REVERT: A   49 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.8074 (t0)
REVERT: A  286 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.6843 (t80)
REVERT: A  328 TYR cc_start: 0.5977 (OUTLIER) cc_final: 0.4577 (t80)
REVERT: A  962 ASN cc_start: 0.7577 (p0) cc_final: 0.7274 (p0)
REVERT: A 1179 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6873 (mp0)
REVERT: A 1415 LYS cc_start: 0.7202 (tttt) cc_final: 0.6677 (tptt)
REVERT: A 1778 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6915 (mtp)
REVERT: A 1861 ILE cc_start: 0.8823 (pt) cc_final: 0.8557 (pt)
  outliers start: 20
  outliers final: 8
  residues processed: 121
  average time/residue: 0.2484
  time to fit residues: 42.4273
Evaluate side-chains
  106 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
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 1035 TYR
Chi-restraints excluded: chain A residue 1103 ASP
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 49 optimal weight:    8.9990
   chunk 59 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 52 optimal weight:    0.1980
   chunk 45 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 95 optimal weight:    4.9990
   chunk 98 optimal weight:    6.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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
A1583 ASN
** 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 = 0.4219 r_free = 0.4219 target = 0.129886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.111201 restraints weight = 21438.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3925 rms_B_bonded: 2.03
r_work: 0.3816 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3679 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3694
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3694 r_free = 0.3694    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 = 0.3694 r_free = 0.3694    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  10665  Z= 0.204
  Angle     :  0.692  14.298  14351  Z= 0.334
  Chirality :  0.045   0.436   1502
  Planarity :  0.004   0.041   1799
  Dihedral  : 18.290 116.354   1588
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 11.16 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.24), residues: 1168
  helix:  0.41 (0.18), residues: 731
  sheet:  None (None), residues: 0
  loop : -2.00 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 560 
 HIS   0.006   0.001   HIS A1666 
 PHE   0.023   0.002   PHE A 158 
 TYR   0.026   0.002   TYR A1663 
 ARG   0.004   0.001   ARG A1720 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00934 (    5)
  link_BETA1-4         : angle       3.83101 (   15)
  hydrogen bonds       : bond        0.04600 (  527)
  hydrogen bonds       : angle       4.20575 ( 1539)
  SS BOND              : bond        0.00488 (    7)
  SS BOND              : angle       1.56963 (   14)
  link_BETA1-3         : bond        0.01740 (    6)
  link_BETA1-3         : angle       5.24191 (   18)
  covalent geometry    : bond        0.00476 (10647)
  covalent geometry    : angle       0.65466 (14304)

*********************** 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
  124 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 1.200 
Fit side-chains
   revert: symmetry clash
REVERT: A  206 TYR cc_start: 0.6739 (m-80) cc_final: 0.6522 (m-80)
REVERT: A  286 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.6882 (t80)
REVERT: A  328 TYR cc_start: 0.5965 (OUTLIER) cc_final: 0.4701 (t80)
REVERT: A  874 ASP cc_start: 0.7296 (t0) cc_final: 0.7064 (t0)
REVERT: A 1304 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6265 (pt0)
REVERT: A 1415 LYS cc_start: 0.7174 (tttt) cc_final: 0.6691 (tptt)
REVERT: A 1778 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.6582 (mmm)
REVERT: A 1953 MET cc_start: 0.7918 (tmm) cc_final: 0.7702 (tmm)
  outliers start: 28
  outliers final: 19
  residues processed: 113
  average time/residue: 0.2352
  time to fit residues: 38.1616
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  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  328 TYR
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue 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 1589 LYS
Chi-restraints excluded: chain A residue 1591 TYR
Chi-restraints excluded: chain A residue 1627 ASN
Chi-restraints excluded: chain A residue 1656 HIS
Chi-restraints excluded: chain A residue 1688 ASP
Chi-restraints excluded: chain A residue 1702 LEU
Chi-restraints excluded: chain A residue 1778 MET
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1915 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 122 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 85 optimal weight:    0.0970
   chunk 20 optimal weight:    0.4980
   chunk 3 optimal weight:    0.0470
   overall best weight:    0.4876

-------------------------------------------------------------------------------
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 571 GLN
** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 956 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 = 0.4243 r_free = 0.4243 target = 0.131657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.113473 restraints weight = 21175.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 1.99
r_work: 0.3857 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3721 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    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 = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10665  Z= 0.135
  Angle     :  0.624  13.387  14351  Z= 0.296
  Chirality :  0.043   0.421   1502
  Planarity :  0.004   0.042   1799
  Dihedral  : 16.754 112.254   1588
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.57 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.24), residues: 1168
  helix:  0.69 (0.19), residues: 737
  sheet:  None (None), residues: 0
  loop : -1.86 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 214 
 HIS   0.005   0.001   HIS A1666 
 PHE   0.021   0.002   PHE A1535 
 TYR   0.031   0.001   TYR A1663 
 ARG   0.003   0.000   ARG A1792 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00941 (    5)
  link_BETA1-4         : angle       3.38977 (   15)
  hydrogen bonds       : bond        0.04012 (  527)
  hydrogen bonds       : angle       3.96857 ( 1539)
  SS BOND              : bond        0.00369 (    7)
  SS BOND              : angle       1.47187 (   14)
  link_BETA1-3         : bond        0.01676 (    6)
  link_BETA1-3         : angle       5.02021 (   18)
  covalent geometry    : bond        0.00300 (10647)
  covalent geometry    : angle       0.58700 (14304)

*********************** 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
  125 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 1.240 
Fit side-chains
REVERT: A  206 TYR cc_start: 0.6726 (m-80) cc_final: 0.6475 (m-80)
REVERT: A  235 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.4554 (mp)
REVERT: A  286 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.7117 (t80)
REVERT: A  328 TYR cc_start: 0.6104 (OUTLIER) cc_final: 0.4862 (t80)
REVERT: A 1030 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8284 (t0)
REVERT: A 1304 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6172 (pt0)
REVERT: A 1415 LYS cc_start: 0.7178 (tttt) cc_final: 0.6703 (tptt)
REVERT: A 1692 ASP cc_start: 0.8199 (t0) cc_final: 0.7964 (t0)
REVERT: A 1778 MET cc_start: 0.7489 (mmm) cc_final: 0.6588 (mmm)
REVERT: A 1861 ILE cc_start: 0.8831 (pt) cc_final: 0.8582 (pt)
REVERT: A 1953 MET cc_start: 0.7888 (tmm) cc_final: 0.7622 (tmm)
  outliers start: 21
  outliers final: 11
  residues processed: 117
  average time/residue: 0.2377
  time to fit residues: 39.6994
Evaluate side-chains
  113 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
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  235 LEU
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  328 TYR
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  993 TYR
Chi-restraints excluded: chain A residue 1030 ASN
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 1591 TYR
Chi-restraints excluded: chain A residue 1702 LEU
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0570
   chunk 54 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.9902

-------------------------------------------------------------------------------
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 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.128444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.110512 restraints weight = 20921.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 1.96
r_work: 0.3808 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3675 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3689
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    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 = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3689
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.2293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  10665  Z= 0.193
  Angle     :  0.664  13.702  14351  Z= 0.319
  Chirality :  0.045   0.414   1502
  Planarity :  0.004   0.040   1799
  Dihedral  : 16.170 110.735   1588
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 13.93 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.24), residues: 1168
  helix:  0.66 (0.19), residues: 734
  sheet:  None (None), residues: 0
  loop : -1.89 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 560 
 HIS   0.011   0.001   HIS A1666 
 PHE   0.025   0.002   PHE A 158 
 TYR   0.027   0.002   TYR A1663 
 ARG   0.005   0.001   ARG A1720 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00857 (    5)
  link_BETA1-4         : angle       3.25129 (   15)
  hydrogen bonds       : bond        0.04283 (  527)
  hydrogen bonds       : angle       4.05267 ( 1539)
  SS BOND              : bond        0.00449 (    7)
  SS BOND              : angle       1.49585 (   14)
  link_BETA1-3         : bond        0.01661 (    6)
  link_BETA1-3         : angle       4.99715 (   18)
  covalent geometry    : bond        0.00454 (10647)
  covalent geometry    : angle       0.63013 (14304)

*********************** 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
  134 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 100
  time to evaluate  : 1.266 
Fit side-chains
REVERT: A  185 MET cc_start: 0.7825 (tpp) cc_final: 0.7427 (tpp)
REVERT: A  206 TYR cc_start: 0.6741 (m-80) cc_final: 0.6438 (m-80)
REVERT: A  286 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7359 (t80)
REVERT: A  328 TYR cc_start: 0.6062 (OUTLIER) cc_final: 0.4979 (t80)
REVERT: A 1030 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8418 (t0)
REVERT: A 1304 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6285 (pt0)
REVERT: A 1415 LYS cc_start: 0.7307 (tttt) cc_final: 0.6825 (tptt)
REVERT: A 1692 ASP cc_start: 0.8128 (t0) cc_final: 0.7912 (t0)
REVERT: A 1778 MET cc_start: 0.7579 (mmm) cc_final: 0.6723 (mmm)
REVERT: A 1861 ILE cc_start: 0.8890 (pt) cc_final: 0.8610 (pt)
REVERT: A 1952 LYS cc_start: 0.5536 (OUTLIER) cc_final: 0.2637 (mmtp)
  outliers start: 34
  outliers final: 21
  residues processed: 124
  average time/residue: 0.2448
  time to fit residues: 43.5528
Evaluate side-chains
  120 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
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 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 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 1688 ASP
Chi-restraints excluded: chain A residue 1702 LEU
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1809 PHE
Chi-restraints excluded: chain A residue 1915 THR
Chi-restraints excluded: chain A residue 1952 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0980
   chunk 51 optimal weight:    0.6980
   chunk 119 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.129346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.111640 restraints weight = 21077.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3935 rms_B_bonded: 1.97
r_work: 0.3828 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3692 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3705 r_free = 0.3705    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3705 r_free = 0.3705    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10665  Z= 0.151
  Angle     :  0.649  13.571  14351  Z= 0.306
  Chirality :  0.044   0.410   1502
  Planarity :  0.003   0.041   1799
  Dihedral  : 15.420 109.267   1588
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.80 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.24), residues: 1168
  helix:  0.81 (0.19), residues: 731
  sheet:  None (None), residues: 0
  loop : -1.82 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 558 
 HIS   0.014   0.001   HIS A1666 
 PHE   0.020   0.002   PHE A 158 
 TYR   0.029   0.001   TYR A1663 
 ARG   0.003   0.000   ARG A1720 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.01078 (    5)
  link_BETA1-4         : angle       3.47897 (   15)
  hydrogen bonds       : bond        0.04027 (  527)
  hydrogen bonds       : angle       3.95094 ( 1539)
  SS BOND              : bond        0.00395 (    7)
  SS BOND              : angle       1.43195 (   14)
  link_BETA1-3         : bond        0.01762 (    6)
  link_BETA1-3         : angle       5.13569 (   18)
  covalent geometry    : bond        0.00345 (10647)
  covalent geometry    : angle       0.61241 (14304)

*********************** 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
  120 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 1.259 
Fit side-chains
REVERT: A  206 TYR cc_start: 0.6732 (m-80) cc_final: 0.6409 (m-80)
REVERT: A  286 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7399 (t80)
REVERT: A  328 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.5011 (t80)
REVERT: A 1304 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6227 (pt0)
REVERT: A 1415 LYS cc_start: 0.7282 (tttt) cc_final: 0.6802 (tptt)
REVERT: A 1692 ASP cc_start: 0.8129 (t0) cc_final: 0.7880 (t0)
REVERT: A 1778 MET cc_start: 0.7553 (mmm) cc_final: 0.6687 (mmm)
REVERT: A 1861 ILE cc_start: 0.8853 (pt) cc_final: 0.8589 (pt)
REVERT: A 1952 LYS cc_start: 0.5476 (OUTLIER) cc_final: 0.2622 (mmtp)
  outliers start: 26
  outliers final: 17
  residues processed: 112
  average time/residue: 0.2728
  time to fit residues: 44.3599
Evaluate side-chains
  113 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 1.169 
-------------------------------------------------------------------------------
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 1006 THR
Chi-restraints excluded: chain A residue 1090 CYS
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1265 VAL
Chi-restraints excluded: chain A residue 1304 GLU
Chi-restraints excluded: chain A residue 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 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1809 PHE
Chi-restraints excluded: chain A residue 1915 THR
Chi-restraints excluded: chain A residue 1952 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 93 optimal weight:    0.0370
   chunk 11 optimal weight:    6.9990
   chunk 18 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0870
   overall best weight:    0.4236

-------------------------------------------------------------------------------
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 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1852 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.130799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.112913 restraints weight = 21499.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3954 rms_B_bonded: 2.00
r_work: 0.3852 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3719 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10665  Z= 0.128
  Angle     :  0.622  13.544  14351  Z= 0.293
  Chirality :  0.042   0.406   1502
  Planarity :  0.003   0.041   1799
  Dihedral  : 14.436 107.112   1588
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.25 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.24), residues: 1168
  helix:  0.99 (0.19), residues: 733
  sheet:  None (None), residues: 0
  loop : -1.74 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 616 
 HIS   0.013   0.001   HIS A1666 
 PHE   0.018   0.002   PHE A 158 
 TYR   0.029   0.001   TYR A1663 
 ARG   0.005   0.000   ARG A 241 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00902 (    5)
  link_BETA1-4         : angle       3.50130 (   15)
  hydrogen bonds       : bond        0.03741 (  527)
  hydrogen bonds       : angle       3.80444 ( 1539)
  SS BOND              : bond        0.00368 (    7)
  SS BOND              : angle       1.42575 (   14)
  link_BETA1-3         : bond        0.01655 (    6)
  link_BETA1-3         : angle       4.93372 (   18)
  covalent geometry    : bond        0.00285 (10647)
  covalent geometry    : angle       0.58542 (14304)

*********************** 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
  131 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 1.712 
Fit side-chains
REVERT: A  206 TYR cc_start: 0.6716 (m-80) cc_final: 0.6366 (m-80)
REVERT: A  286 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7386 (t80)
REVERT: A  328 TYR cc_start: 0.6250 (OUTLIER) cc_final: 0.5207 (t80)
REVERT: A 1304 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6534 (pt0)
REVERT: A 1415 LYS cc_start: 0.7242 (tttt) cc_final: 0.6759 (tptt)
REVERT: A 1692 ASP cc_start: 0.7995 (t0) cc_final: 0.7769 (t0)
REVERT: A 1778 MET cc_start: 0.7514 (mmm) cc_final: 0.6648 (mmm)
REVERT: A 1952 LYS cc_start: 0.5547 (OUTLIER) cc_final: 0.3505 (mmtp)
  outliers start: 25
  outliers final: 16
  residues processed: 124
  average time/residue: 0.3501
  time to fit residues: 62.6583
Evaluate side-chains
  114 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 2.306 
-------------------------------------------------------------------------------
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 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 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0970
   chunk 119 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 110 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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**
** A1666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1852 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.130292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.112698 restraints weight = 20933.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 1.96
r_work: 0.3848 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3715 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3724
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3724 r_free = 0.3724    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3724 r_free = 0.3724    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3724
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10665  Z= 0.137
  Angle     :  0.634  13.366  14351  Z= 0.302
  Chirality :  0.043   0.398   1502
  Planarity :  0.003   0.040   1799
  Dihedral  : 13.697 105.432   1588
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 17.32 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.24), residues: 1168
  helix:  1.02 (0.19), residues: 732
  sheet:  None (None), residues: 0
  loop : -1.69 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 616 
 HIS   0.012   0.001   HIS A1666 
 PHE   0.020   0.002   PHE A 158 
 TYR   0.029   0.001   TYR A1663 
 ARG   0.003   0.000   ARG A1720 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00930 (    5)
  link_BETA1-4         : angle       3.69845 (   15)
  hydrogen bonds       : bond        0.03795 (  527)
  hydrogen bonds       : angle       3.81873 ( 1539)
  SS BOND              : bond        0.00373 (    7)
  SS BOND              : angle       1.42990 (   14)
  link_BETA1-3         : bond        0.01631 (    6)
  link_BETA1-3         : angle       4.88948 (   18)
  covalent geometry    : bond        0.00310 (10647)
  covalent geometry    : angle       0.59785 (14304)

*********************** 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
  121 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 1.441 
Fit side-chains
REVERT: A  286 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7414 (t80)
REVERT: A  328 TYR cc_start: 0.6186 (OUTLIER) cc_final: 0.5318 (t80)
REVERT: A 1304 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6409 (pt0)
REVERT: A 1415 LYS cc_start: 0.7263 (tttt) cc_final: 0.6773 (tptt)
REVERT: A 1778 MET cc_start: 0.7506 (mmm) cc_final: 0.6657 (mmm)
REVERT: A 1952 LYS cc_start: 0.5506 (OUTLIER) cc_final: 0.2417 (mmtp)
  outliers start: 25
  outliers final: 18
  residues processed: 114
  average time/residue: 0.3456
  time to fit residues: 57.5085
Evaluate side-chains
  110 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 1.722 
-------------------------------------------------------------------------------
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  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 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1809 PHE
Chi-restraints excluded: chain A residue 1915 THR
Chi-restraints excluded: chain A residue 1952 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 106 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 34 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 90 optimal weight:    0.0870
   chunk 36 optimal weight:    3.9990
   chunk 108 optimal weight:    0.0870
   chunk 95 optimal weight:    3.9990
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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
** A1666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4223 r_free = 0.4223 target = 0.130432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.112485 restraints weight = 21469.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 2.01
r_work: 0.3846 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3709 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3724
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3724 r_free = 0.3724    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 = 0.3724 r_free = 0.3724    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3724
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10665  Z= 0.137
  Angle     :  0.629  13.243  14351  Z= 0.302
  Chirality :  0.043   0.394   1502
  Planarity :  0.003   0.040   1799
  Dihedral  : 13.421 104.710   1588
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 17.23 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.24), residues: 1168
  helix:  1.05 (0.19), residues: 732
  sheet:  None (None), residues: 0
  loop : -1.70 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 616 
 HIS   0.012   0.001   HIS A1666 
 PHE   0.019   0.002   PHE A 158 
 TYR   0.028   0.001   TYR A1663 
 ARG   0.003   0.000   ARG A1792 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00933 (    5)
  link_BETA1-4         : angle       3.50350 (   15)
  hydrogen bonds       : bond        0.03741 (  527)
  hydrogen bonds       : angle       3.79996 ( 1539)
  SS BOND              : bond        0.00375 (    7)
  SS BOND              : angle       1.42264 (   14)
  link_BETA1-3         : bond        0.01592 (    6)
  link_BETA1-3         : angle       4.87176 (   18)
  covalent geometry    : bond        0.00312 (10647)
  covalent geometry    : angle       0.59312 (14304)

*********************** 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
  119 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 1.244 
Fit side-chains
REVERT: A  179 GLU cc_start: 0.6650 (mm-30) cc_final: 0.6448 (mm-30)
REVERT: A  185 MET cc_start: 0.7720 (tpp) cc_final: 0.7296 (tpp)
REVERT: A  286 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7413 (t80)
REVERT: A  328 TYR cc_start: 0.6181 (OUTLIER) cc_final: 0.5354 (t80)
REVERT: A 1304 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6468 (pt0)
REVERT: A 1415 LYS cc_start: 0.7233 (tttt) cc_final: 0.6738 (tptt)
REVERT: A 1778 MET cc_start: 0.7529 (mmm) cc_final: 0.6693 (mmm)
REVERT: A 1952 LYS cc_start: 0.5512 (OUTLIER) cc_final: 0.2652 (mmtp)
  outliers start: 25
  outliers final: 18
  residues processed: 111
  average time/residue: 0.2358
  time to fit residues: 37.7785
Evaluate side-chains
  115 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  328 TYR
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  993 TYR
Chi-restraints excluded: chain A residue 1090 CYS
Chi-restraints excluded: chain A residue 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 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1809 PHE
Chi-restraints excluded: chain A residue 1915 THR
Chi-restraints excluded: chain A residue 1952 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 95 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 68 optimal weight:    0.0970
   chunk 121 optimal weight:    0.0040
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.4390

-------------------------------------------------------------------------------
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 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1666 HIS
** 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 = 0.4231 r_free = 0.4231 target = 0.130929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.113364 restraints weight = 20950.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3964 rms_B_bonded: 1.95
r_work: 0.3859 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3725 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3733 r_free = 0.3733    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 = 0.3733 r_free = 0.3733    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.2780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10665  Z= 0.127
  Angle     :  0.612  13.006  14351  Z= 0.294
  Chirality :  0.042   0.388   1502
  Planarity :  0.003   0.041   1799
  Dihedral  : 12.839 103.187   1588
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 17.23 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.24), residues: 1168
  helix:  1.16 (0.19), residues: 732
  sheet:  None (None), residues: 0
  loop : -1.63 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 616 
 HIS   0.013   0.001   HIS A1666 
 PHE   0.018   0.001   PHE A 158 
 TYR   0.038   0.001   TYR A1857 
 ARG   0.003   0.000   ARG A1720 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00907 (    5)
  link_BETA1-4         : angle       3.38673 (   15)
  hydrogen bonds       : bond        0.03637 (  527)
  hydrogen bonds       : angle       3.72171 ( 1539)
  SS BOND              : bond        0.00358 (    7)
  SS BOND              : angle       1.40983 (   14)
  link_BETA1-3         : bond        0.01579 (    6)
  link_BETA1-3         : angle       4.78766 (   18)
  covalent geometry    : bond        0.00285 (10647)
  covalent geometry    : angle       0.57743 (14304)

********************** 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
  118 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 1.215 
Fit side-chains
REVERT: A  179 GLU cc_start: 0.6561 (mm-30) cc_final: 0.6343 (mm-30)
REVERT: A  185 MET cc_start: 0.7733 (tpp) cc_final: 0.7391 (tpp)
REVERT: A  274 GLN cc_start: 0.7397 (tt0) cc_final: 0.7145 (tt0)
REVERT: A  286 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7434 (t80)
REVERT: A  328 TYR cc_start: 0.6214 (OUTLIER) cc_final: 0.5433 (t80)
REVERT: A 1304 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6497 (pt0)
REVERT: A 1415 LYS cc_start: 0.7234 (tttt) cc_final: 0.6742 (tptt)
REVERT: A 1753 MET cc_start: 0.7350 (mmt) cc_final: 0.6466 (mmt)
REVERT: A 1778 MET cc_start: 0.7513 (mmm) cc_final: 0.6661 (mmm)
REVERT: A 1952 LYS cc_start: 0.5537 (OUTLIER) cc_final: 0.2637 (mmtp)
  outliers start: 23
  outliers final: 18
  residues processed: 111
  average time/residue: 0.2339
  time to fit residues: 37.8912
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  : 1.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  286 PHE
Chi-restraints excluded: chain A residue  328 TYR
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  936 VAL
Chi-restraints excluded: chain A residue  937 VAL
Chi-restraints excluded: chain A residue  993 TYR
Chi-restraints excluded: chain A residue 1090 CYS
Chi-restraints excluded: chain A residue 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 1780 VAL
Chi-restraints excluded: chain A residue 1803 GLU
Chi-restraints excluded: chain A residue 1809 PHE
Chi-restraints excluded: chain A residue 1915 THR
Chi-restraints excluded: chain A residue 1952 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 122 optimal weight:    0.9980
   chunk 120 optimal weight:    0.4980
   chunk 70 optimal weight:    0.0870
   chunk 27 optimal weight:    0.4980
   chunk 100 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 121 optimal weight:    0.4980
   chunk 3 optimal weight:    0.4980
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.4158

-------------------------------------------------------------------------------
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 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1659 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 = 0.4230 r_free = 0.4230 target = 0.130851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.113142 restraints weight = 21011.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 1.97
r_work: 0.3857 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3722 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3722
-------------------------------------------------------------------------------
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 = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3730
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10665  Z= 0.128
  Angle     :  0.612  12.851  14351  Z= 0.298
  Chirality :  0.042   0.384   1502
  Planarity :  0.003   0.042   1799
  Dihedral  : 12.402 101.543   1588
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.41 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.25), residues: 1168
  helix:  1.21 (0.19), residues: 732
  sheet:  None (None), residues: 0
  loop : -1.59 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 616 
 HIS   0.016   0.001   HIS A1666 
 PHE   0.018   0.001   PHE A 158 
 TYR   0.027   0.001   TYR A1663 
 ARG   0.005   0.000   ARG A1863 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00889 (    5)
  link_BETA1-4         : angle       3.33885 (   15)
  hydrogen bonds       : bond        0.03599 (  527)
  hydrogen bonds       : angle       3.70402 ( 1539)
  SS BOND              : bond        0.00351 (    7)
  SS BOND              : angle       1.40260 (   14)
  link_BETA1-3         : bond        0.01552 (    6)
  link_BETA1-3         : angle       4.74347 (   18)
  covalent geometry    : bond        0.00285 (10647)
  covalent geometry    : angle       0.57813 (14304)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6450.42 seconds
wall clock time: 115 minutes 18.05 seconds (6918.05 seconds total)