Starting phenix.real_space_refine
on Sat Aug 23 12:40:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ela_31178/08_2025/7ela_31178.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ela_31178/08_2025/7ela_31178.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/7ela_31178/08_2025/7ela_31178.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ela_31178/08_2025/7ela_31178.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ela_31178/08_2025/7ela_31178.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ela_31178/08_2025/7ela_31178.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Mn      1      7.51       5
     Zn      2      6.06       5
     P       7      5.49       5
     S      80      5.16       5
     C    7497      2.51       5
     N    1978      2.21       5
     O    2226      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 111 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11791
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 375
          Classifications: {'peptide': 49}
          Link IDs: {'PTRANS': 4, 'TRANS': 44}
    Chain: "C"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 149
          Classifications: {'RNA': 7}
          Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 3, 'rna3p_pyr': 1}
          Link IDs: {'rna2p': 3, 'rna3p': 3}
    Chain: "A"
      Number of atoms: 11264
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1402, 11250
          Classifications: {'peptide': 1402}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 46, 'TRANS': 1355}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 47
      Conformer: "B"
        Number of residues, atoms: 1402, 11250
          Classifications: {'peptide': 1402}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 46, 'TRANS': 1355}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 47
          bond proxies already assigned to first conformer: 11448
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM     55  SG  CYS B  31      75.022  70.911  96.200  1.00 59.29           S
  ATOM     76  SG  CYS B  34      77.728  67.648  96.289  1.00 53.18           S
  ATOM    207  SG  CYS B  50      77.976  71.670  97.807  1.00 71.19           S
  ATOM    229  SG  CYS B  53      77.915  71.242  94.375  1.00 71.71           S
  ATOM    155  SG  CYS B  44      70.342  79.282  92.118  1.00 81.15           S
  ATOM    308  SG  CYS B  64      72.367  77.979  89.642  1.00 84.11           S
  ATOM    329  SG  CYS B  67      69.032  78.503  89.041  1.00 90.04           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATRP A1392 " occ=0.50
      ... (26 atoms not shown)
      pdb=" CH2BTRP A1392 " occ=0.50
  Time building chain proxies: 5.75, per 1000 atoms: 0.49
  Number of scatterers: 11791
  At special positions: 0
  Unit cell: (115, 99, 122, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     Mn      1     24.99
     S      80     16.00
     P       7     15.00
     O    2226      8.00
     N    1978      7.00
     C    7497      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A1692 " - pdb=" SG  CYS A1792 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Conformation dependent library (CDL) restraints added in 913.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 101 "
        pdb="ZN    ZN B 101 " - pdb=" SG  CYS B  53 "
        pdb="ZN    ZN B 101 " - pdb=" SG  CYS B  50 "
        pdb="ZN    ZN B 101 " - pdb=" SG  CYS B  31 "
        pdb="ZN    ZN B 101 " - pdb=" SG  CYS B  34 "
      pdb="  ZN B 102 "
        pdb="ZN    ZN B 102 " - pdb=" NE2 HIS B  47 "
        pdb="ZN    ZN B 102 " - pdb=" SG  CYS B  64 "
        pdb="ZN    ZN B 102 " - pdb=" SG  CYS B  67 "
        pdb="ZN    ZN B 102 " - pdb=" SG  CYS B  44 "
      Number of angles added : 9


  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2784

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 13 sheets defined
      55.9% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'B' and resid 51 through 58
    Processing helix  chain 'A' and resid 2 through 15
    Processing helix  chain 'A' and resid 20 through 30
    Processing helix  chain 'A' and resid 34 through 59
    Processing helix  chain 'A' and resid 68 through 75
    Processing helix  chain 'A' and resid 108 through 132
    Processing helix  chain 'A' and resid 153 through 168
    Processing helix  chain 'A' and resid 171 through 177
    Processing helix  chain 'A' and resid 179 through 191
    Processing helix  chain 'A' and resid 211 through 221
      removed outlier: 4.130A  pdb=" N   GLU A 215 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 252
      removed outlier: 3.776A  pdb=" N   LYS A 235 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 272
    Processing helix  chain 'A' and resid 283 through 292
    Processing helix  chain 'A' and resid 295 through 301
    Processing helix  chain 'A' and resid 320 through 332
    Processing helix  chain 'A' and resid 340 through 363
      removed outlier: 3.659A  pdb=" N   ARG A 362 " --> pdb=" O   HIS A 358 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   LYS A 363 " --> pdb=" O   ASP A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 401
      removed outlier: 3.872A  pdb=" N   VAL A 401 " --> pdb=" O   ARG A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 436
    Processing helix  chain 'A' and resid 440 through 445
      removed outlier: 3.518A  pdb=" N   LYS A 445 " --> pdb=" O   ASP A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 461
    Processing helix  chain 'A' and resid 477 through 481
    Processing helix  chain 'A' and resid 493 through 510
    Processing helix  chain 'A' and resid 578 through 582
    Processing helix  chain 'A' and resid 588 through 603
      removed outlier: 3.850A  pdb=" N   GLN A 593 " --> pdb=" O   ALA A 589 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ILE A 603 " --> pdb=" O   MET A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 607
      removed outlier: 4.393A  pdb=" N   ASN A 607 " --> pdb=" O   GLU A 604 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 604 through 607'
    Processing helix  chain 'A' and resid 612 through 630
    Processing helix  chain 'A' and resid 632 through 650
      removed outlier: 3.697A  pdb=" N   VAL A 650 " --> pdb=" O   ILE A 646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 657 through 663
    Processing helix  chain 'A' and resid 670 through 686
    Processing helix  chain 'A' and resid 693 through 707
    Processing helix  chain 'A' and resid 708 through 711
    Processing helix  chain 'A' and resid 717 through 737
      Proline residue:  A 732  - end of helix
    Processing helix  chain 'A' and resid 748 through 763
      removed outlier: 3.607A  pdb=" N   LEU A 763 " --> pdb=" O   ALA A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 795
    Processing helix  chain 'A' and resid 1139 through 1160
    Processing helix  chain 'A' and resid 1167 through 1184
    Processing helix  chain 'A' and resid 1195 through 1200
      removed outlier: 3.534A  pdb=" N   MET A1199 " --> pdb=" O   LYS A1195 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   MET A1200 " --> pdb=" O   TRP A1196 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1195 through 1200'
    Processing helix  chain 'A' and resid 1201 through 1211
    Processing helix  chain 'A' and resid 1225 through 1238
    Processing helix  chain 'A' and resid 1244 through 1261
    Processing helix  chain 'A' and resid 1269 through 1280
    Processing helix  chain 'A' and resid 1299 through 1323
    Processing helix  chain 'A' and resid 1340 through 1350
    Processing helix  chain 'A' and resid 1350 through 1368
    Processing helix  chain 'A' and resid 1398 through 1409
      removed outlier: 3.530A  pdb=" N   PHE A1402 " --> pdb=" O   LEU A1398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1414 through 1433
    Processing helix  chain 'A' and resid 1435 through 1453
      removed outlier: 3.581A  pdb=" N   ALA A1453 " --> pdb=" O   LEU A1449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1475 through 1488
    Processing helix  chain 'A' and resid 1490 through 1508
      removed outlier: 3.573A  pdb=" N   LYS A1494 " --> pdb=" O   ASP A1490 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   THR A1508 " --> pdb=" O   ASN A1504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1512 through 1520
      removed outlier: 3.732A  pdb=" N   THR A1517 " --> pdb=" O   GLU A1513 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   ASN A1518 " --> pdb=" O   GLU A1514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1523 through 1536
      removed outlier: 3.905A  pdb=" N   LYS A1529 " --> pdb=" O   LEU A1525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1581 through 1586
      removed outlier: 3.814A  pdb=" N   ILE A1586 " --> pdb=" O   ILE A1582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1614 through 1626
    Processing helix  chain 'A' and resid 1640 through 1650
    Processing helix  chain 'A' and resid 1678 through 1681
    Processing helix  chain 'A' and resid 1686 through 1701
    Processing helix  chain 'A' and resid 1703 through 1707
    Processing helix  chain 'A' and resid 1744 through 1753
    Processing helix  chain 'A' and resid 1753 through 1759
    Processing helix  chain 'A' and resid 1782 through 1791
      removed outlier: 4.281A  pdb=" N   ASP A1789 " --> pdb=" O   CYS A1785 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL A1790 " --> pdb=" O   VAL A1786 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ASN A1791 " --> pdb=" O   ALA A1787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1814 through 1819
      removed outlier: 3.590A  pdb=" N   ARG A1818 " --> pdb=" O   SER A1814 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   PHE A1819 " --> pdb=" O   SER A1815 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1814 through 1819'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 41 through 43
    Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62
      removed outlier: 6.552A  pdb=" N   LEU A  98 " --> pdb=" O   ILE A 138 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 62
      removed outlier: 7.471A  pdb=" N   ASP A 142 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   GLU A 102 " --> pdb=" O   ASP A 142 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   ARG A 144 " --> pdb=" O   GLU A 102 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   PHE A 104 " --> pdb=" O   ARG A 144 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 208
      removed outlier: 6.152A  pdb=" N   LEU A 207 " --> pdb=" O   TYR A1109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 258 through 260
    Processing sheet with id=AA6, first strand: chain 'A' and resid 373 through 375
    Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 542
      removed outlier: 6.411A  pdb=" N   LYS A 560 " --> pdb=" O   TYR A 576 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   TYR A 576 " --> pdb=" O   LYS A 560 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   TYR A 562 " --> pdb=" O   SER A 574 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   SER A 574 " --> pdb=" O   TYR A 562 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ILE A 564 " --> pdb=" O   VAL A 572 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1133 through 1138
      removed outlier: 3.584A  pdb=" N   LEU A1123 " --> pdb=" O   GLU A1242 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1383 through 1385
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1548 through 1550
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1631 through 1632
      removed outlier: 3.539A  pdb=" N   VAL A1631 " --> pdb=" O   LEU A1639 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1710 through 1711
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1725 through 1728
      removed outlier: 3.709A  pdb=" N   VAL A1812 " --> pdb=" O   PHE A1726 " (cutoff:3.500A)

    614 hydrogen bonds defined for protein.
    1764 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: 2.68

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3623
        1.34 -     1.46: 1716
        1.46 -     1.57: 6562
        1.57 -     1.69: 13
        1.69 -     1.81: 117
  Bond restraints: 12031
  Sorted by residual:
  bond pdb=" N   VAL A1468 "
       pdb=" CA  VAL A1468 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.25e-02 6.40e+03 9.40e+00
  bond pdb=" N   THR A1466 "
       pdb=" CA  THR A1466 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.34e-02 5.57e+03 6.94e+00
  bond pdb=" N   ARG A1469 "
       pdb=" CA  ARG A1469 "
    ideal  model  delta    sigma   weight residual
    1.460  1.488 -0.028 1.14e-02 7.69e+03 5.95e+00
  bond pdb=" N   GLU A1465 "
       pdb=" CA  GLU A1465 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.25e-02 6.40e+03 5.12e+00
  bond pdb=" N   ASP A1467 "
       pdb=" CA  ASP A1467 "
    ideal  model  delta    sigma   weight residual
    1.460  1.487 -0.028 1.50e-02 4.44e+03 3.41e+00
  ... (remaining 12026 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 15955
        1.68 -     3.36: 278
        3.36 -     5.04: 35
        5.04 -     6.72: 10
        6.72 -     8.40: 4
  Bond angle restraints: 16282
  Sorted by residual:
  angle pdb=" N   ARG A1469 "
        pdb=" CA  ARG A1469 "
        pdb=" C   ARG A1469 "
      ideal   model   delta    sigma   weight residual
     114.62  106.22    8.40 1.14e+00 7.69e-01 5.43e+01
  angle pdb=" CA  ARG A1469 "
        pdb=" C   ARG A1469 "
        pdb=" N   ASP A1470 "
      ideal   model   delta    sigma   weight residual
     119.71  114.52    5.19 1.17e+00 7.31e-01 1.97e+01
  angle pdb=" CA  ASP A1467 "
        pdb=" C   ASP A1467 "
        pdb=" O   ASP A1467 "
      ideal   model   delta    sigma   weight residual
     121.78  117.58    4.20 1.12e+00 7.97e-01 1.41e+01
  angle pdb=" O   ARG A1469 "
        pdb=" C   ARG A1469 "
        pdb=" N   ASP A1470 "
      ideal   model   delta    sigma   weight residual
     121.67  125.93   -4.26 1.30e+00 5.92e-01 1.07e+01
  angle pdb=" CA  THR A1466 "
        pdb=" C   THR A1466 "
        pdb=" O   THR A1466 "
      ideal   model   delta    sigma   weight residual
     121.87  118.25    3.62 1.16e+00 7.43e-01 9.76e+00
  ... (remaining 16277 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.76: 7108
       33.76 -    67.52: 200
       67.52 -   101.28: 25
      101.28 -   135.04: 0
      135.04 -   168.80: 2
  Dihedral angle restraints: 7335
    sinusoidal: 3057
      harmonic: 4278
  Sorted by residual:
  dihedral pdb=" O4'   C C  13 "
           pdb=" C1'   C C  13 "
           pdb=" N1    C C  13 "
           pdb=" C2    C C  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   43.01  156.99     1      1.50e+01 4.44e-03 8.19e+01
  dihedral pdb=" O4'   U C  14 "
           pdb=" C1'   U C  14 "
           pdb=" N1    U C  14 "
           pdb=" C2    U C  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   63.20  168.80     1      1.70e+01 3.46e-03 6.58e+01
  dihedral pdb=" CA  LYS A 363 "
           pdb=" C   LYS A 363 "
           pdb=" N   LYS A 364 "
           pdb=" CA  LYS A 364 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.73  -20.27     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 7332 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1379
       0.039 -    0.079: 383
       0.079 -    0.118: 85
       0.118 -    0.157: 13
       0.157 -    0.196: 2
  Chirality restraints: 1862
  Sorted by residual:
  chirality pdb=" CB  VAL A 133 "
            pdb=" CA  VAL A 133 "
            pdb=" CG1 VAL A 133 "
            pdb=" CG2 VAL A 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.65e-01
  chirality pdb=" CA  ILE A 667 "
            pdb=" N   ILE A 667 "
            pdb=" C   ILE A 667 "
            pdb=" CB  ILE A 667 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.52e-01
  chirality pdb=" CA  ARG A1469 "
            pdb=" N   ARG A1469 "
            pdb=" C   ARG A1469 "
            pdb=" CB  ARG A1469 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.83e-01
  ... (remaining 1859 not shown)

  Planarity restraints: 2028
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A1396 "   -0.023 5.00e-02 4.00e+02   3.56e-02 2.03e+00
        pdb=" N   PRO A1397 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A1397 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A1397 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 152 "    0.023 5.00e-02 4.00e+02   3.50e-02 1.96e+00
        pdb=" N   PRO A 153 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 153 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 153 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  15 "    0.017 2.00e-02 2.50e+03   8.07e-03 1.95e+00
        pdb=" N9    G C  15 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8    G C  15 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    G C  15 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G C  15 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G C  15 "    0.001 2.00e-02 2.50e+03
        pdb=" O6    G C  15 "    0.004 2.00e-02 2.50e+03
        pdb=" N1    G C  15 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    G C  15 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G C  15 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    G C  15 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    G C  15 "    0.000 2.00e-02 2.50e+03
  ... (remaining 2025 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 338
        2.70 -     3.25: 12378
        3.25 -     3.80: 19086
        3.80 -     4.35: 25075
        4.35 -     4.90: 41330
  Nonbonded interactions: 98207
  Sorted by model distance:
  nonbonded pdb=" N   ASP A1470 "
            pdb=" OD1 ASP A1470 "
     model   vdw
     2.153 3.120
  nonbonded pdb=" O   GLY A 683 "
            pdb=" OG  SER A 687 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   ASP A1490 "
            pdb=" OG  SER A1493 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   PRO A1459 "
            pdb=" NE2 GLN A1483 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" O   SER A1373 "
            pdb=" OG  SER A1376 "
     model   vdw
     2.238 3.040
  ... (remaining 98202 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.330
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     19.080
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
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      :  0.004   0.221  12040  Z= 0.163
  Angle     :  0.697  20.428  16293  Z= 0.330
  Chirality :  0.039   0.196   1862
  Planarity :  0.003   0.036   2028
  Dihedral  : 15.708 168.798   4548
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  :  8.60 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.61 (0.20), residues: 1428
  helix: -0.47 (0.17), residues: 773
  sheet: -2.02 (0.49), residues: 91
  loop : -3.56 (0.21), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 380 
 TYR   0.012   0.001   TYR A 302 
 PHE   0.014   0.001   PHE A 541 
 TRP   0.010   0.001   TRP A1666 
 HIS   0.006   0.001   HIS A1744 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (12031)
  covalent geometry    : angle       0.56589 (16282)
  SS BOND              : bond        0.00113 (    1)
  SS BOND              : angle       1.52202 (    2)
  hydrogen bonds       : bond        0.13202 (  606)
  hydrogen bonds       : angle       5.41012 ( 1764)
  metal coordination   : bond        0.09884 (    8)
  metal coordination   : angle      17.32551 (    9)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 236
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: B   50 CYS cc_start: 0.6258 (p) cc_final: 0.5815 (p)
REVERT: B   53 CYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7744 (m)
REVERT: A  343 LYS cc_start: 0.7944 (mmtm) cc_final: 0.7406 (mmtm)
REVERT: A  385 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6872 (pm20)
REVERT: A  669 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7337 (p0)
REVERT: A  751 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7185 (tm-30)
REVERT: A  755 MET cc_start: 0.8687 (tpp) cc_final: 0.8446 (tpp)
REVERT: A 1180 LEU cc_start: 0.8675 (tp) cc_final: 0.8399 (tp)
REVERT: A 1223 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.5590 (tp)
REVERT: A 1366 ASP cc_start: 0.8442 (t70) cc_final: 0.7819 (t0)
REVERT: A 1368 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7324 (mt)
REVERT: A 1467 ASP cc_start: 0.6909 (p0) cc_final: 0.6510 (p0)
REVERT: A 1469 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6387 (tpm170)
REVERT: A 1546 GLU cc_start: 0.7048 (pt0) cc_final: 0.6847 (pt0)
REVERT: A 1579 ILE cc_start: 0.3825 (OUTLIER) cc_final: 0.3028 (tp)
REVERT: A 1810 TYR cc_start: 0.8148 (m-80) cc_final: 0.7741 (m-80)
  outliers start: 37
  outliers final: 23
  residues processed: 268
  average time/residue: 0.1277
  time to fit residues: 48.3118
Evaluate side-chains
  193 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 163
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain A residue  302 TYR
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  475 ARG
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  546 THR
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  669 ASP
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue 1223 ILE
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1267 LYS
Chi-restraints excluded: chain A residue 1294 MET
Chi-restraints excluded: chain A residue 1302 THR
Chi-restraints excluded: chain A residue 1321 VAL
Chi-restraints excluded: chain A residue 1368 LEU
Chi-restraints excluded: chain A residue 1454 ARG
Chi-restraints excluded: chain A residue 1469 ARG
Chi-restraints excluded: chain A residue 1470 ASP
Chi-restraints excluded: chain A residue 1579 ILE
Chi-restraints excluded: chain A residue 1639 LEU
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain A residue 1701 LEU
Chi-restraints excluded: chain A residue 1801 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A  19 ASN
A  58 ASN
A 114 GLN
A 149 ASN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 222 HIS
A 290 GLN
A 360 GLN
A 567 ASN
A 593 GLN
A 607 ASN
A 655 HIS
A 703 ASN
** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 794 ASN
A1128 GLN
A1132 ASN
A1167 ASN
** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1186 HIS
** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1315 ASN
A1335 GLN
A1443 GLN
A1483 GLN
A1524 HIS
A1530 ASN
A1587 GLN
A1664 GLN

Total number of N/Q/H flips: 25

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.177833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.138001 restraints weight = 20502.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 3.59
r_work: 0.3096 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3118
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3118
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12040  Z= 0.168
  Angle     :  0.651  14.137  16293  Z= 0.323
  Chirality :  0.041   0.164   1862
  Planarity :  0.004   0.046   2028
  Dihedral  : 11.889 169.842   1737
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 12.30 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.42 (0.22), residues: 1428
  helix:  0.52 (0.18), residues: 790
  sheet: -1.50 (0.53), residues: 89
  loop : -3.13 (0.24), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  63 
 TYR   0.024   0.002   TYR A1125 
 PHE   0.014   0.001   PHE A1274 
 TRP   0.013   0.002   TRP A 394 
 HIS   0.010   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (12031)
  covalent geometry    : angle       0.64407 (16282)
  SS BOND              : bond        0.01335 (    1)
  SS BOND              : angle       2.01576 (    2)
  hydrogen bonds       : bond        0.03812 (  606)
  hydrogen bonds       : angle       4.38758 ( 1764)
  metal coordination   : bond        0.00603 (    8)
  metal coordination   : angle       4.00942 (    9)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 182
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6265 (mm-30)
REVERT: A  290 GLN cc_start: 0.7953 (tp40) cc_final: 0.7725 (tp-100)
REVERT: A  347 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8895 (mp)
REVERT: A  360 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8161 (pp30)
REVERT: A  384 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8865 (tt)
REVERT: A  647 MET cc_start: 0.8768 (tpt) cc_final: 0.8411 (tpt)
REVERT: A  669 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7853 (p0)
REVERT: A 1144 MET cc_start: 0.8103 (mmt) cc_final: 0.7828 (mmm)
REVERT: A 1150 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8218 (mp0)
REVERT: A 1253 LYS cc_start: 0.8301 (mmmt) cc_final: 0.7753 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8827 (m-10) cc_final: 0.8414 (m-10)
REVERT: A 1311 GLU cc_start: 0.8040 (tp30) cc_final: 0.7538 (tp30)
REVERT: A 1366 ASP cc_start: 0.8885 (t70) cc_final: 0.8343 (t0)
REVERT: A 1368 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8113 (mt)
REVERT: A 1467 ASP cc_start: 0.8062 (p0) cc_final: 0.7582 (p0)
REVERT: A 1546 GLU cc_start: 0.7726 (pt0) cc_final: 0.7365 (pt0)
REVERT: A 1654 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7834 (mm)
REVERT: A 1810 TYR cc_start: 0.8031 (m-80) cc_final: 0.7649 (m-80)
  outliers start: 49
  outliers final: 23
  residues processed: 216
  average time/residue: 0.1149
  time to fit residues: 35.8534
Evaluate side-chains
  192 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 162
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  302 TYR
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  475 ARG
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  546 THR
Chi-restraints excluded: chain A residue  557 GLU
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  669 ASP
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  718 ARG
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue 1150 GLU
Chi-restraints excluded: chain A residue 1267 LYS
Chi-restraints excluded: chain A residue 1302 THR
Chi-restraints excluded: chain A residue 1321 VAL
Chi-restraints excluded: chain A residue 1368 LEU
Chi-restraints excluded: chain A residue 1454 ARG
Chi-restraints excluded: chain A residue 1458 ASP
Chi-restraints excluded: chain A residue 1470 ASP
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain A residue 1701 LEU
Chi-restraints excluded: chain A residue 1706 LEU
Chi-restraints excluded: chain A residue 1801 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 120 optimal weight:    0.8980
   chunk 5 optimal weight:    9.9990
   chunk 41 optimal weight:    0.7980
   chunk 134 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0070
   chunk 112 optimal weight:    0.5980
   chunk 52 optimal weight:    3.9990
   chunk 127 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 109 optimal weight:    0.0770
   overall best weight:    0.4556

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1287 HIS
A1296 GLN
** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1530 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.180461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.141542 restraints weight = 19256.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 3.14
r_work: 0.3205 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3156
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3156
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12040  Z= 0.127
  Angle     :  0.605  11.886  16293  Z= 0.299
  Chirality :  0.040   0.202   1862
  Planarity :  0.004   0.047   2028
  Dihedral  : 11.356 172.126   1715
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 14.42 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.97 (0.22), residues: 1428
  helix:  0.97 (0.18), residues: 788
  sheet: -1.29 (0.55), residues: 89
  loop : -3.08 (0.24), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1469 
 TYR   0.018   0.001   TYR A1125 
 PHE   0.014   0.001   PHE A 541 
 TRP   0.021   0.002   TRP A 369 
 HIS   0.006   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (12031)
  covalent geometry    : angle       0.59933 (16282)
  SS BOND              : bond        0.00219 (    1)
  SS BOND              : angle       1.88667 (    2)
  hydrogen bonds       : bond        0.03533 (  606)
  hydrogen bonds       : angle       4.20177 ( 1764)
  metal coordination   : bond        0.00495 (    8)
  metal coordination   : angle       3.54776 (    9)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 180
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6278 (mm-30)
REVERT: A  268 ASN cc_start: 0.7897 (m-40) cc_final: 0.7562 (t0)
REVERT: A  364 LYS cc_start: 0.6155 (mmtm) cc_final: 0.5923 (mmtt)
REVERT: A  384 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8799 (tt)
REVERT: A  388 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8063 (mttt)
REVERT: A  399 GLN cc_start: 0.7933 (tt0) cc_final: 0.7654 (tm-30)
REVERT: A  647 MET cc_start: 0.8775 (tpt) cc_final: 0.8435 (tpt)
REVERT: A  669 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7720 (p0)
REVERT: A 1150 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8265 (mp0)
REVERT: A 1253 LYS cc_start: 0.8100 (mmmt) cc_final: 0.7626 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8809 (m-10) cc_final: 0.8519 (m-10)
REVERT: A 1311 GLU cc_start: 0.7991 (tp30) cc_final: 0.7481 (tp30)
REVERT: A 1366 ASP cc_start: 0.8770 (t70) cc_final: 0.8235 (t0)
REVERT: A 1368 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8037 (mt)
REVERT: A 1467 ASP cc_start: 0.8066 (p0) cc_final: 0.7532 (p0)
REVERT: A 1546 GLU cc_start: 0.7601 (pt0) cc_final: 0.7223 (pt0)
REVERT: A 1654 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7814 (mm)
REVERT: A 1667 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7187 (ptm160)
REVERT: A 1701 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8035 (pp)
REVERT: A 1810 TYR cc_start: 0.7970 (m-80) cc_final: 0.7579 (m-80)
  outliers start: 44
  outliers final: 29
  residues processed: 214
  average time/residue: 0.1140
  time to fit residues: 34.9007
Evaluate side-chains
  200 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 164
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  302 TYR
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  443 HIS
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  475 ARG
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  557 GLU
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  669 ASP
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  718 ARG
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  741 ILE
Chi-restraints excluded: chain A residue 1150 GLU
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1267 LYS
Chi-restraints excluded: chain A residue 1302 THR
Chi-restraints excluded: chain A residue 1321 VAL
Chi-restraints excluded: chain A residue 1325 THR
Chi-restraints excluded: chain A residue 1368 LEU
Chi-restraints excluded: chain A residue 1454 ARG
Chi-restraints excluded: chain A residue 1458 ASP
Chi-restraints excluded: chain A residue 1470 ASP
Chi-restraints excluded: chain A residue 1639 LEU
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain A residue 1667 ARG
Chi-restraints excluded: chain A residue 1701 LEU
Chi-restraints excluded: chain A residue 1706 LEU
Chi-restraints excluded: chain A residue 1801 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 77 optimal weight:    0.0970
   chunk 91 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0980
   chunk 31 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 5 optimal weight:    8.9990
   chunk 139 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9990
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1301 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 = 0.4022 r_free = 0.4022 target = 0.179867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.140851 restraints weight = 28214.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 5.57
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3537
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12040  Z= 0.132
  Angle     :  0.596   9.190  16293  Z= 0.296
  Chirality :  0.040   0.150   1862
  Planarity :  0.004   0.049   2028
  Dihedral  : 11.273 172.308   1714
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.02 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.22), residues: 1428
  helix:  1.17 (0.18), residues: 790
  sheet: -1.20 (0.55), residues: 89
  loop : -2.94 (0.24), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1355 
 TYR   0.017   0.001   TYR A1125 
 PHE   0.024   0.001   PHE A 583 
 TRP   0.015   0.001   TRP A 394 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (12031)
  covalent geometry    : angle       0.59008 (16282)
  SS BOND              : bond        0.00792 (    1)
  SS BOND              : angle       2.80218 (    2)
  hydrogen bonds       : bond        0.03441 (  606)
  hydrogen bonds       : angle       4.13197 ( 1764)
  metal coordination   : bond        0.00498 (    8)
  metal coordination   : angle       3.41896 (    9)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 174
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6357 (mm-30)
REVERT: A  384 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8691 (tt)
REVERT: A  388 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8217 (mttt)
REVERT: A  399 GLN cc_start: 0.7840 (tt0) cc_final: 0.7586 (tm-30)
REVERT: A  456 TYR cc_start: 0.7549 (t80) cc_final: 0.7346 (t80)
REVERT: A  647 MET cc_start: 0.8370 (tpt) cc_final: 0.7946 (tpt)
REVERT: A  669 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7298 (p0)
REVERT: A  789 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8858 (tp)
REVERT: A 1150 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8075 (mp0)
REVERT: A 1253 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7675 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8712 (m-10) cc_final: 0.8503 (m-10)
REVERT: A 1311 GLU cc_start: 0.7376 (tp30) cc_final: 0.6840 (tp30)
REVERT: A 1366 ASP cc_start: 0.8145 (t70) cc_final: 0.7628 (t0)
REVERT: A 1467 ASP cc_start: 0.7194 (p0) cc_final: 0.6809 (p0)
REVERT: A 1654 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7653 (mm)
REVERT: A 1810 TYR cc_start: 0.7877 (m-80) cc_final: 0.7584 (m-80)
  outliers start: 42
  outliers final: 28
  residues processed: 209
  average time/residue: 0.1161
  time to fit residues: 34.9684
Evaluate side-chains
  195 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 162
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  302 TYR
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  443 HIS
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  475 ARG
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  557 GLU
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  669 ASP
Chi-restraints excluded: chain A residue  718 ARG
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  741 ILE
Chi-restraints excluded: chain A residue  789 LEU
Chi-restraints excluded: chain A residue 1150 GLU
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1267 LYS
Chi-restraints excluded: chain A residue 1302 THR
Chi-restraints excluded: chain A residue 1321 VAL
Chi-restraints excluded: chain A residue 1325 THR
Chi-restraints excluded: chain A residue 1454 ARG
Chi-restraints excluded: chain A residue 1458 ASP
Chi-restraints excluded: chain A residue 1470 ASP
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain A residue 1668 VAL
Chi-restraints excluded: chain A residue 1706 LEU
Chi-restraints excluded: chain A residue 1801 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 139 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0270
   chunk 106 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0010
   chunk 73 optimal weight:    0.8980
   chunk 127 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 132 optimal weight:    2.9990
   chunk 131 optimal weight:    6.9990
   overall best weight:    0.4444

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 GLN
** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1301 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 = 0.4033 r_free = 0.4033 target = 0.180982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.141760 restraints weight = 23991.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 4.86
r_work: 0.3113 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3096
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12040  Z= 0.119
  Angle     :  0.582   8.811  16293  Z= 0.290
  Chirality :  0.039   0.160   1862
  Planarity :  0.004   0.048   2028
  Dihedral  : 11.123 173.128   1709
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 15.09 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.22), residues: 1428
  helix:  1.33 (0.18), residues: 789
  sheet: -0.86 (0.59), residues: 79
  loop : -2.87 (0.24), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 397 
 TYR   0.018   0.001   TYR A 148 
 PHE   0.020   0.001   PHE A 583 
 TRP   0.026   0.002   TRP A 394 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (12031)
  covalent geometry    : angle       0.57634 (16282)
  SS BOND              : bond        0.00421 (    1)
  SS BOND              : angle       2.25469 (    2)
  hydrogen bonds       : bond        0.03346 (  606)
  hydrogen bonds       : angle       4.05268 ( 1764)
  metal coordination   : bond        0.00425 (    8)
  metal coordination   : angle       3.24120 (    9)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 180
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   34 CYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7289 (m)
REVERT: B   53 CYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7403 (m)
REVERT: A  113 GLU cc_start: 0.6786 (mm-30) cc_final: 0.6162 (mm-30)
REVERT: A  388 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8344 (mttt)
REVERT: A  399 GLN cc_start: 0.7959 (tt0) cc_final: 0.7637 (tm-30)
REVERT: A  456 TYR cc_start: 0.7640 (t80) cc_final: 0.7311 (t80)
REVERT: A  640 GLN cc_start: 0.8285 (mt0) cc_final: 0.8081 (mt0)
REVERT: A  647 MET cc_start: 0.8851 (tpt) cc_final: 0.8479 (tpt)
REVERT: A  669 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7849 (p0)
REVERT: A 1150 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8353 (mp0)
REVERT: A 1253 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7608 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8839 (m-10) cc_final: 0.8528 (m-10)
REVERT: A 1311 GLU cc_start: 0.8063 (tp30) cc_final: 0.7579 (tp30)
REVERT: A 1366 ASP cc_start: 0.8811 (t70) cc_final: 0.8296 (t0)
REVERT: A 1368 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8053 (mt)
REVERT: A 1467 ASP cc_start: 0.8201 (p0) cc_final: 0.7645 (p0)
REVERT: A 1654 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7705 (mm)
REVERT: A 1810 TYR cc_start: 0.7867 (m-80) cc_final: 0.7543 (m-80)
  outliers start: 49
  outliers final: 31
  residues processed: 219
  average time/residue: 0.1187
  time to fit residues: 37.0215
Evaluate side-chains
  201 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 164
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  302 TYR
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  443 HIS
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  475 ARG
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  669 ASP
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  718 ARG
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  741 ILE
Chi-restraints excluded: chain A residue 1150 GLU
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1267 LYS
Chi-restraints excluded: chain A residue 1302 THR
Chi-restraints excluded: chain A residue 1321 VAL
Chi-restraints excluded: chain A residue 1325 THR
Chi-restraints excluded: chain A residue 1368 LEU
Chi-restraints excluded: chain A residue 1454 ARG
Chi-restraints excluded: chain A residue 1458 ASP
Chi-restraints excluded: chain A residue 1470 ASP
Chi-restraints excluded: chain A residue 1490 ASP
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain A residue 1668 VAL
Chi-restraints excluded: chain A residue 1706 LEU
Chi-restraints excluded: chain A residue 1801 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 84 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 77 optimal weight:    0.7980
   chunk 68 optimal weight:    0.2980
   chunk 133 optimal weight:    0.6980
   chunk 126 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
A 151 GLN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 GLN
** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.177464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.137541 restraints weight = 25566.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 5.42
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3472
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3472
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12040  Z= 0.180
  Angle     :  0.618  10.078  16293  Z= 0.307
  Chirality :  0.041   0.192   1862
  Planarity :  0.004   0.047   2028
  Dihedral  : 11.165 171.382   1709
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 15.77 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.22), residues: 1428
  helix:  1.28 (0.18), residues: 790
  sheet: -1.40 (0.56), residues: 80
  loop : -2.78 (0.24), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1355 
 TYR   0.017   0.002   TYR A1125 
 PHE   0.021   0.001   PHE A 583 
 TRP   0.028   0.002   TRP A 394 
 HIS   0.005   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (12031)
  covalent geometry    : angle       0.61144 (16282)
  SS BOND              : bond        0.00247 (    1)
  SS BOND              : angle       2.27458 (    2)
  hydrogen bonds       : bond        0.03564 (  606)
  hydrogen bonds       : angle       4.16267 ( 1764)
  metal coordination   : bond        0.00824 (    8)
  metal coordination   : angle       3.71809 (    9)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 163
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 CYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7691 (m)
REVERT: A  360 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7731 (pp30)
REVERT: A  399 GLN cc_start: 0.7836 (tt0) cc_final: 0.7560 (tm-30)
REVERT: A  456 TYR cc_start: 0.7592 (t80) cc_final: 0.7220 (t80)
REVERT: A  640 GLN cc_start: 0.7790 (mt0) cc_final: 0.7561 (mt0)
REVERT: A  647 MET cc_start: 0.8472 (tpt) cc_final: 0.7825 (tpt)
REVERT: A  660 ASP cc_start: 0.7401 (t0) cc_final: 0.7196 (t0)
REVERT: A  669 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7336 (p0)
REVERT: A 1150 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8135 (mp0)
REVERT: A 1253 LYS cc_start: 0.8017 (mmmt) cc_final: 0.7642 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8745 (m-10) cc_final: 0.8512 (m-10)
REVERT: A 1311 GLU cc_start: 0.7677 (tp30) cc_final: 0.7175 (tp30)
REVERT: A 1366 ASP cc_start: 0.8167 (t70) cc_final: 0.7694 (t0)
REVERT: A 1467 ASP cc_start: 0.7292 (p0) cc_final: 0.6930 (p0)
REVERT: A 1810 TYR cc_start: 0.7825 (m-80) cc_final: 0.7495 (m-80)
  outliers start: 47
  outliers final: 33
  residues processed: 201
  average time/residue: 0.1094
  time to fit residues: 31.6340
Evaluate side-chains
  199 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 162
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  302 TYR
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  443 HIS
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  475 ARG
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  669 ASP
Chi-restraints excluded: chain A residue  718 ARG
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  741 ILE
Chi-restraints excluded: chain A residue 1150 GLU
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1267 LYS
Chi-restraints excluded: chain A residue 1272 GLU
Chi-restraints excluded: chain A residue 1302 THR
Chi-restraints excluded: chain A residue 1321 VAL
Chi-restraints excluded: chain A residue 1325 THR
Chi-restraints excluded: chain A residue 1454 ARG
Chi-restraints excluded: chain A residue 1458 ASP
Chi-restraints excluded: chain A residue 1470 ASP
Chi-restraints excluded: chain A residue 1490 ASP
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain A residue 1668 VAL
Chi-restraints excluded: chain A residue 1706 LEU
Chi-restraints excluded: chain A residue 1801 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 138 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 290 GLN
A 360 GLN
** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.177577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.129357 restraints weight = 27263.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 3.06
r_work: 0.3129 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3135
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12040  Z= 0.157
  Angle     :  0.626  14.835  16293  Z= 0.303
  Chirality :  0.040   0.164   1862
  Planarity :  0.004   0.046   2028
  Dihedral  : 11.175 171.718   1709
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 15.77 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.22), residues: 1428
  helix:  1.35 (0.18), residues: 784
  sheet: -1.31 (0.56), residues: 82
  loop : -2.69 (0.25), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1355 
 TYR   0.017   0.001   TYR A1125 
 PHE   0.019   0.001   PHE A 583 
 TRP   0.025   0.002   TRP A 394 
 HIS   0.004   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (12031)
  covalent geometry    : angle       0.60235 (16282)
  SS BOND              : bond        0.00302 (    1)
  SS BOND              : angle       1.96662 (    2)
  hydrogen bonds       : bond        0.03524 (  606)
  hydrogen bonds       : angle       4.14827 ( 1764)
  metal coordination   : bond        0.01800 (    8)
  metal coordination   : angle       7.20658 (    9)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 167
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 CYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7417 (m)
REVERT: A  360 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7874 (pp30)
REVERT: A  399 GLN cc_start: 0.7902 (tt0) cc_final: 0.7642 (tm-30)
REVERT: A  456 TYR cc_start: 0.7642 (t80) cc_final: 0.7177 (t80)
REVERT: A  640 GLN cc_start: 0.8366 (mt0) cc_final: 0.8145 (mt0)
REVERT: A  647 MET cc_start: 0.8916 (tpt) cc_final: 0.8243 (tpt)
REVERT: A  660 ASP cc_start: 0.8229 (t0) cc_final: 0.8018 (t0)
REVERT: A  669 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7782 (p0)
REVERT: A 1150 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8283 (mp0)
REVERT: A 1223 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.5908 (mm)
REVERT: A 1253 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7618 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8878 (m-10) cc_final: 0.8567 (m-10)
REVERT: A 1311 GLU cc_start: 0.8020 (tp30) cc_final: 0.7529 (tp30)
REVERT: A 1366 ASP cc_start: 0.8732 (t70) cc_final: 0.8230 (t0)
REVERT: A 1467 ASP cc_start: 0.8086 (p0) cc_final: 0.7635 (p0)
REVERT: A 1810 TYR cc_start: 0.7985 (m-80) cc_final: 0.7577 (m-80)
  outliers start: 48
  outliers final: 36
  residues processed: 205
  average time/residue: 0.0927
  time to fit residues: 27.4483
Evaluate side-chains
  203 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 162
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  302 TYR
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  443 HIS
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  475 ARG
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  546 THR
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  669 ASP
Chi-restraints excluded: chain A residue  718 ARG
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  741 ILE
Chi-restraints excluded: chain A residue 1150 GLU
Chi-restraints excluded: chain A residue 1223 ILE
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1267 LYS
Chi-restraints excluded: chain A residue 1302 THR
Chi-restraints excluded: chain A residue 1321 VAL
Chi-restraints excluded: chain A residue 1325 THR
Chi-restraints excluded: chain A residue 1400 THR
Chi-restraints excluded: chain A residue 1454 ARG
Chi-restraints excluded: chain A residue 1458 ASP
Chi-restraints excluded: chain A residue 1470 ASP
Chi-restraints excluded: chain A residue 1490 ASP
Chi-restraints excluded: chain A residue 1495 ILE
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain A residue 1668 VAL
Chi-restraints excluded: chain A residue 1706 LEU
Chi-restraints excluded: chain A residue 1801 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 97 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 119 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 2 optimal weight:    9.9990
   chunk 133 optimal weight:    0.5980
   chunk 132 optimal weight:    0.0010
   overall best weight:    1.3192

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 290 GLN
A 360 GLN
** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1301 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.175413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.134575 restraints weight = 19601.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 3.25
r_work: 0.3116 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12040  Z= 0.199
  Angle     :  0.657  14.490  16293  Z= 0.321
  Chirality :  0.042   0.237   1862
  Planarity :  0.004   0.045   2028
  Dihedral  : 11.207 170.459   1709
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 16.15 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.22), residues: 1428
  helix:  1.21 (0.18), residues: 792
  sheet: -1.76 (0.53), residues: 94
  loop : -2.61 (0.25), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1469 
 TYR   0.016   0.002   TYR A1125 
 PHE   0.020   0.002   PHE A 583 
 TRP   0.023   0.002   TRP A 394 
 HIS   0.005   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 (12031)
  covalent geometry    : angle       0.63918 (16282)
  SS BOND              : bond        0.00252 (    1)
  SS BOND              : angle       2.16595 (    2)
  hydrogen bonds       : bond        0.03730 (  606)
  hydrogen bonds       : angle       4.23851 ( 1764)
  metal coordination   : bond        0.01796 (    8)
  metal coordination   : angle       6.35958 (    9)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 166
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 CYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7460 (m)
REVERT: B   60 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7428 (t)
REVERT: A   37 MET cc_start: 0.6180 (tpp) cc_final: 0.5890 (tpp)
REVERT: A  399 GLN cc_start: 0.7884 (tt0) cc_final: 0.7586 (tm-30)
REVERT: A  420 ASN cc_start: 0.8711 (t0) cc_final: 0.8425 (t0)
REVERT: A  456 TYR cc_start: 0.7710 (t80) cc_final: 0.7250 (t80)
REVERT: A  640 GLN cc_start: 0.8448 (mt0) cc_final: 0.8234 (mt0)
REVERT: A  647 MET cc_start: 0.8989 (tpt) cc_final: 0.8370 (tpt)
REVERT: A  669 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7894 (p0)
REVERT: A 1150 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8264 (mp0)
REVERT: A 1223 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6098 (mm)
REVERT: A 1253 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7680 (mtmm)
REVERT: A 1311 GLU cc_start: 0.8122 (tp30) cc_final: 0.7590 (tp30)
REVERT: A 1366 ASP cc_start: 0.8798 (t70) cc_final: 0.8304 (t0)
REVERT: A 1467 ASP cc_start: 0.8284 (p0) cc_final: 0.7882 (p0)
REVERT: A 1810 TYR cc_start: 0.7980 (m-80) cc_final: 0.7567 (m-80)
  outliers start: 48
  outliers final: 39
  residues processed: 204
  average time/residue: 0.0981
  time to fit residues: 28.7965
Evaluate side-chains
  204 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 160
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   52 ASN
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  302 TYR
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  443 HIS
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  475 ARG
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  546 THR
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  669 ASP
Chi-restraints excluded: chain A residue  718 ARG
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  741 ILE
Chi-restraints excluded: chain A residue 1150 GLU
Chi-restraints excluded: chain A residue 1223 ILE
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1267 LYS
Chi-restraints excluded: chain A residue 1272 GLU
Chi-restraints excluded: chain A residue 1302 THR
Chi-restraints excluded: chain A residue 1321 VAL
Chi-restraints excluded: chain A residue 1325 THR
Chi-restraints excluded: chain A residue 1400 THR
Chi-restraints excluded: chain A residue 1454 ARG
Chi-restraints excluded: chain A residue 1458 ASP
Chi-restraints excluded: chain A residue 1470 ASP
Chi-restraints excluded: chain A residue 1490 ASP
Chi-restraints excluded: chain A residue 1495 ILE
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain A residue 1657 LEU
Chi-restraints excluded: chain A residue 1668 VAL
Chi-restraints excluded: chain A residue 1706 LEU
Chi-restraints excluded: chain A residue 1801 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 132 optimal weight:    0.8980
   chunk 98 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 104 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 149 ASN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 GLN
** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 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 = 0.3995 r_free = 0.3995 target = 0.177624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.137187 restraints weight = 18627.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 2.78
r_work: 0.3174 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3124
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3124
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12040  Z= 0.144
  Angle     :  0.623  13.191  16293  Z= 0.307
  Chirality :  0.040   0.224   1862
  Planarity :  0.004   0.046   2028
  Dihedral  : 11.199 173.094   1709
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 16.75 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.22), residues: 1428
  helix:  1.37 (0.18), residues: 786
  sheet: -0.83 (0.63), residues: 70
  loop : -2.64 (0.24), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1469 
 TYR   0.017   0.001   TYR A1125 
 PHE   0.017   0.001   PHE A 583 
 TRP   0.023   0.002   TRP A 394 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (12031)
  covalent geometry    : angle       0.60916 (16282)
  SS BOND              : bond        0.00377 (    1)
  SS BOND              : angle       1.71851 (    2)
  hydrogen bonds       : bond        0.03524 (  606)
  hydrogen bonds       : angle       4.14925 ( 1764)
  metal coordination   : bond        0.01343 (    8)
  metal coordination   : angle       5.62957 (    9)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 167
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 CYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7519 (m)
REVERT: B   60 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.7359 (t)
REVERT: A   37 MET cc_start: 0.6316 (tpp) cc_final: 0.6041 (tpp)
REVERT: A  399 GLN cc_start: 0.7829 (tt0) cc_final: 0.7592 (tm-30)
REVERT: A  420 ASN cc_start: 0.8655 (t0) cc_final: 0.8378 (t0)
REVERT: A  456 TYR cc_start: 0.7651 (t80) cc_final: 0.7212 (t80)
REVERT: A  547 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7978 (mt-10)
REVERT: A  640 GLN cc_start: 0.8298 (mt0) cc_final: 0.8098 (mt0)
REVERT: A  669 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7820 (p0)
REVERT: A 1150 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8189 (mp0)
REVERT: A 1223 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6107 (mm)
REVERT: A 1253 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7730 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8839 (m-10) cc_final: 0.8414 (m-10)
REVERT: A 1290 SER cc_start: 0.8494 (t) cc_final: 0.7938 (m)
REVERT: A 1311 GLU cc_start: 0.8022 (tp30) cc_final: 0.7524 (tp30)
REVERT: A 1366 ASP cc_start: 0.8679 (t70) cc_final: 0.8183 (t0)
REVERT: A 1467 ASP cc_start: 0.8135 (p0) cc_final: 0.7711 (p0)
REVERT: A 1810 TYR cc_start: 0.7932 (m-80) cc_final: 0.7520 (m-80)
  outliers start: 43
  outliers final: 36
  residues processed: 203
  average time/residue: 0.1103
  time to fit residues: 32.1410
Evaluate side-chains
  203 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 162
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  302 TYR
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  443 HIS
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  475 ARG
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  669 ASP
Chi-restraints excluded: chain A residue  718 ARG
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  741 ILE
Chi-restraints excluded: chain A residue 1150 GLU
Chi-restraints excluded: chain A residue 1223 ILE
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1267 LYS
Chi-restraints excluded: chain A residue 1302 THR
Chi-restraints excluded: chain A residue 1321 VAL
Chi-restraints excluded: chain A residue 1325 THR
Chi-restraints excluded: chain A residue 1454 ARG
Chi-restraints excluded: chain A residue 1458 ASP
Chi-restraints excluded: chain A residue 1470 ASP
Chi-restraints excluded: chain A residue 1490 ASP
Chi-restraints excluded: chain A residue 1495 ILE
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain A residue 1668 VAL
Chi-restraints excluded: chain A residue 1706 LEU
Chi-restraints excluded: chain A residue 1801 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 142 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 115 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0770
   chunk 49 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 137 optimal weight:   10.0000
   chunk 127 optimal weight:    2.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.178374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.137980 restraints weight = 21373.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 3.54
r_work: 0.3148 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12040  Z= 0.138
  Angle     :  0.634  12.727  16293  Z= 0.309
  Chirality :  0.040   0.210   1862
  Planarity :  0.004   0.046   2028
  Dihedral  : 11.165 173.543   1709
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 16.91 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.22), residues: 1428
  helix:  1.38 (0.18), residues: 791
  sheet: -0.83 (0.62), residues: 70
  loop : -2.59 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1469 
 TYR   0.016   0.001   TYR A1125 
 PHE   0.018   0.001   PHE A 583 
 TRP   0.023   0.001   TRP A 394 
 HIS   0.003   0.001   HIS A1361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (12031)
  covalent geometry    : angle       0.62141 (16282)
  SS BOND              : bond        0.00443 (    1)
  SS BOND              : angle       1.58643 (    2)
  hydrogen bonds       : bond        0.03475 (  606)
  hydrogen bonds       : angle       4.11521 ( 1764)
  metal coordination   : bond        0.01201 (    8)
  metal coordination   : angle       5.40171 (    9)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 169
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 CYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7509 (m)
REVERT: B   60 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7374 (t)
REVERT: A   37 MET cc_start: 0.6408 (tpp) cc_final: 0.6139 (tpp)
REVERT: A  399 GLN cc_start: 0.7892 (tt0) cc_final: 0.7603 (tm-30)
REVERT: A  420 ASN cc_start: 0.8706 (t0) cc_final: 0.8431 (t0)
REVERT: A  456 TYR cc_start: 0.7703 (t80) cc_final: 0.7191 (t80)
REVERT: A  640 GLN cc_start: 0.8292 (mt0) cc_final: 0.8052 (mt0)
REVERT: A  647 MET cc_start: 0.8770 (tpt) cc_final: 0.8537 (tpt)
REVERT: A  669 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7848 (p0)
REVERT: A 1150 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8323 (mp0)
REVERT: A 1223 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6071 (mm)
REVERT: A 1253 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7683 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8862 (m-10) cc_final: 0.8432 (m-10)
REVERT: A 1290 SER cc_start: 0.8550 (t) cc_final: 0.7976 (m)
REVERT: A 1311 GLU cc_start: 0.8079 (tp30) cc_final: 0.7585 (tp30)
REVERT: A 1366 ASP cc_start: 0.8727 (t70) cc_final: 0.8244 (t0)
REVERT: A 1467 ASP cc_start: 0.8163 (p0) cc_final: 0.7684 (p0)
REVERT: A 1810 TYR cc_start: 0.7880 (m-80) cc_final: 0.7537 (m-80)
  outliers start: 41
  outliers final: 36
  residues processed: 204
  average time/residue: 0.1034
  time to fit residues: 30.2343
Evaluate side-chains
  202 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 161
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  302 TYR
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  443 HIS
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  475 ARG
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  669 ASP
Chi-restraints excluded: chain A residue  718 ARG
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  741 ILE
Chi-restraints excluded: chain A residue 1150 GLU
Chi-restraints excluded: chain A residue 1223 ILE
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1267 LYS
Chi-restraints excluded: chain A residue 1302 THR
Chi-restraints excluded: chain A residue 1321 VAL
Chi-restraints excluded: chain A residue 1325 THR
Chi-restraints excluded: chain A residue 1454 ARG
Chi-restraints excluded: chain A residue 1458 ASP
Chi-restraints excluded: chain A residue 1470 ASP
Chi-restraints excluded: chain A residue 1490 ASP
Chi-restraints excluded: chain A residue 1495 ILE
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain A residue 1668 VAL
Chi-restraints excluded: chain A residue 1706 LEU
Chi-restraints excluded: chain A residue 1801 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 120 optimal weight:    5.9990
   chunk 80 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 123 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 129 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 117 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 132 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.177408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.127386 restraints weight = 29208.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 3.20
r_work: 0.3128 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3160
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12040  Z= 0.154
  Angle     :  0.640  12.708  16293  Z= 0.313
  Chirality :  0.040   0.201   1862
  Planarity :  0.004   0.045   2028
  Dihedral  : 11.148 172.966   1709
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 16.91 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (0.22), residues: 1428
  helix:  1.37 (0.18), residues: 791
  sheet: -0.84 (0.61), residues: 70
  loop : -2.59 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1355 
 TYR   0.016   0.001   TYR A1125 
 PHE   0.019   0.001   PHE A 583 
 TRP   0.025   0.002   TRP A 394 
 HIS   0.003   0.001   HIS A1236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (12031)
  covalent geometry    : angle       0.62706 (16282)
  SS BOND              : bond        0.00411 (    1)
  SS BOND              : angle       1.67086 (    2)
  hydrogen bonds       : bond        0.03512 (  606)
  hydrogen bonds       : angle       4.13597 ( 1764)
  metal coordination   : bond        0.01276 (    8)
  metal coordination   : angle       5.38967 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2882.80 seconds
wall clock time: 50 minutes 24.19 seconds (3024.19 seconds total)