Starting phenix.real_space_refine
on Mon Jun  9 07:10:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wll_32587/06_2025/7wll_32587.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wll_32587/06_2025/7wll_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_32587/06_2025/7wll_32587.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wll_32587/06_2025/7wll_32587.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wll_32587/06_2025/7wll_32587.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wll_32587/06_2025/7wll_32587.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.004 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'ARG:plan': 3, 'TRP:plan': 1}
          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: {'ARG:plan': 3, 'TRP:plan': 1}
          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: {'Y01:plan-2': 1, '3PE:plan-1': 8, '3PE:plan-2': 8, 'Y01:plan-1': 3}
          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: 10.88, per 1000 atoms: 1.14
  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: 2.74
  Conformation dependent library (CDL) restraints added in 2.4 seconds
  

  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: 0.85
  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: 2.89

  Time building geometry restraints manager: 3.13 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:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     32.040
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.060
  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:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.010
-------------------------------------------------------------------------------
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 : 13.97
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (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
 TRP   0.028   0.002   TRP A 231 
 HIS   0.010   0.002   HIS A1169 
 PHE   0.035   0.002   PHE A1181 
 TYR   0.015   0.002   TYR A 165 
 ARG   0.008   0.001   ARG A1585 

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

*********************** 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  : 1.007 
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: 0.1867
  time to fit residues: 65.8135
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  : 1.083 
-------------------------------------------------------------------------------
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 95 optimal weight:    0.9990
   chunk 85 optimal weight:   10.0000
   chunk 47 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:    0.2980
   chunk 88 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0570
   chunk 53 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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
** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.145363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.100705 restraints weight = 22944.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.104301 restraints weight = 9794.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.106564 restraints weight = 6329.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3367
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3367
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9765  Z= 0.138
  Angle     :  0.809  30.057  13235  Z= 0.373
  Chirality :  0.064   1.847   1543
  Planarity :  0.004   0.053   1582
  Dihedral  : 14.059 171.349   1897
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 11.03 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.25), residues: 1130
  helix:  1.01 (0.18), residues: 785
  sheet:  None (None), residues: 0
  loop : -1.88 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1680 
 HIS   0.006   0.001   HIS A1169 
 PHE   0.036   0.002   PHE A1181 
 TYR   0.017   0.001   TYR A 364 
 ARG   0.006   0.001   ARG A 410 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00164 (    1)
  link_NAG-ASN         : angle       0.96610 (    3)
  hydrogen bonds       : bond        0.04470 (  608)
  hydrogen bonds       : angle       4.75961 ( 1734)
  SS BOND              : bond        0.00120 (    5)
  SS BOND              : angle       0.79802 (   10)
  covalent geometry    : bond        0.00294 ( 9758)
  covalent geometry    : angle       0.80908 (13222)
  Misc. bond           : bond        0.00036 (    1)

*********************** 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: 18
    poor density    : 219
  time to evaluate  : 1.190 
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  389 MET cc_start: 0.8239 (tpp) cc_final: 0.7617 (ttt)
REVERT: A  708 ASP cc_start: 0.8878 (m-30) cc_final: 0.8657 (m-30)
REVERT: A  835 SER cc_start: 0.8680 (p) cc_final: 0.8416 (p)
REVERT: A 1436 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8613 (mtpp)
REVERT: A 1592 ILE cc_start: 0.8941 (tp) cc_final: 0.8724 (tp)
REVERT: A 1601 MET cc_start: 0.8705 (mpp) cc_final: 0.7812 (mpp)
REVERT: A 1704 PHE cc_start: 0.8046 (t80) cc_final: 0.7606 (t80)
  outliers start: 18
  outliers final: 11
  residues processed: 227
  average time/residue: 0.1973
  time to fit residues: 68.7965
Evaluate side-chains
  211 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 200
  time to evaluate  : 1.457 
-------------------------------------------------------------------------------
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 1435 HIS
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 24 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0270
   chunk 69 optimal weight:    0.8980
   chunk 89 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 36 optimal weight:    9.9990
   overall best weight:    0.6838

-------------------------------------------------------------------------------
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 = 0.3901 r_free = 0.3901 target = 0.145664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.101432 restraints weight = 28072.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.105788 restraints weight = 11505.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.106590 restraints weight = 6559.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3349
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3349
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9765  Z= 0.132
  Angle     :  0.779  30.202  13235  Z= 0.356
  Chirality :  0.063   1.836   1543
  Planarity :  0.004   0.052   1582
  Dihedral  : 13.342 172.679   1890
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.12 %
    Favored  : 84.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.25), residues: 1130
  helix:  1.33 (0.19), residues: 767
  sheet:  None (None), residues: 0
  loop : -1.61 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A1382 
 HIS   0.005   0.001   HIS A1169 
 PHE   0.029   0.001   PHE A1246 
 TYR   0.018   0.001   TYR A 364 
 ARG   0.005   0.000   ARG A 410 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00073 (    1)
  link_NAG-ASN         : angle       0.91244 (    3)
  hydrogen bonds       : bond        0.03996 (  608)
  hydrogen bonds       : angle       4.60488 ( 1734)
  SS BOND              : bond        0.00073 (    5)
  SS BOND              : angle       0.64066 (   10)
  covalent geometry    : bond        0.00297 ( 9758)
  covalent geometry    : angle       0.77929 (13222)
  Misc. bond           : bond        0.00067 (    1)

*********************** 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
  234 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 212
  time to evaluate  : 1.140 
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: 0.8639 (t0) cc_final: 0.8237 (t70)
REVERT: A  157 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9076 (mp)
REVERT: A  365 TYR cc_start: 0.8342 (m-10) cc_final: 0.8105 (m-10)
REVERT: A  389 MET cc_start: 0.8167 (tpp) cc_final: 0.7546 (ttt)
REVERT: A  708 ASP cc_start: 0.8906 (m-30) cc_final: 0.8651 (m-30)
REVERT: A  835 SER cc_start: 0.8654 (p) cc_final: 0.8387 (p)
REVERT: A 1436 LYS cc_start: 0.8811 (ttmm) cc_final: 0.8565 (mtpp)
REVERT: A 1438 ARG cc_start: 0.8697 (ttp80) cc_final: 0.8311 (tmm-80)
REVERT: A 1592 ILE cc_start: 0.8886 (tp) cc_final: 0.8683 (tp)
REVERT: A 1601 MET cc_start: 0.8706 (mpp) cc_final: 0.7805 (mpp)
REVERT: A 1704 PHE cc_start: 0.8093 (t80) cc_final: 0.7675 (t80)
  outliers start: 22
  outliers final: 10
  residues processed: 220
  average time/residue: 0.2050
  time to fit residues: 68.1403
Evaluate side-chains
  209 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 198
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
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 1409 LEU
Chi-restraints excluded: chain A residue 1556 LEU
Chi-restraints excluded: chain A residue 1644 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 18 optimal weight:    0.0060
   chunk 112 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 84 optimal weight:   20.0000
   chunk 104 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0050
   chunk 49 optimal weight:    0.3980
   overall best weight:    0.4010

-------------------------------------------------------------------------------
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 = 0.3964 r_free = 0.3964 target = 0.151243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.105899 restraints weight = 33819.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.110362 restraints weight = 12310.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.110619 restraints weight = 6625.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3399
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3399
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9765  Z= 0.122
  Angle     :  0.769  30.318  13235  Z= 0.350
  Chirality :  0.062   1.821   1543
  Planarity :  0.004   0.052   1582
  Dihedral  : 12.830 174.180   1890
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.71 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.25), residues: 1130
  helix:  1.46 (0.19), residues: 758
  sheet:  None (None), residues: 0
  loop : -1.57 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A1382 
 HIS   0.004   0.001   HIS A1169 
 PHE   0.024   0.001   PHE A1181 
 TYR   0.017   0.001   TYR A 364 
 ARG   0.005   0.000   ARG A 410 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00132 (    1)
  link_NAG-ASN         : angle       0.80580 (    3)
  hydrogen bonds       : bond        0.03699 (  608)
  hydrogen bonds       : angle       4.50814 ( 1734)
  SS BOND              : bond        0.00050 (    5)
  SS BOND              : angle       0.54198 (   10)
  covalent geometry    : bond        0.00258 ( 9758)
  covalent geometry    : angle       0.76898 (13222)
  Misc. bond           : bond        0.00069 (    1)

*********************** 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
  232 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 213
  time to evaluate  : 0.977 
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: 0.8593 (t0) cc_final: 0.8166 (t70)
REVERT: A  157 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.9084 (mp)
REVERT: A  389 MET cc_start: 0.8109 (tpp) cc_final: 0.7530 (ttt)
REVERT: A  708 ASP cc_start: 0.8749 (m-30) cc_final: 0.8525 (m-30)
REVERT: A  835 SER cc_start: 0.8597 (p) cc_final: 0.8330 (p)
REVERT: A 1311 LEU cc_start: 0.9180 (tp) cc_final: 0.8534 (mt)
REVERT: A 1436 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8462 (mtpp)
REVERT: A 1438 ARG cc_start: 0.8627 (ttp80) cc_final: 0.8235 (tmm-80)
REVERT: A 1483 MET cc_start: 0.5034 (ppp) cc_final: 0.4332 (tmm)
REVERT: A 1564 MET cc_start: 0.9284 (mtm) cc_final: 0.9059 (mtp)
REVERT: A 1592 ILE cc_start: 0.8896 (tp) cc_final: 0.8669 (tp)
REVERT: A 1601 MET cc_start: 0.8744 (mpp) cc_final: 0.7824 (mpp)
REVERT: A 1704 PHE cc_start: 0.8100 (t80) cc_final: 0.7727 (t80)
  outliers start: 19
  outliers final: 12
  residues processed: 224
  average time/residue: 0.1757
  time to fit residues: 58.7472
Evaluate side-chains
  215 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 202
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
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  760 ASP
Chi-restraints excluded: chain A residue 1376 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 70 optimal weight:    0.1980
   chunk 4 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0870
   chunk 72 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    0.8562

-------------------------------------------------------------------------------
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 = 0.3935 r_free = 0.3935 target = 0.147838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.101650 restraints weight = 34583.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.105807 restraints weight = 12126.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.108457 restraints weight = 7101.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3396
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3396 r_free = 0.3396    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3396 r_free = 0.3396    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3396
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2653

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= 0.129
  Angle     :  0.761  30.179  13235  Z= 0.346
  Chirality :  0.062   1.816   1543
  Planarity :  0.004   0.051   1582
  Dihedral  : 12.650 174.714   1890
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.40 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.25), residues: 1130
  helix:  1.54 (0.19), residues: 759
  sheet:  None (None), residues: 0
  loop : -1.50 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1382 
 HIS   0.004   0.001   HIS A1169 
 PHE   0.017   0.001   PHE A 679 
 TYR   0.019   0.001   TYR A 364 
 ARG   0.005   0.000   ARG A1288 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00076 (    1)
  link_NAG-ASN         : angle       0.91770 (    3)
  hydrogen bonds       : bond        0.03691 (  608)
  hydrogen bonds       : angle       4.44963 ( 1734)
  SS BOND              : bond        0.00060 (    5)
  SS BOND              : angle       0.56614 (   10)
  covalent geometry    : bond        0.00291 ( 9758)
  covalent geometry    : angle       0.76073 (13222)
  Misc. bond           : bond        0.00057 (    1)

*********************** 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
  230 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 210
  time to evaluate  : 1.083 
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: 0.8537 (t0) cc_final: 0.8169 (t70)
REVERT: A  157 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9135 (mp)
REVERT: A  389 MET cc_start: 0.8141 (tpp) cc_final: 0.7607 (ttt)
REVERT: A  694 PHE cc_start: 0.6518 (t80) cc_final: 0.6094 (t80)
REVERT: A  708 ASP cc_start: 0.8705 (m-30) cc_final: 0.8491 (m-30)
REVERT: A  835 SER cc_start: 0.8630 (p) cc_final: 0.8374 (p)
REVERT: A 1288 ARG cc_start: 0.8611 (mtt90) cc_final: 0.8375 (mmt-90)
REVERT: A 1438 ARG cc_start: 0.8654 (ttp80) cc_final: 0.8317 (tmm-80)
REVERT: A 1564 MET cc_start: 0.9201 (mtm) cc_final: 0.8985 (mtp)
REVERT: A 1592 ILE cc_start: 0.8936 (tp) cc_final: 0.8685 (tp)
REVERT: A 1601 MET cc_start: 0.8778 (mpp) cc_final: 0.7868 (mpp)
REVERT: A 1704 PHE cc_start: 0.8120 (t80) cc_final: 0.7577 (t80)
  outliers start: 20
  outliers final: 15
  residues processed: 220
  average time/residue: 0.1891
  time to fit residues: 63.2919
Evaluate side-chains
  221 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 205
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
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  748 LEU
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  760 ASP
Chi-restraints excluded: chain A residue 1376 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 1644 LEU
Chi-restraints excluded: chain A residue 1655 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 61 optimal weight:    8.9990
   chunk 72 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.9186

-------------------------------------------------------------------------------
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 = 0.3932 r_free = 0.3932 target = 0.147803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.101273 restraints weight = 34632.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.105396 restraints weight = 12249.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.108081 restraints weight = 7218.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3391
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3391 r_free = 0.3391    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3391 r_free = 0.3391    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3391
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.2736

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= 0.131
  Angle     :  0.779  30.265  13235  Z= 0.352
  Chirality :  0.062   1.807   1543
  Planarity :  0.004   0.050   1582
  Dihedral  : 12.547 175.232   1890
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 16.20 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.26), residues: 1130
  helix:  1.60 (0.19), residues: 761
  sheet:  None (None), residues: 0
  loop : -1.48 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1382 
 HIS   0.004   0.001   HIS A1169 
 PHE   0.024   0.001   PHE A1181 
 TYR   0.018   0.001   TYR A 364 
 ARG   0.004   0.000   ARG A 410 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00089 (    1)
  link_NAG-ASN         : angle       0.92568 (    3)
  hydrogen bonds       : bond        0.03645 (  608)
  hydrogen bonds       : angle       4.39751 ( 1734)
  SS BOND              : bond        0.00074 (    5)
  SS BOND              : angle       0.53334 (   10)
  covalent geometry    : bond        0.00295 ( 9758)
  covalent geometry    : angle       0.77947 (13222)
  Misc. bond           : bond        0.00090 (    1)

*********************** 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
  231 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 209
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
REVERT: A  111 ARG cc_start: 0.5664 (mmt180) cc_final: 0.5358 (ttm110)
REVERT: A  148 ASP cc_start: 0.8569 (t0) cc_final: 0.8194 (t70)
REVERT: A  157 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9123 (mp)
REVERT: A  389 MET cc_start: 0.8134 (tpp) cc_final: 0.7618 (ttt)
REVERT: A  694 PHE cc_start: 0.6365 (t80) cc_final: 0.5745 (t80)
REVERT: A  708 ASP cc_start: 0.8698 (m-30) cc_final: 0.8487 (m-30)
REVERT: A  835 SER cc_start: 0.8627 (p) cc_final: 0.8393 (p)
REVERT: A 1438 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8310 (tmm-80)
REVERT: A 1483 MET cc_start: 0.4459 (ppp) cc_final: 0.3982 (tmm)
REVERT: A 1490 ASP cc_start: 0.8910 (m-30) cc_final: 0.8698 (m-30)
REVERT: A 1564 MET cc_start: 0.9183 (mtm) cc_final: 0.8968 (mtp)
REVERT: A 1586 ILE cc_start: 0.6224 (tp) cc_final: 0.5722 (tp)
REVERT: A 1592 ILE cc_start: 0.8972 (tp) cc_final: 0.8742 (tp)
REVERT: A 1601 MET cc_start: 0.8736 (mpp) cc_final: 0.7884 (mpp)
REVERT: A 1631 PHE cc_start: 0.8390 (t80) cc_final: 0.7990 (t80)
REVERT: A 1731 LYS cc_start: 0.8460 (tptt) cc_final: 0.8051 (tptp)
  outliers start: 22
  outliers final: 14
  residues processed: 220
  average time/residue: 0.1861
  time to fit residues: 61.6354
Evaluate side-chains
  216 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 201
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
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  760 ASP
Chi-restraints excluded: chain A residue 1376 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 1644 LEU
Chi-restraints excluded: chain A residue 1655 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 77 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 97 optimal weight:    8.9990
   chunk 89 optimal weight:    5.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3917 r_free = 0.3917 target = 0.146563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.102812 restraints weight = 23668.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.106368 restraints weight = 11224.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.107033 restraints weight = 6806.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3355
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3355
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9765  Z= 0.152
  Angle     :  0.792  30.374  13235  Z= 0.362
  Chirality :  0.063   1.807   1543
  Planarity :  0.004   0.050   1582
  Dihedral  : 12.575 175.110   1890
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 16.70 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.26), residues: 1130
  helix:  1.55 (0.19), residues: 761
  sheet:  None (None), residues: 0
  loop : -1.51 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1382 
 HIS   0.005   0.001   HIS A1169 
 PHE   0.022   0.001   PHE A1181 
 TYR   0.019   0.001   TYR A 364 
 ARG   0.004   0.000   ARG A1288 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00056 (    1)
  link_NAG-ASN         : angle       1.05617 (    3)
  hydrogen bonds       : bond        0.03821 (  608)
  hydrogen bonds       : angle       4.44592 ( 1734)
  SS BOND              : bond        0.00102 (    5)
  SS BOND              : angle       0.56870 (   10)
  covalent geometry    : bond        0.00353 ( 9758)
  covalent geometry    : angle       0.79215 (13222)
  Misc. bond           : bond        0.00106 (    1)

*********************** 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
  226 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 204
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
REVERT: A  157 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.9077 (mp)
REVERT: A  389 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7764 (ttt)
REVERT: A  694 PHE cc_start: 0.6437 (t80) cc_final: 0.5846 (t80)
REVERT: A  708 ASP cc_start: 0.8782 (m-30) cc_final: 0.8562 (m-30)
REVERT: A 1483 MET cc_start: 0.4550 (ppp) cc_final: 0.4024 (tmm)
REVERT: A 1490 ASP cc_start: 0.8918 (m-30) cc_final: 0.8709 (m-30)
REVERT: A 1586 ILE cc_start: 0.6063 (tp) cc_final: 0.5771 (tp)
REVERT: A 1592 ILE cc_start: 0.8934 (tp) cc_final: 0.8698 (tp)
REVERT: A 1601 MET cc_start: 0.8737 (mpp) cc_final: 0.7847 (mpp)
REVERT: A 1631 PHE cc_start: 0.8417 (t80) cc_final: 0.8055 (t80)
REVERT: A 1731 LYS cc_start: 0.8423 (tptt) cc_final: 0.8018 (tptp)
  outliers start: 22
  outliers final: 17
  residues processed: 215
  average time/residue: 0.2042
  time to fit residues: 67.9408
Evaluate side-chains
  218 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 199
  time to evaluate  : 1.367 
-------------------------------------------------------------------------------
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  389 MET
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  642 PHE
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  760 ASP
Chi-restraints excluded: chain A residue 1376 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 1616 LEU
Chi-restraints excluded: chain A residue 1644 LEU
Chi-restraints excluded: chain A residue 1655 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 39 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0980
   chunk 87 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9990
   chunk 104 optimal weight:    0.0770
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.5140

-------------------------------------------------------------------------------
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 653 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.149553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.103251 restraints weight = 32636.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.107382 restraints weight = 11873.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.110042 restraints weight = 7073.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3420
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3420 r_free = 0.3420    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.43   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 = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3419
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9765  Z= 0.120
  Angle     :  0.782  30.381  13235  Z= 0.353
  Chirality :  0.061   1.792   1543
  Planarity :  0.004   0.050   1582
  Dihedral  : 12.385 176.051   1890
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 17.00 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.26), residues: 1130
  helix:  1.60 (0.19), residues: 761
  sheet:  None (None), residues: 0
  loop : -1.46 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1382 
 HIS   0.004   0.001   HIS A1169 
 PHE   0.020   0.001   PHE A1181 
 TYR   0.016   0.001   TYR A 364 
 ARG   0.004   0.000   ARG A1288 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00179 (    1)
  link_NAG-ASN         : angle       0.78635 (    3)
  hydrogen bonds       : bond        0.03516 (  608)
  hydrogen bonds       : angle       4.38298 ( 1734)
  SS BOND              : bond        0.00064 (    5)
  SS BOND              : angle       0.49139 (   10)
  covalent geometry    : bond        0.00260 ( 9758)
  covalent geometry    : angle       0.78200 (13222)
  Misc. bond           : bond        0.00070 (    1)

*********************** 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
  229 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 209
  time to evaluate  : 2.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
REVERT: A  105 MET cc_start: 0.7615 (mpp) cc_final: 0.7259 (mmp)
REVERT: A  157 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9114 (mp)
REVERT: A  389 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7665 (ttt)
REVERT: A  694 PHE cc_start: 0.6365 (t80) cc_final: 0.5805 (t80)
REVERT: A  708 ASP cc_start: 0.8756 (m-30) cc_final: 0.8536 (m-30)
REVERT: A  835 SER cc_start: 0.8565 (p) cc_final: 0.8343 (p)
REVERT: A 1174 TYR cc_start: 0.8402 (m-10) cc_final: 0.8038 (m-80)
REVERT: A 1438 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8253 (tmm-80)
REVERT: A 1483 MET cc_start: 0.4498 (ppp) cc_final: 0.4049 (tmm)
REVERT: A 1507 GLU cc_start: 0.7856 (tt0) cc_final: 0.7532 (tt0)
REVERT: A 1586 ILE cc_start: 0.6094 (tp) cc_final: 0.5745 (tp)
REVERT: A 1592 ILE cc_start: 0.8982 (tp) cc_final: 0.8725 (tp)
REVERT: A 1601 MET cc_start: 0.8724 (mpp) cc_final: 0.7880 (mpp)
REVERT: A 1687 THR cc_start: 0.9400 (t) cc_final: 0.9162 (t)
REVERT: A 1731 LYS cc_start: 0.8473 (tptt) cc_final: 0.8240 (tptp)
  outliers start: 20
  outliers final: 14
  residues processed: 221
  average time/residue: 0.1823
  time to fit residues: 60.6264
Evaluate side-chains
  220 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 204
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
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  389 MET
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  642 PHE
Chi-restraints excluded: chain A residue  748 LEU
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 1499 LEU
Chi-restraints excluded: chain A residue 1644 LEU
Chi-restraints excluded: chain A residue 1655 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 84 optimal weight:   20.0000
   chunk 102 optimal weight:    0.3980
   chunk 14 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.8788

-------------------------------------------------------------------------------
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 = 0.3941 r_free = 0.3941 target = 0.148343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.106050 restraints weight = 20966.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.107469 restraints weight = 9722.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.108112 restraints weight = 6963.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3383
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3383 r_free = 0.3383    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3383 r_free = 0.3383    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3383
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9765  Z= 0.135
  Angle     :  0.806  30.348  13235  Z= 0.366
  Chirality :  0.062   1.797   1543
  Planarity :  0.005   0.107   1582
  Dihedral  : 12.477 175.593   1890
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 17.69 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.26), residues: 1130
  helix:  1.56 (0.19), residues: 762
  sheet:  None (None), residues: 0
  loop : -1.47 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1382 
 HIS   0.004   0.001   HIS A1169 
 PHE   0.022   0.001   PHE A1181 
 TYR   0.019   0.001   TYR A 364 
 ARG   0.023   0.001   ARG A1585 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00115 (    1)
  link_NAG-ASN         : angle       0.87358 (    3)
  hydrogen bonds       : bond        0.03639 (  608)
  hydrogen bonds       : angle       4.38238 ( 1734)
  SS BOND              : bond        0.00069 (    5)
  SS BOND              : angle       0.52664 (   10)
  covalent geometry    : bond        0.00306 ( 9758)
  covalent geometry    : angle       0.80656 (13222)
  Misc. bond           : bond        0.00522 (    1)

*********************** 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
  220 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 203
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
REVERT: A  105 MET cc_start: 0.7770 (mpp) cc_final: 0.7501 (mmp)
REVERT: A  157 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9102 (mp)
REVERT: A  389 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7720 (ttt)
REVERT: A  694 PHE cc_start: 0.6363 (t80) cc_final: 0.5844 (t80)
REVERT: A  760 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7074 (t0)
REVERT: A  835 SER cc_start: 0.8613 (p) cc_final: 0.8402 (p)
REVERT: A 1174 TYR cc_start: 0.8425 (m-10) cc_final: 0.8071 (m-80)
REVERT: A 1507 GLU cc_start: 0.7864 (tt0) cc_final: 0.7543 (tt0)
REVERT: A 1592 ILE cc_start: 0.8982 (tp) cc_final: 0.8719 (tp)
REVERT: A 1601 MET cc_start: 0.8724 (mpp) cc_final: 0.7876 (mpp)
REVERT: A 1631 PHE cc_start: 0.8321 (t80) cc_final: 0.7988 (t80)
REVERT: A 1731 LYS cc_start: 0.8462 (tptt) cc_final: 0.8234 (tptp)
  outliers start: 17
  outliers final: 13
  residues processed: 215
  average time/residue: 0.1786
  time to fit residues: 59.0723
Evaluate side-chains
  215 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 199
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  179 THR
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  748 LEU
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  760 ASP
Chi-restraints excluded: chain A residue 1376 LEU
Chi-restraints excluded: chain A residue 1409 LEU
Chi-restraints excluded: chain A residue 1499 LEU
Chi-restraints excluded: chain A residue 1616 LEU
Chi-restraints excluded: chain A residue 1644 LEU
Chi-restraints excluded: chain A residue 1655 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 46 optimal weight:    0.3980
   chunk 0 optimal weight:   20.0000
   chunk 101 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0670
   chunk 31 optimal weight:    0.0020
   chunk 2 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   overall best weight:    0.4926

-------------------------------------------------------------------------------
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 = 0.3964 r_free = 0.3964 target = 0.150218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.106059 restraints weight = 26211.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.109485 restraints weight = 11833.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.111170 restraints weight = 6637.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3418
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3418 r_free = 0.3418    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3418 r_free = 0.3418    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3418
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9765  Z= 0.124
  Angle     :  0.825  30.370  13235  Z= 0.372
  Chirality :  0.062   1.793   1543
  Planarity :  0.004   0.089   1582
  Dihedral  : 12.335 176.168   1890
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 18.29 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.26), residues: 1130
  helix:  1.58 (0.19), residues: 761
  sheet:  None (None), residues: 0
  loop : -1.45 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1382 
 HIS   0.003   0.001   HIS A1169 
 PHE   0.027   0.001   PHE A1546 
 TYR   0.017   0.001   TYR A 364 
 ARG   0.017   0.000   ARG A1585 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00182 (    1)
  link_NAG-ASN         : angle       0.75390 (    3)
  hydrogen bonds       : bond        0.03546 (  608)
  hydrogen bonds       : angle       4.35244 ( 1734)
  SS BOND              : bond        0.00056 (    5)
  SS BOND              : angle       0.50536 (   10)
  covalent geometry    : bond        0.00270 ( 9758)
  covalent geometry    : angle       0.82507 (13222)
  Misc. bond           : bond        0.00380 (    1)

********************** 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
  222 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 206
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
REVERT: A  157 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9061 (mp)
REVERT: A  389 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7702 (ttt)
REVERT: A  760 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7084 (t0)
REVERT: A  835 SER cc_start: 0.8539 (p) cc_final: 0.8334 (p)
REVERT: A 1174 TYR cc_start: 0.8409 (m-10) cc_final: 0.8045 (m-80)
REVERT: A 1507 GLU cc_start: 0.7890 (tt0) cc_final: 0.7584 (tt0)
REVERT: A 1592 ILE cc_start: 0.8886 (tp) cc_final: 0.8644 (tp)
REVERT: A 1601 MET cc_start: 0.8688 (mpp) cc_final: 0.7819 (mpp)
REVERT: A 1687 THR cc_start: 0.9365 (t) cc_final: 0.9107 (t)
REVERT: A 1704 PHE cc_start: 0.8101 (t80) cc_final: 0.7555 (t80)
REVERT: A 1731 LYS cc_start: 0.8401 (tptt) cc_final: 0.8168 (tptp)
  outliers start: 16
  outliers final: 11
  residues processed: 216
  average time/residue: 0.1707
  time to fit residues: 56.1495
Evaluate side-chains
  216 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 202
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  157 ILE
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  748 LEU
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  760 ASP
Chi-restraints excluded: chain A residue 1376 LEU
Chi-restraints excluded: chain A residue 1409 LEU
Chi-restraints excluded: chain A residue 1499 LEU
Chi-restraints excluded: chain A residue 1644 LEU
Chi-restraints excluded: chain A residue 1655 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 39 optimal weight:    0.0970
   chunk 111 optimal weight:    0.7980
   chunk 93 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0040
   chunk 49 optimal weight:    0.7980
   chunk 23 optimal weight:    9.9990
   chunk 109 optimal weight:    3.9990
   chunk 7 optimal weight:    8.9990
   chunk 34 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.4990

-------------------------------------------------------------------------------
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 = 0.3968 r_free = 0.3968 target = 0.150553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.104711 restraints weight = 30369.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.108844 restraints weight = 11350.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.111476 restraints weight = 6834.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.3473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9765  Z= 0.124
  Angle     :  0.816  30.361  13235  Z= 0.370
  Chirality :  0.062   1.794   1543
  Planarity :  0.004   0.080   1582
  Dihedral  : 12.267 175.947   1890
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 18.49 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.26), residues: 1130
  helix:  1.58 (0.19), residues: 762
  sheet:  None (None), residues: 0
  loop : -1.43 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1382 
 HIS   0.003   0.001   HIS A1169 
 PHE   0.028   0.001   PHE A1546 
 TYR   0.016   0.001   TYR A 364 
 ARG   0.014   0.000   ARG A1585 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00176 (    1)
  link_NAG-ASN         : angle       0.75828 (    3)
  hydrogen bonds       : bond        0.03546 (  608)
  hydrogen bonds       : angle       4.33274 ( 1734)
  SS BOND              : bond        0.00037 (    5)
  SS BOND              : angle       0.49438 (   10)
  covalent geometry    : bond        0.00270 ( 9758)
  covalent geometry    : angle       0.81574 (13222)
  Misc. bond           : bond        0.00322 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4093.25 seconds
wall clock time: 73 minutes 10.72 seconds (4390.72 seconds total)