Starting phenix.real_space_refine
on Wed Mar  4 03:07:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wll_32587/03_2026/7wll_32587.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wll_32587/03_2026/7wll_32587.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wll_32587/03_2026/7wll_32587.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wll_32587/03_2026/7wll_32587.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wll_32587/03_2026/7wll_32587.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wll_32587/03_2026/7wll_32587.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.004 sd=   0.106
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
     Ca      2      9.91       5
     P       1      5.49       5
     S      78      5.16       5
     C    6358      2.51       5
     N    1504      2.21       5
     O    1595      1.98       5
     F       2      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9540
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9111
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1135, 9100
          Classifications: {'peptide': 1135}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 31, 'TRANS': 1103}
          Chain breaks: 3
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 24
      Conformer: "B"
        Number of residues, atoms: 1135, 9100
          Classifications: {'peptide': 1135}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 31, 'TRANS': 1103}
          Chain breaks: 3
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 24
          bond proxies already assigned to first conformer: 9289
    Chain: "A"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 429
          Unusual residues: {' CA': 2, '1II': 1, '3PE': 9, 'NAG': 2, 'Y01': 7}
          Classifications: {'undetermined': 21}
          Link IDs: {None: 20}
          Unresolved non-hydrogen bonds: 341
          Unresolved non-hydrogen angles: 395
          Unresolved non-hydrogen dihedrals: 351
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'3PE:plan-1': 8, '3PE:plan-2': 8, 'Y01:plan-1': 3, 'Y01:plan-2': 1}
          Unresolved non-hydrogen planarities: 68
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE A 854 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 854 " occ=0.50
  Time building chain proxies: 4.09, per 1000 atoms: 0.43
  Number of scatterers: 9540
  At special positions: 0
  Unit cell: (111.28, 122.72, 109.2, 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)
     Ca      2     19.99
     S      78     16.00
     P       1     15.00
     F       2      9.00
     O    1595      8.00
     N    1504      7.00
     C    6358      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 239 " - pdb=" SG  CYS A 280 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 269 " - pdb=" SG  CYS A 326 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1335 " - pdb=" SG  CYS A1349 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1646 " - pdb=" SG  CYS A1652 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1691 " - pdb=" SG  CYS A1698 " 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=1, symmetry=0
  Links applied
    NAG-ASN
      " NAG A2313 " - " ASN A1345 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 886.7 milliseconds
  

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2150

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 1 sheets defined
      74.8% alpha, 0.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 77
      removed outlier: 4.243A  pdb=" N   CYS A  72 " --> pdb=" O   PRO A  68 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   LYS A  74 " --> pdb=" O   ASN A  70 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   MET A  75 " --> pdb=" O   TRP A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 98
      removed outlier: 3.566A  pdb=" N   GLU A  82 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 138
    Processing helix  chain 'A' and resid 144 through 147
    Processing helix  chain 'A' and resid 148 through 170
    Processing helix  chain 'A' and resid 177 through 191
      Proline residue:  A 185  - end of helix
      removed outlier: 3.578A  pdb=" N   ASN A 190 " --> pdb=" O   LYS A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 206
    Processing helix  chain 'A' and resid 209 through 231
      removed outlier: 4.304A  pdb=" N   PHE A 223 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 237
    Processing helix  chain 'A' and resid 318 through 323
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 343 through 355
    Processing helix  chain 'A' and resid 358 through 370
      removed outlier: 4.021A  pdb=" N   ILE A 362 " --> pdb=" O   GLY A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 386
    Processing helix  chain 'A' and resid 389 through 413
      removed outlier: 3.680A  pdb=" N   MET A 412 " --> pdb=" O   GLU A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 638
      removed outlier: 3.912A  pdb=" N   ILE A 636 " --> pdb=" O   LYS A 632 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ASP A 638 " --> pdb=" O   ARG A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 660
      removed outlier: 3.530A  pdb=" N   ILE A 659 " --> pdb=" O   VAL A 655 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   GLU A 660 " --> pdb=" O   SER A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 695
      removed outlier: 3.933A  pdb=" N   ASN A 670 " --> pdb=" O   GLU A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 695 through 702
      removed outlier: 4.337A  pdb=" N   ASN A 702 " --> pdb=" O   ASP A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 721
      removed outlier: 3.783A  pdb=" N   ILE A 706 " --> pdb=" O   ASN A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 730
    Processing helix  chain 'A' and resid 731 through 744
      removed outlier: 3.931A  pdb=" N   LEU A 735 " --> pdb=" O   THR A 732 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL A 742 " --> pdb=" O   LEU A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 784
      removed outlier: 3.674A  pdb=" N   ARG A 750 " --> pdb=" O   PRO A 746 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   LEU A 752 " --> pdb=" O   LEU A 748 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ASN A 761 " --> pdb=" O   LYS A 757 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   THR A 764 " --> pdb=" O   ASP A 760 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   PHE A 765 " --> pdb=" O   ASN A 761 " (cutoff:3.500A)
WARNING: missing atoms!
    Processing helix  chain 'A' and resid 806 through 819
    Processing helix  chain 'A' and resid 822 through 832
      removed outlier: 3.827A  pdb=" N   VAL A 826 " --> pdb=" O   ASP A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 837
      No H-bonds generated for 'chain 'A' and resid 835 through 837'
    Processing helix  chain 'A' and resid 838 through 851
      removed outlier: 3.914A  pdb=" N   PHE A 842 " --> pdb=" O   ALA A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 852 through 865
    Processing helix  chain 'A' and resid 1171 through 1188
      removed outlier: 3.701A  pdb=" N   VAL A1175 " --> pdb=" O   LEU A1171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1198 through 1227
    Processing helix  chain 'A' and resid 1238 through 1260
    Processing helix  chain 'A' and resid 1267 through 1279
    Processing helix  chain 'A' and resid 1289 through 1304
      removed outlier: 3.595A  pdb=" N   LYS A1304 " --> pdb=" O   ILE A1300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1306 through 1328
    Processing helix  chain 'A' and resid 1345 through 1353
    Processing helix  chain 'A' and resid 1366 through 1378
    Processing helix  chain 'A' and resid 1381 through 1392
      removed outlier: 3.627A  pdb=" N   ILE A1385 " --> pdb=" O   GLY A1381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1404 through 1406
      No H-bonds generated for 'chain 'A' and resid 1404 through 1406'
    Processing helix  chain 'A' and resid 1407 through 1462
      removed outlier: 4.051A  pdb=" N   LEU A1415 " --> pdb=" O   PHE A1411 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLU A1442 " --> pdb=" O   ARG A1438 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   ALA A1443 " --> pdb=" O   GLN A1439 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   GLU A1444 " --> pdb=" O   HIS A1440 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ARG A1447 " --> pdb=" O   ALA A1443 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A1454 " --> pdb=" O   GLU A1450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1486 through 1505
      removed outlier: 3.540A  pdb=" N   ASP A1490 " --> pdb=" O   SER A1486 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   PHE A1492 " --> pdb=" O   TYR A1488 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE A1493 " --> pdb=" O   LEU A1489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1512 through 1541
    Processing helix  chain 'A' and resid 1542 through 1547
      removed outlier: 3.630A  pdb=" N   PHE A1546 " --> pdb=" O   GLY A1542 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE A1547 " --> pdb=" O   LEU A1543 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1542 through 1547'
    Processing helix  chain 'A' and resid 1551 through 1575
      removed outlier: 3.589A  pdb=" N   ASP A1555 " --> pdb=" O   TRP A1551 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLU A1570 " --> pdb=" O   ILE A1566 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE A1571 " --> pdb=" O   THR A1567 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLU A1572 " --> pdb=" O   LEU A1568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1580 through 1591
      removed outlier: 3.892A  pdb=" N   ILE A1584 " --> pdb=" O   ASN A1580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1592 through 1601
      removed outlier: 3.806A  pdb=" N   LYS A1597 " --> pdb=" O   ARG A1594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1602 through 1614
    Processing helix  chain 'A' and resid 1615 through 1642
    Processing helix  chain 'A' and resid 1664 through 1676
      removed outlier: 3.601A  pdb=" N   THR A1670 " --> pdb=" O   MET A1666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1679 through 1688
    Processing helix  chain 'A' and resid 1701 through 1738
      Proline residue:  A1707  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1333 through 1334

    608 hydrogen bonds defined for protein.
    1734 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.44

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1427
        1.29 -     1.42: 2525
        1.42 -     1.55: 5558
        1.55 -     1.68: 121
        1.68 -     1.82: 127
  Bond restraints: 9758
  Sorted by residual:
  bond pdb=" C12 1II A2301 "
       pdb=" N04 1II A2301 "
    ideal  model  delta    sigma   weight residual
    1.449  1.204  0.245 2.00e-02 2.50e+03 1.50e+02
  bond pdb=" C16 1II A2301 "
       pdb=" O03 1II A2301 "
    ideal  model  delta    sigma   weight residual
    1.219  1.396 -0.177 2.00e-02 2.50e+03 7.79e+01
  bond pdb=" C21 3PE A2302 "
       pdb=" O21 3PE A2302 "
    ideal  model  delta    sigma   weight residual
    1.316  1.469 -0.153 2.00e-02 2.50e+03 5.82e+01
  bond pdb=" C31 3PE A2302 "
       pdb=" O31 3PE A2302 "
    ideal  model  delta    sigma   weight residual
    1.331  1.471 -0.140 2.00e-02 2.50e+03 4.88e+01
  bond pdb=" C   PRO A 333 "
       pdb=" O   PRO A 333 "
    ideal  model  delta    sigma   weight residual
    1.233  1.160  0.073 1.18e-02 7.18e+03 3.88e+01
  ... (remaining 9753 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.88: 13175
        5.88 -    11.76: 41
       11.76 -    17.64: 3
       17.64 -    23.52: 0
       23.52 -    29.40: 3
  Bond angle restraints: 13222
  Sorted by residual:
  angle pdb=" N   THR A1186 "
        pdb=" CA  THR A1186 "
        pdb=" C   THR A1186 "
      ideal   model   delta    sigma   weight residual
     113.50   97.99   15.51 1.23e+00 6.61e-01 1.59e+02
  angle pdb=" CAE Y01 A2312 "
        pdb=" CBI Y01 A2312 "
        pdb=" CAU Y01 A2312 "
      ideal   model   delta    sigma   weight residual
     111.22   81.82   29.40 3.00e+00 1.11e-01 9.60e+01
  angle pdb=" CAE Y01 A2312 "
        pdb=" CBI Y01 A2312 "
        pdb=" CBE Y01 A2312 "
      ideal   model   delta    sigma   weight residual
     110.21   81.25   28.96 3.00e+00 1.11e-01 9.32e+01
  angle pdb=" CA  PHE A1426 "
        pdb=" CB  PHE A1426 "
        pdb=" CG  PHE A1426 "
      ideal   model   delta    sigma   weight residual
     113.80  123.17   -9.37 1.00e+00 1.00e+00 8.77e+01
  angle pdb=" CAE Y01 A2312 "
        pdb=" CBI Y01 A2312 "
        pdb=" CBG Y01 A2312 "
      ideal   model   delta    sigma   weight residual
     112.07   88.02   24.05 3.00e+00 1.11e-01 6.43e+01
  ... (remaining 13217 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.62: 5972
       35.62 -    71.24: 188
       71.24 -   106.87: 9
      106.87 -   142.49: 1
      142.49 -   178.11: 5
  Dihedral angle restraints: 6175
    sinusoidal: 2856
      harmonic: 3319
  Sorted by residual:
  dihedral pdb=" CB  CYS A1646 "
           pdb=" SG  CYS A1646 "
           pdb=" SG  CYS A1652 "
           pdb=" CB  CYS A1652 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.65  -75.65     1      1.00e+01 1.00e-02 7.22e+01
  dihedral pdb=" CB  CYS A 239 "
           pdb=" SG  CYS A 239 "
           pdb=" SG  CYS A 280 "
           pdb=" CB  CYS A 280 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.60  -63.60     1      1.00e+01 1.00e-02 5.33e+01
  dihedral pdb=" CB  CYS A1691 "
           pdb=" SG  CYS A1691 "
           pdb=" SG  CYS A1698 "
           pdb=" CB  CYS A1698 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -38.88  -47.12     1      1.00e+01 1.00e-02 3.07e+01
  ... (remaining 6172 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.377: 1535
       0.377 -    0.753: 7
       0.753 -    1.130: 0
       1.130 -    1.506: 0
       1.506 -    1.883: 1
  Chirality restraints: 1543
  Sorted by residual:
  chirality pdb=" CBI Y01 A2312 "
            pdb=" CAU Y01 A2312 "
            pdb=" CBE Y01 A2312 "
            pdb=" CBG Y01 A2312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.94    1.05    1.88 2.00e-01 2.50e+01 8.86e+01
  chirality pdb=" CBG Y01 A2314 "
            pdb=" CAQ Y01 A2314 "
            pdb=" CBD Y01 A2314 "
            pdb=" CBI Y01 A2314 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.88    0.54 2.00e-01 2.50e+01 7.42e+00
  chirality pdb=" CBG Y01 A2315 "
            pdb=" CAQ Y01 A2315 "
            pdb=" CBD Y01 A2315 "
            pdb=" CBI Y01 A2315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.83    0.49 2.00e-01 2.50e+01 6.09e+00
  ... (remaining 1540 not shown)

  Planarity restraints: 1583
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A1426 "    0.014 2.00e-02 2.50e+03   2.85e-02 8.10e+00
        pdb=" C   PHE A1426 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   PHE A1426 "    0.019 2.00e-02 2.50e+03
        pdb=" N   VAL A1427 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A1185 "   -0.014 2.00e-02 2.50e+03   2.81e-02 7.87e+00
        pdb=" C   ILE A1185 "    0.049 2.00e-02 2.50e+03
        pdb=" O   ILE A1185 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   THR A1186 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 331 "    0.013 2.00e-02 2.50e+03   2.79e-02 7.78e+00
        pdb=" C   ALA A 331 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   ALA A 331 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASN A 332 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1580 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 95
        2.60 -     3.18: 9029
        3.18 -     3.75: 14414
        3.75 -     4.33: 19773
        4.33 -     4.90: 31754
  Nonbonded interactions: 75065
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 850 "
            pdb=" O03 1II A2301 "
     model   vdw
     2.026 3.040
  nonbonded pdb=" OE2 GLU A1445 "
            pdb=" OD1 ASP A1734 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" OH  TYR A1524 "
            pdb=" OE1 GLU A1569 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" OD1 ASN A1345 "
            pdb=" OG  SER A1347 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OG  SER A1238 "
            pdb=" OD1 ASN A1241 "
     model   vdw
     2.170 3.040
  ... (remaining 75060 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 group one per residue
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:             1.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.870
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.245   9765  Z= 0.615
  Angle     :  1.189  29.399  13235  Z= 0.600
  Chirality :  0.084   1.883   1543
  Planarity :  0.005   0.057   1582
  Dihedral  : 16.938 178.108   4010
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.28 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  0.40 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.25), residues: 1130
  helix:  0.49 (0.19), residues: 774
  sheet:  None (None), residues: 0
  loop : -1.93 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1585 
 TYR   0.015   0.002   TYR A 165 
 PHE   0.035   0.002   PHE A1181 
 TRP   0.028   0.002   TRP A 231 
 HIS   0.010   0.002   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.01218 ( 9758)
  covalent geometry    : angle       1.18847 (13222)
  SS BOND              : bond        0.00198 (    5)
  SS BOND              : angle       1.04773 (   10)
  hydrogen bonds       : bond        0.14829 (  608)
  hydrogen bonds       : angle       6.00006 ( 1734)
  Misc. bond           : bond        0.00232 (    1)
  link_NAG-ASN         : bond        0.00048 (    1)
  link_NAG-ASN         : angle       2.12582 (    3)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 235
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  124 ILE cc_start: 0.9301 (mt) cc_final: 0.8854 (mt)
REVERT: A  156 PHE cc_start: 0.9226 (t80) cc_final: 0.8984 (t80)
REVERT: A  177 ILE cc_start: 0.9273 (tt) cc_final: 0.8992 (tt)
REVERT: A  708 ASP cc_start: 0.8876 (m-30) cc_final: 0.8637 (m-30)
REVERT: A  866 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6086 (mt0)
REVERT: A 1259 LEU cc_start: 0.8962 (mm) cc_final: 0.8726 (mm)
REVERT: A 1438 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8407 (tmm-80)
REVERT: A 1592 ILE cc_start: 0.9073 (tp) cc_final: 0.8872 (tp)
REVERT: A 1601 MET cc_start: 0.8670 (mpp) cc_final: 0.7958 (mpp)
REVERT: A 1639 GLU cc_start: 0.8429 (tp30) cc_final: 0.8188 (tp30)
  outliers start: 5
  outliers final: 0
  residues processed: 240
  average time/residue: 0.0775
  time to fit residues: 27.9565
Evaluate side-chains
  192 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 190
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  866 GLN
Chi-restraints excluded: chain A residue 1438 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 761 ASN
A1183 ASN
A1424 ASN
** A1500 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 = 0.3891 r_free = 0.3891 target = 0.144777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.099558 restraints weight = 25488.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.103270 restraints weight = 10406.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.105564 restraints weight = 6569.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.106888 restraints weight = 5274.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.107334 restraints weight = 4746.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3380
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3380
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9765  Z= 0.142
  Angle     :  0.808  30.242  13235  Z= 0.373
  Chirality :  0.063   1.836   1543
  Planarity :  0.004   0.053   1582
  Dihedral  : 14.026 171.848   1897
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 11.23 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.25), residues: 1130
  helix:  0.99 (0.18), residues: 785
  sheet:  None (None), residues: 0
  loop : -1.89 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 410 
 TYR   0.017   0.001   TYR A 364 
 PHE   0.037   0.002   PHE A1181 
 TRP   0.014   0.001   TRP A1680 
 HIS   0.006   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9758)
  covalent geometry    : angle       0.80767 (13222)
  SS BOND              : bond        0.00120 (    5)
  SS BOND              : angle       0.81530 (   10)
  hydrogen bonds       : bond        0.04420 (  608)
  hydrogen bonds       : angle       4.76271 ( 1734)
  Misc. bond           : bond        0.00055 (    1)
  link_NAG-ASN         : bond        0.00160 (    1)
  link_NAG-ASN         : angle       1.06329 (    3)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 217
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  364 TYR cc_start: 0.8323 (m-10) cc_final: 0.8119 (m-10)
REVERT: A  389 MET cc_start: 0.8203 (tpp) cc_final: 0.7591 (ttt)
REVERT: A  708 ASP cc_start: 0.8859 (m-30) cc_final: 0.8653 (m-30)
REVERT: A  835 SER cc_start: 0.8688 (p) cc_final: 0.8428 (p)
REVERT: A 1436 LYS cc_start: 0.8959 (ttmm) cc_final: 0.8646 (mtpp)
REVERT: A 1592 ILE cc_start: 0.8950 (tp) cc_final: 0.8732 (tp)
REVERT: A 1601 MET cc_start: 0.8697 (mpp) cc_final: 0.7797 (mpp)
REVERT: A 1610 ASP cc_start: 0.8755 (t70) cc_final: 0.8555 (t70)
REVERT: A 1704 PHE cc_start: 0.8062 (t80) cc_final: 0.7623 (t80)
  outliers start: 20
  outliers final: 10
  residues processed: 226
  average time/residue: 0.0736
  time to fit residues: 25.6582
Evaluate side-chains
  214 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 204
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  164 GLU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  642 PHE
Chi-restraints excluded: chain A residue 1409 LEU
Chi-restraints excluded: chain A residue 1556 LEU
Chi-restraints excluded: chain A residue 1644 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 44 optimal weight:    8.9990
   chunk 83 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 109 optimal weight:    4.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1500 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.143569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.097861 restraints weight = 30504.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.101735 restraints weight = 11550.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.104200 restraints weight = 7006.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.105523 restraints weight = 5508.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.106050 restraints weight = 4929.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3353
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3353 r_free = 0.3353    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3353 r_free = 0.3353    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3353
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9765  Z= 0.160
  Angle     :  0.789  30.021  13235  Z= 0.363
  Chirality :  0.063   1.836   1543
  Planarity :  0.004   0.052   1582
  Dihedral  : 13.430 172.744   1890
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.62 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.25), residues: 1130
  helix:  1.24 (0.19), residues: 769
  sheet:  None (None), residues: 0
  loop : -1.62 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 410 
 TYR   0.013   0.001   TYR A 364 
 PHE   0.030   0.002   PHE A1246 
 TRP   0.024   0.002   TRP A1382 
 HIS   0.006   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 9758)
  covalent geometry    : angle       0.78846 (13222)
  SS BOND              : bond        0.00100 (    5)
  SS BOND              : angle       0.70847 (   10)
  hydrogen bonds       : bond        0.04184 (  608)
  hydrogen bonds       : angle       4.68600 ( 1734)
  Misc. bond           : bond        0.00114 (    1)
  link_NAG-ASN         : bond        0.00031 (    1)
  link_NAG-ASN         : angle       1.23069 (    3)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 214
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
REVERT: A  148 ASP cc_start: 0.8659 (t0) cc_final: 0.8378 (t70)
REVERT: A  157 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9133 (mp)
REVERT: A  167 LEU cc_start: 0.9456 (mm) cc_final: 0.9202 (mp)
REVERT: A  364 TYR cc_start: 0.8392 (m-10) cc_final: 0.8103 (m-10)
REVERT: A  365 TYR cc_start: 0.8463 (m-10) cc_final: 0.7926 (m-10)
REVERT: A  389 MET cc_start: 0.8135 (tpp) cc_final: 0.7513 (ttt)
REVERT: A  679 PHE cc_start: 0.9085 (m-80) cc_final: 0.8868 (m-80)
REVERT: A  708 ASP cc_start: 0.8884 (m-30) cc_final: 0.8647 (m-30)
REVERT: A 1436 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8601 (mtpp)
REVERT: A 1438 ARG cc_start: 0.8707 (ttp80) cc_final: 0.8388 (tmm-80)
REVERT: A 1564 MET cc_start: 0.9248 (mtm) cc_final: 0.8994 (mtp)
REVERT: A 1601 MET cc_start: 0.8698 (mpp) cc_final: 0.7814 (mpp)
REVERT: A 1610 ASP cc_start: 0.8690 (t70) cc_final: 0.8388 (t0)
REVERT: A 1631 PHE cc_start: 0.8563 (t80) cc_final: 0.8209 (t80)
REVERT: A 1704 PHE cc_start: 0.8102 (t80) cc_final: 0.7710 (t80)
  outliers start: 21
  outliers final: 12
  residues processed: 222
  average time/residue: 0.0721
  time to fit residues: 24.3932
Evaluate side-chains
  211 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 198
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  164 GLU
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  642 PHE
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue 1409 LEU
Chi-restraints excluded: chain A residue 1556 LEU
Chi-restraints excluded: chain A residue 1644 LEU
Chi-restraints excluded: chain A residue 1655 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 105 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 70 optimal weight:    0.2980
   chunk 88 optimal weight:    7.9990
   chunk 56 optimal weight:    8.9990
   chunk 106 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    1.8588

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

Flipped N/Q/H residues before XYZ refinement:
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.140388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.093900 restraints weight = 35582.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.097807 restraints weight = 12546.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.100298 restraints weight = 7323.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.101728 restraints weight = 5611.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.102460 restraints weight = 4943.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3295
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3295
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9765  Z= 0.189
  Angle     :  0.805  30.368  13235  Z= 0.373
  Chirality :  0.063   1.822   1543
  Planarity :  0.004   0.052   1582
  Dihedral  : 13.192 173.716   1890
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 15.01 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.25), residues: 1130
  helix:  1.24 (0.19), residues: 771
  sheet:  None (None), residues: 0
  loop : -1.69 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 410 
 TYR   0.013   0.001   TYR A 364 
 PHE   0.026   0.002   PHE A1181 
 TRP   0.024   0.002   TRP A1382 
 HIS   0.007   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 9758)
  covalent geometry    : angle       0.80520 (13222)
  SS BOND              : bond        0.00165 (    5)
  SS BOND              : angle       0.73602 (   10)
  hydrogen bonds       : bond        0.04229 (  608)
  hydrogen bonds       : angle       4.68536 ( 1734)
  Misc. bond           : bond        0.00143 (    1)
  link_NAG-ASN         : bond        0.00058 (    1)
  link_NAG-ASN         : angle       1.40763 (    3)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 205
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
REVERT: A  148 ASP cc_start: 0.8668 (t0) cc_final: 0.8359 (t70)
REVERT: A  157 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9136 (mp)
REVERT: A  365 TYR cc_start: 0.8550 (m-10) cc_final: 0.7948 (m-10)
REVERT: A  389 MET cc_start: 0.8188 (tpp) cc_final: 0.7654 (ttt)
REVERT: A 1483 MET cc_start: 0.4928 (ppp) cc_final: 0.4153 (tmm)
REVERT: A 1498 CYS cc_start: 0.9031 (m) cc_final: 0.8735 (m)
REVERT: A 1564 MET cc_start: 0.9233 (mtm) cc_final: 0.8831 (mtm)
REVERT: A 1601 MET cc_start: 0.8763 (mpp) cc_final: 0.7874 (mpp)
REVERT: A 1610 ASP cc_start: 0.8704 (t70) cc_final: 0.8412 (t70)
REVERT: A 1631 PHE cc_start: 0.8588 (t80) cc_final: 0.8287 (t80)
REVERT: A 1655 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7856 (ptm)
REVERT: A 1704 PHE cc_start: 0.8228 (t80) cc_final: 0.7843 (t80)
  outliers start: 20
  outliers final: 12
  residues processed: 215
  average time/residue: 0.0666
  time to fit residues: 22.5150
Evaluate side-chains
  204 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 190
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  164 GLU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  388 PHE
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  642 PHE
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  760 ASP
Chi-restraints excluded: chain A residue 1409 LEU
Chi-restraints excluded: chain A residue 1556 LEU
Chi-restraints excluded: chain A residue 1644 LEU
Chi-restraints excluded: chain A residue 1655 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 61 optimal weight:    8.9990
   chunk 40 optimal weight:    8.9990
   chunk 73 optimal weight:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 37 optimal weight:    0.7980
   chunk 56 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   chunk 48 optimal weight:    0.0670
   chunk 105 optimal weight:    3.9990
   overall best weight:    3.3724

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

Flipped N/Q/H residues before XYZ refinement:
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 761 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.140538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.095063 restraints weight = 32486.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.099502 restraints weight = 12236.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.100579 restraints weight = 6697.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.100854 restraints weight = 6245.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.100778 restraints weight = 5818.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3269
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062   9765  Z= 0.302
  Angle     :  0.886  30.784  13235  Z= 0.415
  Chirality :  0.066   1.826   1543
  Planarity :  0.005   0.053   1582
  Dihedral  : 13.625 173.677   1890
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 16.70 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.25), residues: 1130
  helix:  0.98 (0.18), residues: 773
  sheet:  None (None), residues: 0
  loop : -1.77 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1585 
 TYR   0.024   0.002   TYR A 364 
 PHE   0.023   0.002   PHE A1713 
 TRP   0.023   0.002   TRP A1382 
 HIS   0.009   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00715 ( 9758)
  covalent geometry    : angle       0.88561 (13222)
  SS BOND              : bond        0.00309 (    5)
  SS BOND              : angle       0.93458 (   10)
  hydrogen bonds       : bond        0.04798 (  608)
  hydrogen bonds       : angle       4.94339 ( 1734)
  Misc. bond           : bond        0.00228 (    1)
  link_NAG-ASN         : bond        0.00219 (    1)
  link_NAG-ASN         : angle       2.13382 (    3)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 191
  time to evaluate  : 0.343 
Fit side-chains
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
REVERT: A   98 MET cc_start: 0.7826 (mmm) cc_final: 0.7387 (tpt)
REVERT: A  157 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9090 (mp)
REVERT: A  164 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8108 (tp30)
REVERT: A  365 TYR cc_start: 0.8681 (m-10) cc_final: 0.8391 (m-10)
REVERT: A  389 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7900 (ttt)
REVERT: A 1564 MET cc_start: 0.9300 (mtm) cc_final: 0.8861 (mtm)
REVERT: A 1601 MET cc_start: 0.8758 (mpp) cc_final: 0.7990 (mpp)
REVERT: A 1610 ASP cc_start: 0.8768 (t70) cc_final: 0.8491 (t70)
REVERT: A 1704 PHE cc_start: 0.8331 (t80) cc_final: 0.7740 (t80)
  outliers start: 23
  outliers final: 15
  residues processed: 202
  average time/residue: 0.0660
  time to fit residues: 20.8955
Evaluate side-chains
  207 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 189
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  164 GLU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  388 PHE
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  642 PHE
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  760 ASP
Chi-restraints excluded: chain A residue 1277 LEU
Chi-restraints excluded: chain A residue 1409 LEU
Chi-restraints excluded: chain A residue 1499 LEU
Chi-restraints excluded: chain A residue 1556 LEU
Chi-restraints excluded: chain A residue 1611 THR
Chi-restraints excluded: chain A residue 1616 LEU
Chi-restraints excluded: chain A residue 1644 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 96 optimal weight:    9.9990
   chunk 91 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 84 optimal weight:   20.0000
   chunk 25 optimal weight:    0.5980
   chunk 86 optimal weight:    0.2980
   chunk 82 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.149058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.102779 restraints weight = 31782.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.106897 restraints weight = 11570.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.109520 restraints weight = 6924.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.110919 restraints weight = 5380.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.111430 restraints weight = 4791.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3419
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3419 r_free = 0.3419    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3419 r_free = 0.3419    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3419
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9765  Z= 0.123
  Angle     :  0.779  30.589  13235  Z= 0.352
  Chirality :  0.062   1.791   1543
  Planarity :  0.004   0.053   1582
  Dihedral  : 13.015 176.509   1890
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.30 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.25), residues: 1130
  helix:  1.42 (0.19), residues: 760
  sheet:  None (None), residues: 0
  loop : -1.66 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 410 
 TYR   0.016   0.001   TYR A 364 
 PHE   0.017   0.001   PHE A 772 
 TRP   0.020   0.001   TRP A1382 
 HIS   0.004   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9758)
  covalent geometry    : angle       0.77878 (13222)
  SS BOND              : bond        0.00126 (    5)
  SS BOND              : angle       0.64786 (   10)
  hydrogen bonds       : bond        0.03802 (  608)
  hydrogen bonds       : angle       4.56062 ( 1734)
  Misc. bond           : bond        0.00072 (    1)
  link_NAG-ASN         : bond        0.00247 (    1)
  link_NAG-ASN         : angle       0.84532 (    3)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 206
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
REVERT: A  115 LEU cc_start: 0.9326 (mm) cc_final: 0.9039 (mm)
REVERT: A  148 ASP cc_start: 0.8639 (t0) cc_final: 0.8226 (t70)
REVERT: A  157 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9112 (mp)
REVERT: A  208 MET cc_start: 0.8595 (mpp) cc_final: 0.8386 (mpp)
REVERT: A  389 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7622 (ttt)
REVERT: A  835 SER cc_start: 0.8548 (p) cc_final: 0.8328 (p)
REVERT: A 1174 TYR cc_start: 0.8314 (m-80) cc_final: 0.7915 (m-80)
REVERT: A 1483 MET cc_start: 0.4715 (ppp) cc_final: 0.4342 (tmm)
REVERT: A 1564 MET cc_start: 0.9169 (mtm) cc_final: 0.8943 (mtp)
REVERT: A 1601 MET cc_start: 0.8639 (mpp) cc_final: 0.7866 (mpp)
REVERT: A 1631 PHE cc_start: 0.8378 (t80) cc_final: 0.7974 (t80)
REVERT: A 1687 THR cc_start: 0.9402 (t) cc_final: 0.9139 (t)
REVERT: A 1704 PHE cc_start: 0.8194 (t80) cc_final: 0.7634 (t80)
  outliers start: 23
  outliers final: 11
  residues processed: 218
  average time/residue: 0.0684
  time to fit residues: 23.1335
Evaluate side-chains
  210 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 197
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  164 GLU
Chi-restraints excluded: chain A residue  359 TRP
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  642 PHE
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  760 ASP
Chi-restraints excluded: chain A residue 1409 LEU
Chi-restraints excluded: chain A residue 1644 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 101 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 95 optimal weight:   10.0000
   chunk 84 optimal weight:   20.0000
   chunk 72 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 49 optimal weight:    0.4980
   chunk 88 optimal weight:    6.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 761 ASN
A1365 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.145887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.099896 restraints weight = 30132.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.103884 restraints weight = 11399.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.106384 restraints weight = 6964.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.107745 restraints weight = 5498.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.108266 restraints weight = 4936.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3392
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3392 r_free = 0.3392    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3392 r_free = 0.3392    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3392
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9765  Z= 0.139
  Angle     :  0.798  30.318  13235  Z= 0.361
  Chirality :  0.062   1.806   1543
  Planarity :  0.005   0.105   1582
  Dihedral  : 12.997 175.470   1890
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 17.79 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.25), residues: 1130
  helix:  1.46 (0.19), residues: 760
  sheet:  None (None), residues: 0
  loop : -1.60 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A1585 
 TYR   0.020   0.001   TYR A 364 
 PHE   0.016   0.001   PHE A 772 
 TRP   0.018   0.001   TRP A1382 
 HIS   0.005   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9758)
  covalent geometry    : angle       0.79761 (13222)
  SS BOND              : bond        0.00103 (    5)
  SS BOND              : angle       0.59186 (   10)
  hydrogen bonds       : bond        0.03839 (  608)
  hydrogen bonds       : angle       4.51172 ( 1734)
  Misc. bond           : bond        0.00302 (    1)
  link_NAG-ASN         : bond        0.00116 (    1)
  link_NAG-ASN         : angle       0.96980 (    3)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 201
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
REVERT: A  115 LEU cc_start: 0.9371 (mm) cc_final: 0.9076 (mm)
REVERT: A  148 ASP cc_start: 0.8626 (t0) cc_final: 0.8236 (t70)
REVERT: A  157 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9146 (mp)
REVERT: A  389 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7641 (ttt)
REVERT: A  835 SER cc_start: 0.8617 (p) cc_final: 0.8409 (p)
REVERT: A 1274 LEU cc_start: 0.9020 (mt) cc_final: 0.8803 (mt)
REVERT: A 1483 MET cc_start: 0.4622 (ppp) cc_final: 0.3947 (tmm)
REVERT: A 1564 MET cc_start: 0.9116 (mtm) cc_final: 0.8901 (mtp)
REVERT: A 1601 MET cc_start: 0.8603 (mpp) cc_final: 0.7860 (mpp)
REVERT: A 1687 THR cc_start: 0.9443 (t) cc_final: 0.9184 (t)
  outliers start: 21
  outliers final: 16
  residues processed: 210
  average time/residue: 0.0691
  time to fit residues: 22.6642
Evaluate side-chains
  212 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 194
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  164 GLU
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  359 TRP
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  642 PHE
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  760 ASP
Chi-restraints excluded: chain A residue  831 MET
Chi-restraints excluded: chain A residue 1409 LEU
Chi-restraints excluded: chain A residue 1499 LEU
Chi-restraints excluded: chain A residue 1556 LEU
Chi-restraints excluded: chain A residue 1644 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 44 optimal weight:    7.9990
   chunk 56 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 108 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1365 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.142522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.095932 restraints weight = 32254.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.099833 restraints weight = 11904.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.102295 restraints weight = 7203.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.103401 restraints weight = 5666.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.104279 restraints weight = 5120.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3340
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3340
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   9765  Z= 0.242
  Angle     :  0.872  30.656  13235  Z= 0.404
  Chirality :  0.065   1.820   1543
  Planarity :  0.005   0.100   1582
  Dihedral  : 13.268 174.970   1890
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 18.69 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.26), residues: 1130
  helix:  1.31 (0.19), residues: 764
  sheet:  None (None), residues: 0
  loop : -1.60 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A1585 
 TYR   0.027   0.002   TYR A 364 
 PHE   0.020   0.002   PHE A 772 
 TRP   0.015   0.002   TRP A1382 
 HIS   0.008   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 ( 9758)
  covalent geometry    : angle       0.87163 (13222)
  SS BOND              : bond        0.00231 (    5)
  SS BOND              : angle       0.82633 (   10)
  hydrogen bonds       : bond        0.04426 (  608)
  hydrogen bonds       : angle       4.71610 ( 1734)
  Misc. bond           : bond        0.00437 (    1)
  link_NAG-ASN         : bond        0.00068 (    1)
  link_NAG-ASN         : angle       1.69896 (    3)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 198
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
REVERT: A  115 LEU cc_start: 0.9377 (mm) cc_final: 0.9093 (mm)
REVERT: A  157 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9158 (mp)
REVERT: A  389 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7831 (ttt)
REVERT: A 1483 MET cc_start: 0.4472 (ppp) cc_final: 0.3738 (tmm)
REVERT: A 1564 MET cc_start: 0.9153 (mtm) cc_final: 0.8931 (mtp)
REVERT: A 1601 MET cc_start: 0.8621 (mpp) cc_final: 0.8048 (mpp)
REVERT: A 1731 LYS cc_start: 0.8691 (tptt) cc_final: 0.7933 (ttmm)
  outliers start: 19
  outliers final: 16
  residues processed: 205
  average time/residue: 0.0699
  time to fit residues: 22.1997
Evaluate side-chains
  211 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 193
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  164 GLU
Chi-restraints excluded: chain A residue  359 TRP
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  642 PHE
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  760 ASP
Chi-restraints excluded: chain A residue 1277 LEU
Chi-restraints excluded: chain A residue 1409 LEU
Chi-restraints excluded: chain A residue 1499 LEU
Chi-restraints excluded: chain A residue 1556 LEU
Chi-restraints excluded: chain A residue 1611 THR
Chi-restraints excluded: chain A residue 1644 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 87 optimal weight:   10.0000
   chunk 54 optimal weight:    0.6980
   chunk 105 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 89 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A1435 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.146267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.099690 restraints weight = 33909.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.103790 restraints weight = 12008.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.106396 restraints weight = 7101.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.107868 restraints weight = 5514.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.108224 restraints weight = 4902.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3392
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3392 r_free = 0.3392    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3392 r_free = 0.3392    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3392
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9765  Z= 0.135
  Angle     :  0.809  30.580  13235  Z= 0.368
  Chirality :  0.062   1.796   1543
  Planarity :  0.004   0.066   1582
  Dihedral  : 12.939 176.728   1890
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 19.09 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.26), residues: 1130
  helix:  1.47 (0.19), residues: 762
  sheet:  None (None), residues: 0
  loop : -1.57 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A1585 
 TYR   0.019   0.001   TYR A 364 
 PHE   0.020   0.001   PHE A1546 
 TRP   0.017   0.001   TRP A1382 
 HIS   0.004   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9758)
  covalent geometry    : angle       0.80920 (13222)
  SS BOND              : bond        0.00110 (    5)
  SS BOND              : angle       0.64230 (   10)
  hydrogen bonds       : bond        0.03815 (  608)
  hydrogen bonds       : angle       4.48692 ( 1734)
  Misc. bond           : bond        0.00287 (    1)
  link_NAG-ASN         : bond        0.00202 (    1)
  link_NAG-ASN         : angle       0.92153 (    3)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 200
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
REVERT: A   75 MET cc_start: 0.7957 (mpp) cc_final: 0.7461 (ptp)
REVERT: A  115 LEU cc_start: 0.9374 (mm) cc_final: 0.9100 (mm)
REVERT: A  157 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9128 (mp)
REVERT: A  389 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7614 (ttt)
REVERT: A  694 PHE cc_start: 0.6744 (t80) cc_final: 0.6354 (t80)
REVERT: A 1174 TYR cc_start: 0.8372 (m-10) cc_final: 0.7954 (m-80)
REVERT: A 1274 LEU cc_start: 0.9022 (mt) cc_final: 0.8809 (mt)
REVERT: A 1483 MET cc_start: 0.4435 (ppp) cc_final: 0.3941 (tmm)
REVERT: A 1601 MET cc_start: 0.8552 (mpp) cc_final: 0.8017 (mpp)
REVERT: A 1704 PHE cc_start: 0.8079 (t80) cc_final: 0.7529 (t80)
REVERT: A 1731 LYS cc_start: 0.8600 (tptt) cc_final: 0.7823 (ttmm)
  outliers start: 19
  outliers final: 14
  residues processed: 208
  average time/residue: 0.0695
  time to fit residues: 22.4786
Evaluate side-chains
  211 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 195
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  164 GLU
Chi-restraints excluded: chain A residue  359 TRP
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  642 PHE
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  760 ASP
Chi-restraints excluded: chain A residue 1259 LEU
Chi-restraints excluded: chain A residue 1409 LEU
Chi-restraints excluded: chain A residue 1435 HIS
Chi-restraints excluded: chain A residue 1499 LEU
Chi-restraints excluded: chain A residue 1644 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 106 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 87 optimal weight:   10.0000
   chunk 93 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 111 optimal weight:    0.5980
   chunk 52 optimal weight:    0.3980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A1365 ASN
A1435 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.146658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.100681 restraints weight = 37822.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.106177 restraints weight = 13077.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.106591 restraints weight = 6386.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.106714 restraints weight = 6661.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.107179 restraints weight = 6190.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3356
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3356 r_free = 0.3356    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3356 r_free = 0.3356    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3356
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.3046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9765  Z= 0.134
  Angle     :  0.825  30.318  13235  Z= 0.375
  Chirality :  0.063   1.802   1543
  Planarity :  0.004   0.063   1582
  Dihedral  : 12.848 176.104   1890
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 20.28 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.26), residues: 1130
  helix:  1.52 (0.19), residues: 762
  sheet:  None (None), residues: 0
  loop : -1.59 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1585 
 TYR   0.022   0.001   TYR A 364 
 PHE   0.027   0.002   PHE A1546 
 TRP   0.015   0.001   TRP A1382 
 HIS   0.004   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9758)
  covalent geometry    : angle       0.82560 (13222)
  SS BOND              : bond        0.00095 (    5)
  SS BOND              : angle       0.57810 (   10)
  hydrogen bonds       : bond        0.03783 (  608)
  hydrogen bonds       : angle       4.45652 ( 1734)
  Misc. bond           : bond        0.00268 (    1)
  link_NAG-ASN         : bond        0.00197 (    1)
  link_NAG-ASN         : angle       0.85600 (    3)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 200
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
REVERT: A   75 MET cc_start: 0.8079 (mpp) cc_final: 0.7698 (ptp)
REVERT: A  115 LEU cc_start: 0.9328 (mm) cc_final: 0.9085 (mm)
REVERT: A  157 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9091 (mp)
REVERT: A  389 MET cc_start: 0.8127 (tpp) cc_final: 0.7705 (ttt)
REVERT: A  694 PHE cc_start: 0.6645 (t80) cc_final: 0.6282 (t80)
REVERT: A 1174 TYR cc_start: 0.8406 (m-10) cc_final: 0.8041 (m-80)
REVERT: A 1274 LEU cc_start: 0.8994 (mt) cc_final: 0.8781 (mt)
REVERT: A 1483 MET cc_start: 0.4668 (ppp) cc_final: 0.4013 (tmm)
REVERT: A 1601 MET cc_start: 0.8609 (mpp) cc_final: 0.8033 (mpp)
REVERT: A 1704 PHE cc_start: 0.8157 (t80) cc_final: 0.7626 (t80)
REVERT: A 1731 LYS cc_start: 0.8574 (tptt) cc_final: 0.7975 (ttmm)
  outliers start: 15
  outliers final: 13
  residues processed: 208
  average time/residue: 0.0723
  time to fit residues: 23.4743
Evaluate side-chains
  212 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 198
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  155 PHE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  359 TRP
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  642 PHE
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  760 ASP
Chi-restraints excluded: chain A residue 1259 LEU
Chi-restraints excluded: chain A residue 1409 LEU
Chi-restraints excluded: chain A residue 1435 HIS
Chi-restraints excluded: chain A residue 1499 LEU
Chi-restraints excluded: chain A residue 1644 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0970
   chunk 111 optimal weight:    0.6980
   chunk 94 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0000
   chunk 58 optimal weight:    4.9990
   chunk 107 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.4382

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

Flipped N/Q/H residues before XYZ refinement:
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1365 ASN
A1435 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.147983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.101778 restraints weight = 37934.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.107407 restraints weight = 13208.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.107900 restraints weight = 6473.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107914 restraints weight = 6652.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.108327 restraints weight = 6256.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3371
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3371
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9765  Z= 0.125
  Angle     :  0.817  30.305  13235  Z= 0.368
  Chirality :  0.062   1.798   1543
  Planarity :  0.004   0.054   1582
  Dihedral  : 12.732 176.632   1890
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 19.78 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.26), residues: 1130
  helix:  1.57 (0.19), residues: 761
  sheet:  None (None), residues: 0
  loop : -1.55 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1585 
 TYR   0.018   0.001   TYR A 364 
 PHE   0.028   0.001   PHE A1546 
 TRP   0.016   0.001   TRP A1382 
 HIS   0.005   0.001   HIS A1435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9758)
  covalent geometry    : angle       0.81711 (13222)
  SS BOND              : bond        0.00074 (    5)
  SS BOND              : angle       0.54529 (   10)
  hydrogen bonds       : bond        0.03637 (  608)
  hydrogen bonds       : angle       4.38934 ( 1734)
  Misc. bond           : bond        0.00239 (    1)
  link_NAG-ASN         : bond        0.00240 (    1)
  link_NAG-ASN         : angle       0.73235 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1946.90 seconds
wall clock time: 34 minutes 5.26 seconds (2045.26 seconds total)