Starting phenix.real_space_refine
on Wed Jul 30 07:07:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ela_31178/07_2025/7ela_31178.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ela_31178/07_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_31178/07_2025/7ela_31178.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ela_31178/07_2025/7ela_31178.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ela_31178/07_2025/7ela_31178.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ela_31178/07_2025/7ela_31178.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 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): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5}
          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: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5}
          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: 12.58, per 1000 atoms: 1.07
  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: 2.86
  Conformation dependent library (CDL) restraints added in 3.0 seconds
  
  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: 1.84
  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: 5.23

  Time building geometry restraints manager: 3.40 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:                  0.000
  Normalize map: mean=0, sd=1:             1.290
  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:          0.550
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     43.120
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.210
-------------------------------------------------------------------------------
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 : 11.82
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (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
 TRP   0.010   0.001   TRP A1666 
 HIS   0.006   0.001   HIS A1744 
 PHE   0.014   0.001   PHE A 541 
 TYR   0.012   0.001   TYR A 302 
 ARG   0.002   0.000   ARG A 380 

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

*********************** 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  : 1.470 
Fit side-chains
   revert: symmetry clash
REVERT: B   50 CYS cc_start: 0.6258 (p) cc_final: 0.5814 (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: 0.7407 (mmtm)
REVERT: A  385 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6870 (pm20)
REVERT: A  669 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7332 (p0)
REVERT: A  751 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7219 (tm-30)
REVERT: A  755 MET cc_start: 0.8687 (tpp) cc_final: 0.8429 (tpp)
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: 0.7816 (t0)
REVERT: A 1467 ASP cc_start: 0.6909 (p0) cc_final: 0.6512 (p0)
REVERT: A 1469 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6386 (tpm170)
REVERT: A 1546 GLU cc_start: 0.7048 (pt0) cc_final: 0.6848 (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: 0.7740 (m-80)
  outliers start: 37
  outliers final: 24
  residues processed: 268
  average time/residue: 0.3186
  time to fit residues: 119.9766
Evaluate side-chains
  194 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 164
  time to evaluate  : 1.554 
-------------------------------------------------------------------------------
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 121 optimal weight:   10.0000
   chunk 109 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 73 optimal weight:    0.4980
   chunk 58 optimal weight:    1.9990
   chunk 112 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 68 optimal weight:    0.3980
   chunk 84 optimal weight:    0.6980
   chunk 130 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 290 GLN
A 360 GLN
A 567 ASN
A 593 GLN
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**
A1278 ASN
** 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: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.179304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.140563 restraints weight = 22772.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 4.04
r_work: 0.3129 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12040  Z= 0.143
  Angle     :  0.632  14.241  16293  Z= 0.313
  Chirality :  0.040   0.160   1862
  Planarity :  0.004   0.046   2028
  Dihedral  : 11.868 170.626   1737
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 12.30 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.22), residues: 1428
  helix:  0.55 (0.18), residues: 788
  sheet: -1.56 (0.53), residues: 89
  loop : -3.20 (0.23), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 394 
 HIS   0.003   0.001   HIS A 289 
 PHE   0.012   0.001   PHE A 541 
 TYR   0.024   0.001   TYR A1125 
 ARG   0.005   0.001   ARG B  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03868 (  606)
  hydrogen bonds       : angle       4.35517 ( 1764)
  metal coordination   : bond        0.00514 (    8)
  metal coordination   : angle       3.89419 (    9)
  SS BOND              : bond        0.00053 (    1)
  SS BOND              : angle       2.28892 (    2)
  covalent geometry    : bond        0.00325 (12031)
  covalent geometry    : angle       0.62541 (16282)

*********************** 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
  227 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 181
  time to evaluate  : 1.305 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6254 (mm-30)
REVERT: A  347 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8882 (mp)
REVERT: A  360 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8202 (pp30)
REVERT: A  384 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8834 (tt)
REVERT: A  647 MET cc_start: 0.8799 (tpt) cc_final: 0.8469 (tpt)
REVERT: A  669 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7851 (p0)
REVERT: A  717 ASP cc_start: 0.7856 (p0) cc_final: 0.7629 (p0)
REVERT: A  751 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7583 (tm-30)
REVERT: A 1150 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8276 (mp0)
REVERT: A 1253 LYS cc_start: 0.8320 (mmmt) cc_final: 0.7739 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8821 (m-10) cc_final: 0.8389 (m-10)
REVERT: A 1311 GLU cc_start: 0.8063 (tp30) cc_final: 0.7555 (tp30)
REVERT: A 1366 ASP cc_start: 0.8911 (t70) cc_final: 0.8338 (t0)
REVERT: A 1368 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8051 (mt)
REVERT: A 1467 ASP cc_start: 0.8044 (p0) cc_final: 0.7562 (p0)
REVERT: A 1469 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6870 (ttt90)
REVERT: A 1546 GLU cc_start: 0.7761 (pt0) cc_final: 0.7403 (pt0)
REVERT: A 1654 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7914 (mm)
REVERT: A 1810 TYR cc_start: 0.7983 (m-80) cc_final: 0.7617 (m-80)
  outliers start: 46
  outliers final: 22
  residues processed: 212
  average time/residue: 0.2519
  time to fit residues: 76.3918
Evaluate side-chains
  194 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 164
  time to evaluate  : 1.348 
-------------------------------------------------------------------------------
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  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 1469 ARG
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 17 optimal weight:    6.9990
   chunk 107 optimal weight:    0.6980
   chunk 99 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 128 optimal weight:    1.9990
   chunk 139 optimal weight:    8.9990
   chunk 110 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 140 optimal weight:    0.9980
   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 151 GLN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 222 HIS
A 290 GLN
A 607 ASN
A 703 ASN
** 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: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.178036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.127245 restraints weight = 30458.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 3.24
r_work: 0.3096 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3149
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3149
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12040  Z= 0.161
  Angle     :  0.622  13.570  16293  Z= 0.308
  Chirality :  0.040   0.150   1862
  Planarity :  0.004   0.047   2028
  Dihedral  : 11.475 170.748   1719
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 14.79 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.22), residues: 1428
  helix:  0.84 (0.18), residues: 796
  sheet: -1.62 (0.52), residues: 101
  loop : -3.04 (0.25), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1688 
 HIS   0.011   0.001   HIS A 213 
 PHE   0.015   0.001   PHE A 541 
 TYR   0.016   0.001   TYR A1125 
 ARG   0.004   0.000   ARG A 397 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03674 (  606)
  hydrogen bonds       : angle       4.26161 ( 1764)
  metal coordination   : bond        0.00554 (    8)
  metal coordination   : angle       3.62279 (    9)
  SS BOND              : bond        0.00885 (    1)
  SS BOND              : angle       1.86052 (    2)
  covalent geometry    : bond        0.00375 (12031)
  covalent geometry    : angle       0.61565 (16282)

*********************** 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
  220 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 176
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6236 (mm-30)
REVERT: A  268 ASN cc_start: 0.7889 (m-40) cc_final: 0.7524 (t0)
REVERT: A  360 GLN cc_start: 0.8505 (pp30) cc_final: 0.8147 (pp30)
REVERT: A  364 LYS cc_start: 0.6328 (mmtm) cc_final: 0.6057 (mmtt)
REVERT: A  384 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9007 (tt)
REVERT: A  388 LYS cc_start: 0.8449 (mtpt) cc_final: 0.8043 (mttt)
REVERT: A  399 GLN cc_start: 0.8080 (tt0) cc_final: 0.7752 (tm-30)
REVERT: A  622 MET cc_start: 0.9108 (mtm) cc_final: 0.8888 (mtm)
REVERT: A  647 MET cc_start: 0.8859 (tpt) cc_final: 0.8387 (tpt)
REVERT: A  669 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7876 (p0)
REVERT: A  717 ASP cc_start: 0.7787 (p0) cc_final: 0.7583 (p0)
REVERT: A 1150 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8238 (mp0)
REVERT: A 1253 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7573 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8882 (m-10) cc_final: 0.8481 (m-10)
REVERT: A 1311 GLU cc_start: 0.8058 (tp30) cc_final: 0.7559 (tp30)
REVERT: A 1366 ASP cc_start: 0.8892 (t70) cc_final: 0.8369 (t0)
REVERT: A 1368 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8116 (mt)
REVERT: A 1467 ASP cc_start: 0.8158 (p0) cc_final: 0.7601 (p0)
REVERT: A 1469 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6993 (ttt90)
REVERT: A 1546 GLU cc_start: 0.7682 (pt0) cc_final: 0.7278 (pt0)
REVERT: A 1654 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7754 (mm)
REVERT: A 1701 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8009 (pp)
REVERT: A 1810 TYR cc_start: 0.7936 (m-80) cc_final: 0.7520 (m-80)
  outliers start: 44
  outliers final: 29
  residues processed: 210
  average time/residue: 0.2725
  time to fit residues: 81.9459
Evaluate side-chains
  194 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 158
  time to evaluate  : 1.252 
-------------------------------------------------------------------------------
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  230 THR
Chi-restraints excluded: chain A residue  261 VAL
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  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  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 1469 ARG
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 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 124 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 4 optimal weight:    0.4980
   chunk 41 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0980
   chunk 74 optimal weight:    0.0670
   chunk 48 optimal weight:   10.0000
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.180025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.139505 restraints weight = 21172.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 3.67
r_work: 0.3104 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3144
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3144
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
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   0.030  12040  Z= 0.125
  Angle     :  0.592  11.842  16293  Z= 0.293
  Chirality :  0.039   0.150   1862
  Planarity :  0.004   0.046   2028
  Dihedral  : 11.366 172.496   1717
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 14.87 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.22), residues: 1428
  helix:  1.20 (0.18), residues: 784
  sheet: -0.91 (0.60), residues: 79
  loop : -2.92 (0.24), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 369 
 HIS   0.007   0.001   HIS A 213 
 PHE   0.011   0.001   PHE A 541 
 TYR   0.017   0.001   TYR A1125 
 ARG   0.003   0.000   ARG A1141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03398 (  606)
  hydrogen bonds       : angle       4.12247 ( 1764)
  metal coordination   : bond        0.00497 (    8)
  metal coordination   : angle       3.35501 (    9)
  SS BOND              : bond        0.01166 (    1)
  SS BOND              : angle       2.96947 (    2)
  covalent geometry    : bond        0.00284 (12031)
  covalent geometry    : angle       0.58577 (16282)

*********************** 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
  221 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 172
  time to evaluate  : 1.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 CYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7564 (m)
REVERT: A  113 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6218 (mm-30)
REVERT: A  268 ASN cc_start: 0.7795 (m-40) cc_final: 0.7523 (t0)
REVERT: A  388 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8291 (mttt)
REVERT: A  399 GLN cc_start: 0.7975 (tt0) cc_final: 0.7672 (tm-30)
REVERT: A  456 TYR cc_start: 0.7693 (t80) cc_final: 0.7407 (t80)
REVERT: A  640 GLN cc_start: 0.8290 (mt0) cc_final: 0.7999 (mt0)
REVERT: A  647 MET cc_start: 0.8828 (tpt) cc_final: 0.8359 (tpt)
REVERT: A  669 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7836 (p0)
REVERT: A 1150 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8342 (mp0)
REVERT: A 1253 LYS cc_start: 0.8082 (mmmt) cc_final: 0.7606 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8847 (m-10) cc_final: 0.8529 (m-10)
REVERT: A 1311 GLU cc_start: 0.8064 (tp30) cc_final: 0.7574 (tp30)
REVERT: A 1366 ASP cc_start: 0.8821 (t70) cc_final: 0.8297 (t0)
REVERT: A 1368 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8070 (mt)
REVERT: A 1467 ASP cc_start: 0.8152 (p0) cc_final: 0.7617 (p0)
REVERT: A 1546 GLU cc_start: 0.7698 (pt0) cc_final: 0.7224 (pt0)
REVERT: A 1654 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7800 (mm)
REVERT: A 1667 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6587 (ptm160)
REVERT: A 1810 TYR cc_start: 0.7876 (m-80) cc_final: 0.7535 (m-80)
  outliers start: 49
  outliers final: 31
  residues processed: 215
  average time/residue: 0.2782
  time to fit residues: 86.3866
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  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  273 LEU
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  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 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 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 1472 VAL
Chi-restraints excluded: chain A residue 1490 ASP
Chi-restraints excluded: chain A residue 1495 ILE
Chi-restraints excluded: chain A residue 1528 LEU
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain A residue 1667 ARG
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 121 optimal weight:    0.1980
   chunk 88 optimal weight:    0.6980
   chunk 115 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   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 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 636 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.176211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.141049 restraints weight = 34860.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 6.44
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3570
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3570
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12040  Z= 0.184
  Angle     :  0.629  12.677  16293  Z= 0.311
  Chirality :  0.041   0.166   1862
  Planarity :  0.004   0.045   2028
  Dihedral  : 11.207 170.327   1711
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 15.25 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.23), residues: 1428
  helix:  1.20 (0.18), residues: 784
  sheet: -1.67 (0.55), residues: 92
  loop : -2.67 (0.25), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 394 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.014   0.001   PHE A 258 
 TYR   0.016   0.002   TYR A1125 
 ARG   0.004   0.000   ARG A 397 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03666 (  606)
  hydrogen bonds       : angle       4.20385 ( 1764)
  metal coordination   : bond        0.00941 (    8)
  metal coordination   : angle       4.10475 (    9)
  SS BOND              : bond        0.00236 (    1)
  SS BOND              : angle       2.70711 (    2)
  covalent geometry    : bond        0.00434 (12031)
  covalent geometry    : angle       0.62132 (16282)

*********************** 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
  222 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 170
  time to evaluate  : 1.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   34 CYS cc_start: 0.7335 (OUTLIER) cc_final: 0.7011 (m)
REVERT: B   53 CYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7671 (m)
REVERT: A  343 LYS cc_start: 0.7691 (mmtm) cc_final: 0.7351 (mmtm)
REVERT: A  456 TYR cc_start: 0.7538 (t80) cc_final: 0.7217 (t80)
REVERT: A  622 MET cc_start: 0.8311 (mtm) cc_final: 0.8062 (mtm)
REVERT: A  647 MET cc_start: 0.8465 (tpt) cc_final: 0.7739 (tpt)
REVERT: A  660 ASP cc_start: 0.7756 (t0) cc_final: 0.7552 (t0)
REVERT: A  669 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7383 (p0)
REVERT: A  751 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7914 (tm-30)
REVERT: A 1150 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8163 (mp0)
REVERT: A 1253 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7787 (mtmm)
REVERT: A 1311 GLU cc_start: 0.7542 (tp30) cc_final: 0.6981 (tp30)
REVERT: A 1366 ASP cc_start: 0.8175 (t70) cc_final: 0.7703 (t0)
REVERT: A 1467 ASP cc_start: 0.7418 (p0) cc_final: 0.7108 (p0)
REVERT: A 1654 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7515 (mm)
REVERT: A 1810 TYR cc_start: 0.8080 (m-80) cc_final: 0.7748 (m-80)
  outliers start: 52
  outliers final: 37
  residues processed: 213
  average time/residue: 0.2947
  time to fit residues: 90.4483
Evaluate side-chains
  207 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 165
  time to evaluate  : 1.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   52 ASN
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  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  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 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 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 1472 VAL
Chi-restraints excluded: chain A residue 1490 ASP
Chi-restraints excluded: chain A residue 1495 ILE
Chi-restraints excluded: chain A residue 1528 LEU
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 138 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0670
   chunk 140 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 11 optimal weight:    5.9990
   chunk 124 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 113 optimal weight:    0.2980
   chunk 128 optimal weight:    0.9990
   overall best weight:    0.4718

-------------------------------------------------------------------------------
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 = 0.4015 r_free = 0.4015 target = 0.179522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.139269 restraints weight = 25505.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 4.87
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3501
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3501 r_free = 0.3501    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3501 r_free = 0.3501    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3501
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  12040  Z= 0.126
  Angle     :  0.606  12.268  16293  Z= 0.297
  Chirality :  0.039   0.151   1862
  Planarity :  0.004   0.045   2028
  Dihedral  : 11.169 172.798   1709
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 16.08 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.23), residues: 1428
  helix:  1.38 (0.18), residues: 783
  sheet: -0.98 (0.63), residues: 70
  loop : -2.66 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 394 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.011   0.001   PHE A1274 
 TYR   0.018   0.001   TYR A1125 
 ARG   0.004   0.000   ARG B  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03394 (  606)
  hydrogen bonds       : angle       4.08009 ( 1764)
  metal coordination   : bond        0.02653 (    8)
  metal coordination   : angle       4.79723 (    9)
  SS BOND              : bond        0.00439 (    1)
  SS BOND              : angle       1.86002 (    2)
  covalent geometry    : bond        0.00287 (12031)
  covalent geometry    : angle       0.59499 (16282)

*********************** 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
  230 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 184
  time to evaluate  : 1.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   34 CYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7114 (m)
REVERT: B   53 CYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7782 (m)
REVERT: A  420 ASN cc_start: 0.8141 (t0) cc_final: 0.7871 (t0)
REVERT: A  456 TYR cc_start: 0.7588 (t80) cc_final: 0.7222 (t80)
REVERT: A  647 MET cc_start: 0.8386 (tpt) cc_final: 0.7720 (tpt)
REVERT: A  660 ASP cc_start: 0.7436 (t0) cc_final: 0.7189 (t0)
REVERT: A  669 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7288 (p0)
REVERT: A 1253 LYS cc_start: 0.8024 (mmmt) cc_final: 0.7685 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8733 (m-10) cc_final: 0.8498 (m-10)
REVERT: A 1311 GLU cc_start: 0.7417 (tp30) cc_final: 0.6909 (tp30)
REVERT: A 1366 ASP cc_start: 0.8113 (t70) cc_final: 0.7646 (t0)
REVERT: A 1467 ASP cc_start: 0.7388 (p0) cc_final: 0.6968 (p0)
REVERT: A 1810 TYR cc_start: 0.7839 (m-80) cc_final: 0.7567 (m-80)
  outliers start: 46
  outliers final: 35
  residues processed: 223
  average time/residue: 0.3980
  time to fit residues: 129.9710
Evaluate side-chains
  204 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 166
  time to evaluate  : 1.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   34 CYS
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  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  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  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 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 1470 ASP
Chi-restraints excluded: chain A residue 1472 VAL
Chi-restraints excluded: chain A residue 1490 ASP
Chi-restraints excluded: chain A residue 1495 ILE
Chi-restraints excluded: chain A residue 1528 LEU
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 79 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 57 optimal weight:    0.4980
   chunk 87 optimal weight:    4.9990
   chunk 44 optimal weight:    0.5980
   chunk 113 optimal weight:    0.9990
   chunk 125 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 95 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 290 GLN
A 360 GLN
A 399 GLN
A 703 ASN
** 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

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.178460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.138639 restraints weight = 24350.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 4.86
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3489
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3489 r_free = 0.3489    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3489 r_free = 0.3489    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3489
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  12040  Z= 0.147
  Angle     :  0.612  11.164  16293  Z= 0.301
  Chirality :  0.041   0.206   1862
  Planarity :  0.004   0.044   2028
  Dihedral  : 11.142 172.375   1709
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 16.45 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.22), residues: 1428
  helix:  1.34 (0.18), residues: 783
  sheet: -1.35 (0.57), residues: 80
  loop : -2.60 (0.25), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A1688 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.012   0.001   PHE A1274 
 TYR   0.018   0.001   TYR A1125 
 ARG   0.003   0.000   ARG A1133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03456 (  606)
  hydrogen bonds       : angle       4.13058 ( 1764)
  metal coordination   : bond        0.01357 (    8)
  metal coordination   : angle       4.23280 (    9)
  SS BOND              : bond        0.00424 (    1)
  SS BOND              : angle       1.88987 (    2)
  covalent geometry    : bond        0.00344 (12031)
  covalent geometry    : angle       0.60381 (16282)

*********************** 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
  223 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 175
  time to evaluate  : 1.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 CYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7801 (m)
REVERT: B   60 VAL cc_start: 0.7525 (OUTLIER) cc_final: 0.6932 (t)
REVERT: A  420 ASN cc_start: 0.8281 (t0) cc_final: 0.8005 (t0)
REVERT: A  660 ASP cc_start: 0.7448 (t0) cc_final: 0.7193 (t0)
REVERT: A  669 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7249 (p0)
REVERT: A 1150 GLU cc_start: 0.8194 (mp0) cc_final: 0.7930 (mp0)
REVERT: A 1253 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7617 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8777 (m-10) cc_final: 0.8557 (m-10)
REVERT: A 1311 GLU cc_start: 0.7435 (tp30) cc_final: 0.6908 (tp30)
REVERT: A 1366 ASP cc_start: 0.8157 (t70) cc_final: 0.7681 (t0)
REVERT: A 1467 ASP cc_start: 0.7367 (p0) cc_final: 0.6946 (p0)
  outliers start: 48
  outliers final: 36
  residues processed: 215
  average time/residue: 0.2517
  time to fit residues: 78.6313
Evaluate side-chains
  208 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 169
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
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  193 THR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  261 VAL
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  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  718 ARG
Chi-restraints excluded: chain A residue  725 CYS
Chi-restraints excluded: chain A residue  741 ILE
Chi-restraints excluded: chain A residue  781 VAL
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 131 optimal weight:    0.1980
   chunk 59 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 76 optimal weight:    0.1980
   chunk 61 optimal weight:    0.5980
   chunk 135 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 132 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1635 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.179856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.140489 restraints weight = 25463.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 4.97
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3498
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2378

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= 0.128
  Angle     :  0.627  13.802  16293  Z= 0.305
  Chirality :  0.040   0.243   1862
  Planarity :  0.004   0.043   2028
  Dihedral  : 11.094 173.166   1709
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 17.43 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.22), residues: 1428
  helix:  1.37 (0.18), residues: 785
  sheet: -1.02 (0.63), residues: 70
  loop : -2.57 (0.24), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 394 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.011   0.001   PHE A1274 
 TYR   0.017   0.001   TYR A1125 
 ARG   0.002   0.000   ARG A1141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03386 (  606)
  hydrogen bonds       : angle       4.08958 ( 1764)
  metal coordination   : bond        0.01221 (    8)
  metal coordination   : angle       5.93445 (    9)
  SS BOND              : bond        0.00414 (    1)
  SS BOND              : angle       1.65219 (    2)
  covalent geometry    : bond        0.00292 (12031)
  covalent geometry    : angle       0.61105 (16282)

*********************** 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
  216 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 175
  time to evaluate  : 1.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   60 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.6906 (t)
REVERT: A   37 MET cc_start: 0.6137 (tpp) cc_final: 0.5891 (tpp)
REVERT: A  420 ASN cc_start: 0.8222 (t0) cc_final: 0.7962 (t0)
REVERT: A  660 ASP cc_start: 0.7413 (t0) cc_final: 0.7139 (t0)
REVERT: A  664 GLU cc_start: 0.6562 (pp20) cc_final: 0.6319 (tm-30)
REVERT: A  669 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7248 (p0)
REVERT: A  694 MET cc_start: 0.8666 (tpt) cc_final: 0.8273 (tpt)
REVERT: A  714 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7237 (mt-10)
REVERT: A  751 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7882 (tm-30)
REVERT: A 1223 ILE cc_start: 0.6901 (OUTLIER) cc_final: 0.6008 (mm)
REVERT: A 1253 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7600 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8726 (m-10) cc_final: 0.8511 (m-10)
REVERT: A 1311 GLU cc_start: 0.7568 (tp30) cc_final: 0.7053 (tp30)
REVERT: A 1467 ASP cc_start: 0.7308 (p0) cc_final: 0.6885 (p0)
REVERT: A 1810 TYR cc_start: 0.7670 (m-80) cc_final: 0.7364 (m-80)
  outliers start: 41
  outliers final: 33
  residues processed: 208
  average time/residue: 0.2421
  time to fit residues: 73.7806
Evaluate side-chains
  203 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 167
  time to evaluate  : 1.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
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  273 LEU
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  446 ILE
Chi-restraints excluded: chain A residue  475 ARG
Chi-restraints excluded: chain A residue  546 THR
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  781 VAL
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 1528 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 105 optimal weight:    0.1980
   chunk 19 optimal weight:    0.7980
   chunk 117 optimal weight:    0.0980
   chunk 119 optimal weight:    0.0980
   chunk 86 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 136 optimal weight:    0.0470
   chunk 101 optimal weight:    0.9990
   chunk 114 optimal weight:    0.7980
   chunk 112 optimal weight:    0.5980
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.2078

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 399 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.182538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.142433 restraints weight = 20641.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 3.34
r_work: 0.3227 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3182
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12040  Z= 0.118
  Angle     :  0.617  16.910  16293  Z= 0.299
  Chirality :  0.040   0.208   1862
  Planarity :  0.004   0.045   2028
  Dihedral  : 11.027 174.444   1708
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 17.96 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.22), residues: 1428
  helix:  1.41 (0.18), residues: 780
  sheet: -0.93 (0.63), residues: 70
  loop : -2.51 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 394 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.010   0.001   PHE A1274 
 TYR   0.018   0.001   TYR A1125 
 ARG   0.002   0.000   ARG A1141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03310 (  606)
  hydrogen bonds       : angle       4.05939 ( 1764)
  metal coordination   : bond        0.01147 (    8)
  metal coordination   : angle       6.22832 (    9)
  SS BOND              : bond        0.00585 (    1)
  SS BOND              : angle       1.34533 (    2)
  covalent geometry    : bond        0.00253 (12031)
  covalent geometry    : angle       0.59927 (16282)

*********************** 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: 34
    poor density    : 176
  time to evaluate  : 1.411 
Fit side-chains
   revert: symmetry clash
REVERT: B   60 VAL cc_start: 0.7721 (OUTLIER) cc_final: 0.7104 (t)
REVERT: A   37 MET cc_start: 0.6393 (tpp) cc_final: 0.6123 (tpp)
REVERT: A  420 ASN cc_start: 0.8625 (t0) cc_final: 0.8359 (t0)
REVERT: A  547 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8034 (mt-10)
REVERT: A  660 ASP cc_start: 0.8375 (t0) cc_final: 0.8055 (t0)
REVERT: A  664 GLU cc_start: 0.6676 (pp20) cc_final: 0.6301 (tm-30)
REVERT: A  669 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7778 (p0)
REVERT: A  694 MET cc_start: 0.8849 (tpt) cc_final: 0.8466 (tpt)
REVERT: A  751 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7944 (tm-30)
REVERT: A 1150 GLU cc_start: 0.8141 (mp0) cc_final: 0.7930 (mp0)
REVERT: A 1223 ILE cc_start: 0.6932 (OUTLIER) cc_final: 0.5980 (mm)
REVERT: A 1253 LYS cc_start: 0.8077 (mmmt) cc_final: 0.7620 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8796 (m-10) cc_final: 0.8515 (m-10)
REVERT: A 1290 SER cc_start: 0.8542 (t) cc_final: 0.7995 (m)
REVERT: A 1311 GLU cc_start: 0.8035 (tp30) cc_final: 0.7552 (tp30)
REVERT: A 1467 ASP cc_start: 0.8140 (p0) cc_final: 0.7645 (p0)
REVERT: A 1667 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7328 (ptm160)
  outliers start: 34
  outliers final: 24
  residues processed: 205
  average time/residue: 0.2473
  time to fit residues: 72.9029
Evaluate side-chains
  197 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 169
  time to evaluate  : 1.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  261 VAL
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  384 LEU
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  475 ARG
Chi-restraints excluded: chain A residue  546 THR
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 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 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 1667 ARG
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 89 optimal weight:    0.5980
   chunk 98 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 79 optimal weight:    0.2980
   chunk 62 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0670
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 72 optimal weight:    0.4980
   chunk 140 optimal weight:    2.9990
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 ASN
** A 399 GLN ** 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 = 0.4037 r_free = 0.4037 target = 0.181589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.143703 restraints weight = 30526.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 6.03
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3594
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3594
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12040  Z= 0.126
  Angle     :  0.615  14.627  16293  Z= 0.299
  Chirality :  0.040   0.200   1862
  Planarity :  0.004   0.043   2028
  Dihedral  : 10.948 174.176   1707
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 18.79 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.22), residues: 1428
  helix:  1.42 (0.18), residues: 781
  sheet: -1.00 (0.62), residues: 70
  loop : -2.49 (0.25), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 394 
 HIS   0.003   0.001   HIS A 443 
 PHE   0.016   0.001   PHE A 645 
 TYR   0.018   0.001   TYR A1125 
 ARG   0.003   0.000   ARG A1133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03322 (  606)
  hydrogen bonds       : angle       4.04346 ( 1764)
  metal coordination   : bond        0.01147 (    8)
  metal coordination   : angle       5.48222 (    9)
  SS BOND              : bond        0.00451 (    1)
  SS BOND              : angle       1.48961 (    2)
  covalent geometry    : bond        0.00287 (12031)
  covalent geometry    : angle       0.60085 (16282)

********************** 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
  193 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 166
  time to evaluate  : 1.964 
Fit side-chains
REVERT: B   60 VAL cc_start: 0.7262 (OUTLIER) cc_final: 0.6657 (t)
REVERT: A   37 MET cc_start: 0.6113 (tpp) cc_final: 0.5913 (tpp)
REVERT: A  359 ASP cc_start: 0.7874 (t70) cc_final: 0.7638 (t0)
REVERT: A  420 ASN cc_start: 0.8086 (t0) cc_final: 0.7793 (t0)
REVERT: A  547 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7160 (mt-10)
REVERT: A  660 ASP cc_start: 0.7555 (t0) cc_final: 0.7243 (t0)
REVERT: A  669 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7431 (p0)
REVERT: A  694 MET cc_start: 0.8619 (tpt) cc_final: 0.8315 (tpt)
REVERT: A  751 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7874 (tm-30)
REVERT: A 1223 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6017 (mm)
REVERT: A 1253 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7743 (mtmm)
REVERT: A 1276 TYR cc_start: 0.8699 (m-10) cc_final: 0.8476 (m-10)
REVERT: A 1290 SER cc_start: 0.8464 (t) cc_final: 0.7935 (m)
REVERT: A 1311 GLU cc_start: 0.7458 (tp30) cc_final: 0.6945 (tp30)
REVERT: A 1467 ASP cc_start: 0.7337 (p0) cc_final: 0.6962 (p0)
  outliers start: 27
  outliers final: 22
  residues processed: 190
  average time/residue: 0.3090
  time to fit residues: 84.3383
Evaluate side-chains
  187 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 162
  time to evaluate  : 2.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   67 CYS
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  446 ILE
Chi-restraints excluded: chain A residue  475 ARG
Chi-restraints excluded: chain A residue  546 THR
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 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 1454 ARG
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 1801 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 81 optimal weight:    0.6980
   chunk 104 optimal weight:    0.5980
   chunk 69 optimal weight:    0.5980
   chunk 54 optimal weight:    0.5980
   chunk 135 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 20 optimal weight:    0.4980
   chunk 82 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 136 optimal weight:    6.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.180603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.142333 restraints weight = 30695.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 6.37
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3586
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12040  Z= 0.134
  Angle     :  0.620  13.890  16293  Z= 0.303
  Chirality :  0.040   0.181   1862
  Planarity :  0.004   0.043   2028
  Dihedral  : 10.929 174.068   1707
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 18.57 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.22), residues: 1428
  helix:  1.43 (0.18), residues: 780
  sheet: -1.02 (0.61), residues: 70
  loop : -2.51 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 394 
 HIS   0.003   0.000   HIS A1361 
 PHE   0.014   0.001   PHE A 583 
 TYR   0.017   0.001   TYR A1125 
 ARG   0.003   0.000   ARG A1133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03379 (  606)
  hydrogen bonds       : angle       4.09872 ( 1764)
  metal coordination   : bond        0.01149 (    8)
  metal coordination   : angle       5.21203 (    9)
  SS BOND              : bond        0.00439 (    1)
  SS BOND              : angle       1.53856 (    2)
  covalent geometry    : bond        0.00309 (12031)
  covalent geometry    : angle       0.60802 (16282)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6124.81 seconds
wall clock time: 110 minutes 2.25 seconds (6602.25 seconds total)