Starting phenix.real_space_refine
on Wed Mar  4 02:47:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wlj_32585/03_2026/7wlj_32585.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wlj_32585/03_2026/7wlj_32585.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wlj_32585/03_2026/7wlj_32585.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wlj_32585/03_2026/7wlj_32585.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wlj_32585/03_2026/7wlj_32585.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wlj_32585/03_2026/7wlj_32585.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.009 sd=   0.094
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      1      9.91       5
     P       1      5.49       5
     S      78      5.16       5
     C    6272      2.51       5
     N    1504      2.21       5
     O    1593      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9450
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9111
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1135, 9100
          Classifications: {'peptide': 1135}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 31, 'TRANS': 1103}
          Chain breaks: 3
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 24
      Conformer: "B"
        Number of residues, atoms: 1135, 9100
          Classifications: {'peptide': 1135}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 31, 'TRANS': 1103}
          Chain breaks: 3
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 24
          bond proxies already assigned to first conformer: 9289
    Chain: "A"
      Number of atoms: 339
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 339
          Unusual residues: {' CA': 1, '3PE': 5, 'MWV': 1, 'NAG': 2, 'Y01': 6}
          Classifications: {'undetermined': 15}
          Link IDs: {None: 14}
          Unresolved non-hydrogen bonds: 193
          Unresolved non-hydrogen angles: 223
          Unresolved non-hydrogen dihedrals: 199
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'3PE:plan-1': 4, '3PE:plan-2': 4, 'Y01:plan-1': 3, 'Y01:plan-2': 1}
          Unresolved non-hydrogen planarities: 41
  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: 3.87, per 1000 atoms: 0.41
  Number of scatterers: 9450
  At special positions: 0
  Unit cell: (113.36, 123.76, 108.16, 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      1     19.99
     S      78     16.00
     P       1     15.00
     F       1      9.00
     O    1593      8.00
     N    1504      7.00
     C    6272      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=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A2310 " - " ASN A1345 "
      " NAG A2312 " - " ASN A1342 "
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 686.8 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 2 sheets defined
      77.9% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 78
      removed outlier: 4.226A  pdb=" N   CYS A  72 " --> pdb=" O   PRO A  68 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ILE A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   LYS A  74 " --> pdb=" O   ASN A  70 " (cutoff:3.500A)
      removed outlier: 5.645A  pdb=" N   MET A  75 " --> pdb=" O   TRP A  71 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL A  76 " --> pdb=" O   CYS A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 98
      removed outlier: 3.853A  pdb=" N   GLU A  82 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 136
    Processing helix  chain 'A' and resid 144 through 147
    Processing helix  chain 'A' and resid 148 through 170
    Processing helix  chain 'A' and resid 180 through 191
      Proline residue:  A 185  - end of helix
      removed outlier: 3.963A  pdb=" N   ILE A 189 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
      removed outlier: 3.787A  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: 3.812A  pdb=" N   PHE A 223 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 237
      removed outlier: 3.547A  pdb=" N   ARG A 236 " --> pdb=" O   GLY A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 264
      removed outlier: 3.706A  pdb=" N   ASP A 263 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 323
      removed outlier: 3.561A  pdb=" N   ARG A 321 " --> pdb=" O   ASN A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 342 through 355
      removed outlier: 3.747A  pdb=" N   ALA A 346 " --> pdb=" O   ASN A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 370
    Processing helix  chain 'A' and resid 371 through 373
      No H-bonds generated for 'chain 'A' and resid 371 through 373'
    Processing helix  chain 'A' and resid 374 through 383
    Processing helix  chain 'A' and resid 389 through 413
    Processing helix  chain 'A' and resid 628 through 638
      removed outlier: 3.808A  pdb=" N   LYS A 632 " --> pdb=" O   GLU A 628 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   GLY A 635 " --> pdb=" O   ALA A 631 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ILE A 636 " --> pdb=" O   LYS A 632 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL A 637 " --> pdb=" O   LEU A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 660
      removed outlier: 3.960A  pdb=" N   GLU A 660 " --> pdb=" O   SER A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 695
      removed outlier: 3.586A  pdb=" N   ASN A 670 " --> pdb=" O   GLU A 666 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ALA A 692 " --> pdb=" O   ILE A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 695 through 702
      removed outlier: 4.247A  pdb=" N   ASN A 702 " --> pdb=" O   ASP A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 721
      removed outlier: 3.935A  pdb=" N   ILE A 706 " --> pdb=" O   ASN A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 730
      removed outlier: 3.790A  pdb=" N   VAL A 729 " --> pdb=" O   GLY A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 744
      removed outlier: 3.865A  pdb=" N   LEU A 735 " --> pdb=" O   THR A 732 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A 736 " --> pdb=" O   PHE A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 785
      removed outlier: 3.825A  pdb=" N   ARG A 749 " --> pdb=" O   MET A 745 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ARG A 750 " --> pdb=" O   PRO A 746 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ASN A 761 " --> pdb=" O   LYS A 757 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   THR A 764 " --> pdb=" O   ASP A 760 " (cutoff:3.500A)
      removed outlier: 4.085A  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: 4.318A  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: 3.898A  pdb=" N   PHE A 842 " --> pdb=" O   ALA A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 866
      removed outlier: 3.504A  pdb=" N   VAL A 858 " --> pdb=" O  BPHE A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1171 through 1188
    Processing helix  chain 'A' and resid 1198 through 1227
    Processing helix  chain 'A' and resid 1234 through 1237
      removed outlier: 3.740A  pdb=" N   ARG A1237 " --> pdb=" O   ALA A1234 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1234 through 1237'
    Processing helix  chain 'A' and resid 1238 through 1260
    Processing helix  chain 'A' and resid 1267 through 1281
    Processing helix  chain 'A' and resid 1284 through 1289
    Processing helix  chain 'A' and resid 1289 through 1304
      removed outlier: 3.850A  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 1365 through 1377
    Processing helix  chain 'A' and resid 1381 through 1392
      removed outlier: 3.606A  pdb=" N   ILE A1385 " --> pdb=" O   GLY A1381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1406 through 1444
      removed outlier: 4.012A  pdb=" N   TYR A1410 " --> pdb=" O   TRP A1406 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU A1415 " --> pdb=" O   PHE A1411 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   HIS A1440 " --> pdb=" O   LYS A1436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1444 through 1460
      removed outlier: 3.621A  pdb=" N   ARG A1448 " --> pdb=" O   GLU A1444 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   GLU A1450 " --> pdb=" O   ALA A1446 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   GLU A1451 " --> pdb=" O   ARG A1447 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   ARG A1453 " --> pdb=" O   ARG A1449 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU A1454 " --> pdb=" O   GLU A1450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1461 through 1463
      No H-bonds generated for 'chain 'A' and resid 1461 through 1463'
    Processing helix  chain 'A' and resid 1468 through 1473
      removed outlier: 4.210A  pdb=" N   THR A1472 " --> pdb=" O   PRO A1468 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   TYR A1473 " --> pdb=" O   TYR A1469 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1468 through 1473'
    Processing helix  chain 'A' and resid 1482 through 1485
    Processing helix  chain 'A' and resid 1486 through 1505
      removed outlier: 3.704A  pdb=" N   ASP A1490 " --> pdb=" O   SER A1486 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   PHE A1492 " --> pdb=" O   TYR A1488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1512 through 1541
    Processing helix  chain 'A' and resid 1542 through 1549
      removed outlier: 3.936A  pdb=" N   PHE A1546 " --> pdb=" O   GLY A1542 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   PHE A1547 " --> pdb=" O   LEU A1543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1551 through 1574
      removed outlier: 3.597A  pdb=" N   LEU A1568 " --> pdb=" O   MET A1564 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLU A1569 " --> pdb=" O   GLY A1565 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLU A1570 " --> pdb=" O   ILE A1566 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE A1571 " --> pdb=" O   THR A1567 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU A1572 " --> pdb=" O   LEU A1568 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ASN A1574 " --> pdb=" O   GLU A1570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1580 through 1591
    Processing helix  chain 'A' and resid 1592 through 1596
    Processing helix  chain 'A' and resid 1597 through 1602
      removed outlier: 4.001A  pdb=" N   MET A1601 " --> pdb=" O   LYS A1597 " (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 1663 through 1675
      removed outlier: 3.668A  pdb=" N   ALA A1667 " --> pdb=" O   ASN A1663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1679 through 1688
    Processing helix  chain 'A' and resid 1695 through 1700
      removed outlier: 4.063A  pdb=" N   LEU A1699 " --> pdb=" O   GLU A1695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1701 through 1738
      removed outlier: 3.619A  pdb=" N   VAL A1705 " --> pdb=" O   SER A1701 " (cutoff:3.500A)
      Proline residue:  A1707  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 238 through 239
      removed outlier: 3.526A  pdb=" N   ARG A 238 " --> pdb=" O   ARG A 327 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG A 327 " --> pdb=" O   ARG A 238 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1333 through 1335

    596 hydrogen bonds defined for protein.
    1725 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.48

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1432
        1.32 -     1.44: 2587
        1.44 -     1.57: 5459
        1.57 -     1.69: 64
        1.69 -     1.82: 127
  Bond restraints: 9669
  Sorted by residual:
  bond pdb=" C21 3PE A2302 "
       pdb=" O21 3PE A2302 "
    ideal  model  delta    sigma   weight residual
    1.316  1.465 -0.149 2.00e-02 2.50e+03 5.56e+01
  bond pdb=" C31 3PE A2302 "
       pdb=" O31 3PE A2302 "
    ideal  model  delta    sigma   weight residual
    1.331  1.469 -0.138 2.00e-02 2.50e+03 4.75e+01
  bond pdb=" C04 MWV A2301 "
       pdb=" O06 MWV A2301 "
    ideal  model  delta    sigma   weight residual
    1.322  1.432 -0.110 2.00e-02 2.50e+03 3.05e+01
  bond pdb=" C21 3PE A2302 "
       pdb=" C22 3PE A2302 "
    ideal  model  delta    sigma   weight residual
    1.502  1.602 -0.100 2.00e-02 2.50e+03 2.50e+01
  bond pdb=" C31 3PE A2306 "
       pdb=" C32 3PE A2306 "
    ideal  model  delta    sigma   weight residual
    1.504  1.604 -0.100 2.00e-02 2.50e+03 2.48e+01
  ... (remaining 9664 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 12782
        2.87 -     5.75: 283
        5.75 -     8.62: 42
        8.62 -    11.50: 10
       11.50 -    14.37: 2
  Bond angle restraints: 13119
  Sorted by residual:
  angle pdb=" O12 3PE A2302 "
        pdb=" P   3PE A2302 "
        pdb=" O14 3PE A2302 "
      ideal   model   delta    sigma   weight residual
     123.79  109.42   14.37 3.00e+00 1.11e-01 2.30e+01
  angle pdb=" N   ILE A 177 "
        pdb=" CA  ILE A 177 "
        pdb=" C   ILE A 177 "
      ideal   model   delta    sigma   weight residual
     113.39  106.40    6.99 1.47e+00 4.63e-01 2.26e+01
  angle pdb=" C   ARG A1341 "
        pdb=" N   ASN A1342 "
        pdb=" CA  ASN A1342 "
      ideal   model   delta    sigma   weight residual
     122.61  129.43   -6.82 1.56e+00 4.11e-01 1.91e+01
  angle pdb=" N   ALA A 176 "
        pdb=" CA  ALA A 176 "
        pdb=" C   ALA A 176 "
      ideal   model   delta    sigma   weight residual
     114.39  108.37    6.02 1.45e+00 4.76e-01 1.73e+01
  angle pdb=" CB  MET A 687 "
        pdb=" CG  MET A 687 "
        pdb=" SD  MET A 687 "
      ideal   model   delta    sigma   weight residual
     112.70  124.37  -11.67 3.00e+00 1.11e-01 1.51e+01
  ... (remaining 13114 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.67: 5893
       35.67 -    71.34: 149
       71.34 -   107.01: 18
      107.01 -   142.68: 3
      142.68 -   178.35: 3
  Dihedral angle restraints: 6066
    sinusoidal: 2747
      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  166.57  -73.57     1      1.00e+01 1.00e-02 6.88e+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  146.34  -53.34     1      1.00e+01 1.00e-02 3.87e+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  -40.00  -46.00     1      1.00e+01 1.00e-02 2.93e+01
  ... (remaining 6063 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.953: 1536
       0.953 -    1.906: 0
       1.906 -    2.859: 0
       2.859 -    3.812: 0
       3.812 -    4.766: 1
  Chirality restraints: 1537
  Sorted by residual:
  chirality pdb=" C33 MWV A2301 "
            pdb=" C07 MWV A2301 "
            pdb=" C27 MWV A2301 "
            pdb=" C34 MWV A2301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.33   -2.44    4.77 2.00e-01 2.50e+01 5.68e+02
  chirality pdb=" CBG Y01 A2311 "
            pdb=" CAQ Y01 A2311 "
            pdb=" CBD Y01 A2311 "
            pdb=" CBI Y01 A2311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.84    0.51 2.00e-01 2.50e+01 6.48e+00
  chirality pdb=" CBG Y01 A2313 "
            pdb=" CAQ Y01 A2313 "
            pdb=" CBD Y01 A2313 "
            pdb=" CBI Y01 A2313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.83    0.50 2.00e-01 2.50e+01 6.26e+00
  ... (remaining 1534 not shown)

  Planarity restraints: 1582
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 702 "   -0.033 5.00e-02 4.00e+02   4.99e-02 3.99e+00
        pdb=" N   PRO A 703 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 703 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 703 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 192 "    0.032 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO A 193 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 193 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 193 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A1191 "   -0.031 5.00e-02 4.00e+02   4.74e-02 3.59e+00
        pdb=" N   PRO A1192 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A1192 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A1192 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1579 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 57
        2.51 -     3.11: 7724
        3.11 -     3.70: 14803
        3.70 -     4.30: 20488
        4.30 -     4.90: 32605
  Nonbonded interactions: 75677
  Sorted by model distance:
  nonbonded pdb=" CD  ARG A1191 "
            pdb=" CA  ASN A1663 "
     model   vdw
     1.912 3.870
  nonbonded pdb=" CG  ARG A1191 "
            pdb=" O   GLU A1662 "
     model   vdw
     2.067 3.440
  nonbonded pdb=" CD1 LEU A 861 "
            pdb=" CD2 LEU A1423 "
     model   vdw
     2.092 3.880
  nonbonded pdb=" O   TYR A1633 "
            pdb=" OH  TYR A1709 "
     model   vdw
     2.130 3.040
  nonbonded pdb=" OD1 ASP A1380 "
            pdb=" ND2 ASN A1681 "
     model   vdw
     2.185 3.120
  ... (remaining 75672 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:             1.100
  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:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.650
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
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      :  0.009   0.149   9676  Z= 0.437
  Angle     :  1.015  14.374  13135  Z= 0.497
  Chirality :  0.138   4.766   1537
  Planarity :  0.004   0.050   1580
  Dihedral  : 16.923 178.349   3901
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 18.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.20 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.26), residues: 1130
  helix:  0.85 (0.19), residues: 746
  sheet:  None (None), residues: 0
  loop : -1.61 (0.34), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1278 
 TYR   0.014   0.002   TYR A1473 
 PHE   0.029   0.002   PHE A 772 
 TRP   0.020   0.002   TRP A 231 
 HIS   0.014   0.001   HIS A1440 

Details of bonding type rmsd
  covalent geometry    : bond        0.00884 ( 9669)
  covalent geometry    : angle       1.01173 (13119)
  SS BOND              : bond        0.00145 (    5)
  SS BOND              : angle       0.77660 (   10)
  hydrogen bonds       : bond        0.14507 (  596)
  hydrogen bonds       : angle       6.12922 ( 1725)
  link_NAG-ASN         : bond        0.00651 (    2)
  link_NAG-ASN         : angle       4.01906 (    6)

*********************** 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
  256 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 255
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  208 MET cc_start: 0.7518 (mtm) cc_final: 0.6461 (mtm)
REVERT: A  373 TYR cc_start: 0.8538 (m-80) cc_final: 0.8123 (m-10)
REVERT: A  387 PHE cc_start: 0.8873 (t80) cc_final: 0.8655 (t80)
REVERT: A  400 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8465 (mm-40)
REVERT: A  694 PHE cc_start: 0.8407 (m-80) cc_final: 0.7991 (m-10)
REVERT: A  767 MET cc_start: 0.7189 (mtt) cc_final: 0.6484 (mmt)
REVERT: A  839 SER cc_start: 0.9509 (p) cc_final: 0.9303 (p)
REVERT: A 1181 PHE cc_start: 0.8662 (t80) cc_final: 0.8422 (t80)
REVERT: A 1244 ASP cc_start: 0.9079 (m-30) cc_final: 0.8856 (m-30)
REVERT: A 1386 MET cc_start: 0.8989 (ttp) cc_final: 0.8569 (ttp)
REVERT: A 1501 VAL cc_start: 0.9655 (t) cc_final: 0.9396 (t)
REVERT: A 1504 MET cc_start: 0.8741 (mpp) cc_final: 0.8251 (mpp)
REVERT: A 1522 CYS cc_start: 0.9503 (m) cc_final: 0.9214 (p)
REVERT: A 1662 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7964 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 256
  average time/residue: 0.0717
  time to fit residues: 28.1734
Evaluate side-chains
  190 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0370
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
A 116 GLN
A 229 GLN
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 HIS
A 653 ASN
A 820 GLN
A 855 ASN
A1241 ASN
A1362 ASN
** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1510 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.123856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.090653 restraints weight = 24244.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.093734 restraints weight = 11458.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.095604 restraints weight = 7704.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.096603 restraints weight = 6347.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.096974 restraints weight = 5785.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3460
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3460
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9676  Z= 0.154
  Angle     :  0.815  13.200  13135  Z= 0.398
  Chirality :  0.045   0.236   1537
  Planarity :  0.005   0.043   1580
  Dihedral  : 12.900 139.438   1781
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.22 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.25), residues: 1130
  helix:  0.83 (0.18), residues: 786
  sheet:  None (None), residues: 0
  loop : -2.05 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1355 
 TYR   0.031   0.002   TYR A1473 
 PHE   0.026   0.002   PHE A1546 
 TRP   0.016   0.002   TRP A 823 
 HIS   0.015   0.002   HIS A1440 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 9669)
  covalent geometry    : angle       0.81203 (13119)
  SS BOND              : bond        0.00115 (    5)
  SS BOND              : angle       0.99868 (   10)
  hydrogen bonds       : bond        0.04430 (  596)
  hydrogen bonds       : angle       5.01309 ( 1725)
  link_NAG-ASN         : bond        0.00415 (    2)
  link_NAG-ASN         : angle       3.37686 (    6)

*********************** 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
  238 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 221
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  208 MET cc_start: 0.7462 (mtm) cc_final: 0.6590 (mtm)
REVERT: A  387 PHE cc_start: 0.8785 (t80) cc_final: 0.8540 (t80)
REVERT: A  400 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8228 (mm110)
REVERT: A  694 PHE cc_start: 0.7920 (m-80) cc_final: 0.7667 (m-80)
REVERT: A  717 TRP cc_start: 0.8671 (m100) cc_final: 0.8468 (t60)
REVERT: A  759 MET cc_start: 0.8672 (ppp) cc_final: 0.8268 (tmm)
REVERT: A  767 MET cc_start: 0.6737 (mtt) cc_final: 0.6342 (mmt)
REVERT: A  778 ILE cc_start: 0.9339 (mm) cc_final: 0.9065 (tt)
REVERT: A 1181 PHE cc_start: 0.8444 (t80) cc_final: 0.8180 (t80)
REVERT: A 1364 ASP cc_start: 0.8192 (m-30) cc_final: 0.7930 (t0)
REVERT: A 1488 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.6832 (m-80)
REVERT: A 1519 LEU cc_start: 0.9569 (mp) cc_final: 0.8845 (pp)
REVERT: A 1662 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7574 (mm-30)
REVERT: A 1704 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7598 (t80)
  outliers start: 17
  outliers final: 10
  residues processed: 230
  average time/residue: 0.0715
  time to fit residues: 24.9608
Evaluate side-chains
  202 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 190
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  409 HIS
Chi-restraints excluded: chain A residue  707 PHE
Chi-restraints excluded: chain A residue  761 ASN
Chi-restraints excluded: chain A residue 1203 PHE
Chi-restraints excluded: chain A residue 1323 LEU
Chi-restraints excluded: chain A residue 1362 ASN
Chi-restraints excluded: chain A residue 1488 TYR
Chi-restraints excluded: chain A residue 1704 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 50 optimal weight:    0.2980
   chunk 70 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 105 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 106 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 56 optimal weight:    8.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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**
** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1552 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.124143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.090957 restraints weight = 39246.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.093479 restraints weight = 15820.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.094604 restraints weight = 9336.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.094969 restraints weight = 8765.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.094972 restraints weight = 7907.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3409
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3409 r_free = 0.3409    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3409 r_free = 0.3409    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3409
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9676  Z= 0.144
  Angle     :  0.768  13.572  13135  Z= 0.378
  Chirality :  0.045   0.239   1537
  Planarity :  0.004   0.047   1580
  Dihedral  : 12.041 133.799   1781
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 16.40 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.25), residues: 1130
  helix:  0.79 (0.19), residues: 781
  sheet:  None (None), residues: 0
  loop : -2.05 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1355 
 TYR   0.028   0.001   TYR A1473 
 PHE   0.023   0.002   PHE A1246 
 TRP   0.012   0.001   TRP A 319 
 HIS   0.004   0.001   HIS A1481 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 9669)
  covalent geometry    : angle       0.76538 (13119)
  SS BOND              : bond        0.00081 (    5)
  SS BOND              : angle       0.80312 (   10)
  hydrogen bonds       : bond        0.04124 (  596)
  hydrogen bonds       : angle       4.83051 ( 1725)
  link_NAG-ASN         : bond        0.00439 (    2)
  link_NAG-ASN         : angle       3.06734 (    6)

*********************** 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  : 0.367 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  123 PHE cc_start: 0.8856 (t80) cc_final: 0.8551 (t80)
REVERT: A  125 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8600 (t80)
REVERT: A  133 LYS cc_start: 0.9211 (ttpp) cc_final: 0.8944 (tptp)
REVERT: A  208 MET cc_start: 0.7577 (mtm) cc_final: 0.6705 (mtm)
REVERT: A  387 PHE cc_start: 0.8766 (t80) cc_final: 0.8482 (t80)
REVERT: A  389 MET cc_start: 0.7309 (ttm) cc_final: 0.7026 (ttm)
REVERT: A  400 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8187 (mm110)
REVERT: A  694 PHE cc_start: 0.8132 (m-80) cc_final: 0.7918 (m-80)
REVERT: A  717 TRP cc_start: 0.8751 (m100) cc_final: 0.8526 (t60)
REVERT: A  759 MET cc_start: 0.8663 (ppp) cc_final: 0.8356 (tmm)
REVERT: A  767 MET cc_start: 0.6827 (mtt) cc_final: 0.6433 (mmt)
REVERT: A  778 ILE cc_start: 0.9354 (mm) cc_final: 0.9146 (tt)
REVERT: A 1364 ASP cc_start: 0.8112 (m-30) cc_final: 0.7774 (t0)
REVERT: A 1488 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.6936 (m-80)
REVERT: A 1598 LEU cc_start: 0.9570 (mp) cc_final: 0.8902 (mm)
REVERT: A 1662 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7610 (mm-30)
REVERT: A 1704 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7641 (t80)
  outliers start: 22
  outliers final: 9
  residues processed: 221
  average time/residue: 0.0691
  time to fit residues: 23.3148
Evaluate side-chains
  206 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 194
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  707 PHE
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1203 PHE
Chi-restraints excluded: chain A residue 1323 LEU
Chi-restraints excluded: chain A residue 1488 TYR
Chi-restraints excluded: chain A residue 1704 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   chunk 101 optimal weight:    0.0970
   chunk 56 optimal weight:    0.9990
   chunk 10 optimal weight:   10.0000
   chunk 51 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 87 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 339 ASN
** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1650 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.123955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.087408 restraints weight = 50142.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.091464 restraints weight = 17086.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.094067 restraints weight = 9578.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.095544 restraints weight = 7116.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.096069 restraints weight = 6159.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3441
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3441 r_free = 0.3441    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3441 r_free = 0.3441    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3441
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9676  Z= 0.143
  Angle     :  0.771  13.662  13135  Z= 0.378
  Chirality :  0.045   0.242   1537
  Planarity :  0.004   0.046   1580
  Dihedral  : 11.278 145.108   1781
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 19.09 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.25), residues: 1130
  helix:  0.86 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop : -2.03 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1191 
 TYR   0.020   0.001   TYR A 364 
 PHE   0.024   0.001   PHE A1246 
 TRP   0.012   0.001   TRP A 319 
 HIS   0.005   0.001   HIS A1358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9669)
  covalent geometry    : angle       0.76863 (13119)
  SS BOND              : bond        0.00104 (    5)
  SS BOND              : angle       0.64949 (   10)
  hydrogen bonds       : bond        0.03926 (  596)
  hydrogen bonds       : angle       4.82289 ( 1725)
  link_NAG-ASN         : bond        0.00410 (    2)
  link_NAG-ASN         : angle       2.86099 (    6)

*********************** 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
  223 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 207
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  125 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8530 (t80)
REVERT: A  133 LYS cc_start: 0.9111 (ttpp) cc_final: 0.8910 (tptp)
REVERT: A  194 SER cc_start: 0.8938 (p) cc_final: 0.8669 (t)
REVERT: A  208 MET cc_start: 0.7412 (mtm) cc_final: 0.6503 (mtm)
REVERT: A  345 TYR cc_start: 0.8430 (m-80) cc_final: 0.8079 (m-80)
REVERT: A  387 PHE cc_start: 0.8772 (t80) cc_final: 0.8522 (t80)
REVERT: A  389 MET cc_start: 0.7235 (ttm) cc_final: 0.6982 (ttm)
REVERT: A  400 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8083 (mm110)
REVERT: A  759 MET cc_start: 0.8445 (ppp) cc_final: 0.8002 (tmm)
REVERT: A  767 MET cc_start: 0.6684 (mtt) cc_final: 0.6369 (mmt)
REVERT: A  778 ILE cc_start: 0.9416 (mm) cc_final: 0.9116 (tt)
REVERT: A 1364 ASP cc_start: 0.8076 (m-30) cc_final: 0.7721 (t0)
REVERT: A 1449 ARG cc_start: 0.8827 (ptt90) cc_final: 0.8392 (ptt-90)
REVERT: A 1488 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6849 (m-80)
REVERT: A 1601 MET cc_start: 0.7988 (pmm) cc_final: 0.7758 (tpt)
REVERT: A 1609 LEU cc_start: 0.9038 (mm) cc_final: 0.8291 (pp)
REVERT: A 1662 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7527 (mm-30)
REVERT: A 1704 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7590 (t80)
  outliers start: 16
  outliers final: 9
  residues processed: 215
  average time/residue: 0.0646
  time to fit residues: 21.6690
Evaluate side-chains
  209 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 197
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  707 PHE
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1323 LEU
Chi-restraints excluded: chain A residue 1488 TYR
Chi-restraints excluded: chain A residue 1704 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 73 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 50 optimal weight:    0.5980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A1362 ASN
** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1723 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.121001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.083878 restraints weight = 42485.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.087480 restraints weight = 16576.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.089775 restraints weight = 9962.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.091075 restraints weight = 7675.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.091726 restraints weight = 6766.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9676  Z= 0.180
  Angle     :  0.791  14.550  13135  Z= 0.394
  Chirality :  0.046   0.245   1537
  Planarity :  0.004   0.049   1580
  Dihedral  : 10.984 151.401   1781
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 20.58 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.25), residues: 1130
  helix:  0.78 (0.19), residues: 786
  sheet:  None (None), residues: 0
  loop : -2.16 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1191 
 TYR   0.025   0.001   TYR A1473 
 PHE   0.027   0.002   PHE A 765 
 TRP   0.012   0.001   TRP A1382 
 HIS   0.007   0.001   HIS A1358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 9669)
  covalent geometry    : angle       0.78953 (13119)
  SS BOND              : bond        0.00140 (    5)
  SS BOND              : angle       0.62791 (   10)
  hydrogen bonds       : bond        0.04025 (  596)
  hydrogen bonds       : angle       4.91341 ( 1725)
  link_NAG-ASN         : bond        0.00298 (    2)
  link_NAG-ASN         : angle       2.75813 (    6)

*********************** 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
  223 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 201
  time to evaluate  : 0.349 
Fit side-chains
TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  125 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8552 (t80)
REVERT: A  363 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.7837 (tmm)
REVERT: A  387 PHE cc_start: 0.8823 (t80) cc_final: 0.8551 (t80)
REVERT: A  759 MET cc_start: 0.8459 (ppp) cc_final: 0.8003 (tmm)
REVERT: A  767 MET cc_start: 0.6849 (mtt) cc_final: 0.6536 (mmt)
REVERT: A  778 ILE cc_start: 0.9408 (mm) cc_final: 0.9107 (tt)
REVERT: A  822 ASP cc_start: 0.8381 (t0) cc_final: 0.8120 (t70)
REVERT: A  855 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.7931 (t0)
REVERT: A 1364 ASP cc_start: 0.8114 (m-30) cc_final: 0.7764 (t0)
REVERT: A 1407 MET cc_start: 0.8692 (mmp) cc_final: 0.8428 (mmt)
REVERT: A 1449 ARG cc_start: 0.8889 (ptt90) cc_final: 0.8517 (ptt-90)
REVERT: A 1704 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7506 (t80)
  outliers start: 22
  outliers final: 16
  residues processed: 211
  average time/residue: 0.0621
  time to fit residues: 20.2259
Evaluate side-chains
  211 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 191
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 PHE
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  409 HIS
Chi-restraints excluded: chain A residue  707 PHE
Chi-restraints excluded: chain A residue  717 TRP
Chi-restraints excluded: chain A residue  761 ASN
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain A residue  855 ASN
Chi-restraints excluded: chain A residue 1171 LEU
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1208 ASN
Chi-restraints excluded: chain A residue 1323 LEU
Chi-restraints excluded: chain A residue 1362 ASN
Chi-restraints excluded: chain A residue 1704 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 88 optimal weight:    7.9990
   chunk 74 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 19 optimal weight:    0.4980
   chunk 99 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 103 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.119958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.084131 restraints weight = 43109.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.088356 restraints weight = 16548.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.090121 restraints weight = 8670.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.090007 restraints weight = 7495.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.089886 restraints weight = 7410.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3305
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3305
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9676  Z= 0.141
  Angle     :  0.790  13.501  13135  Z= 0.386
  Chirality :  0.045   0.236   1537
  Planarity :  0.004   0.045   1580
  Dihedral  : 10.441 149.711   1781
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 20.78 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.25), residues: 1130
  helix:  0.87 (0.19), residues: 785
  sheet:  None (None), residues: 0
  loop : -2.14 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 191 
 TYR   0.012   0.001   TYR A 699 
 PHE   0.027   0.001   PHE A1246 
 TRP   0.011   0.001   TRP A1382 
 HIS   0.005   0.001   HIS A1403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9669)
  covalent geometry    : angle       0.78862 (13119)
  SS BOND              : bond        0.00113 (    5)
  SS BOND              : angle       0.51099 (   10)
  hydrogen bonds       : bond        0.03894 (  596)
  hydrogen bonds       : angle       4.81778 ( 1725)
  link_NAG-ASN         : bond        0.00410 (    2)
  link_NAG-ASN         : angle       2.40109 (    6)

*********************** 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
  225 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 200
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  124 ILE cc_start: 0.9548 (mt) cc_final: 0.9268 (tp)
REVERT: A  125 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8706 (t80)
REVERT: A  190 ASN cc_start: 0.8228 (p0) cc_final: 0.6533 (p0)
REVERT: A  218 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8411 (t80)
REVERT: A  363 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.7747 (tmm)
REVERT: A  387 PHE cc_start: 0.8847 (t80) cc_final: 0.8548 (t80)
REVERT: A  400 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8101 (mm-40)
REVERT: A  759 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8027 (tmm)
REVERT: A  767 MET cc_start: 0.7065 (mtt) cc_final: 0.6615 (mmt)
REVERT: A  778 ILE cc_start: 0.9312 (mm) cc_final: 0.9097 (tt)
REVERT: A  807 LEU cc_start: 0.8543 (tp) cc_final: 0.8269 (tp)
REVERT: A  822 ASP cc_start: 0.8424 (t0) cc_final: 0.8131 (t70)
REVERT: A  855 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.7743 (t0)
REVERT: A 1364 ASP cc_start: 0.8144 (m-30) cc_final: 0.7796 (t0)
REVERT: A 1449 ARG cc_start: 0.8996 (ptt90) cc_final: 0.8541 (ptt-90)
REVERT: A 1488 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.6925 (m-80)
REVERT: A 1497 ILE cc_start: 0.9603 (mm) cc_final: 0.9219 (tt)
REVERT: A 1609 LEU cc_start: 0.9034 (mm) cc_final: 0.8259 (pp)
REVERT: A 1662 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7589 (mm-30)
REVERT: A 1704 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7643 (t80)
  outliers start: 25
  outliers final: 13
  residues processed: 211
  average time/residue: 0.0685
  time to fit residues: 22.5282
Evaluate side-chains
  207 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 187
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 PHE
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  218 PHE
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  707 PHE
Chi-restraints excluded: chain A residue  717 TRP
Chi-restraints excluded: chain A residue  759 MET
Chi-restraints excluded: chain A residue  839 SER
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain A residue  855 ASN
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1208 ASN
Chi-restraints excluded: chain A residue 1323 LEU
Chi-restraints excluded: chain A residue 1488 TYR
Chi-restraints excluded: chain A residue 1684 MET
Chi-restraints excluded: chain A residue 1704 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 23 optimal weight:    8.9990
   chunk 41 optimal weight:   10.0000
   chunk 86 optimal weight:    0.7980
   chunk 56 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.119376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.084403 restraints weight = 29581.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.087516 restraints weight = 13308.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.089444 restraints weight = 8667.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.090318 restraints weight = 6962.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.090997 restraints weight = 6311.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3336
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3336
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9676  Z= 0.148
  Angle     :  0.813  14.885  13135  Z= 0.396
  Chirality :  0.045   0.236   1537
  Planarity :  0.004   0.050   1580
  Dihedral  : 10.057 142.813   1781
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 22.17 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.25), residues: 1130
  helix:  0.88 (0.19), residues: 787
  sheet:  None (None), residues: 0
  loop : -2.08 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 191 
 TYR   0.021   0.001   TYR A1473 
 PHE   0.029   0.002   PHE A1246 
 TRP   0.010   0.001   TRP A 319 
 HIS   0.004   0.001   HIS A1358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 9669)
  covalent geometry    : angle       0.81190 (13119)
  SS BOND              : bond        0.00106 (    5)
  SS BOND              : angle       0.50642 (   10)
  hydrogen bonds       : bond        0.03814 (  596)
  hydrogen bonds       : angle       4.84833 ( 1725)
  link_NAG-ASN         : bond        0.00360 (    2)
  link_NAG-ASN         : angle       2.23827 (    6)

*********************** 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
  217 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 196
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  124 ILE cc_start: 0.9552 (mt) cc_final: 0.9283 (tp)
REVERT: A  125 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8647 (t80)
REVERT: A  363 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.7716 (tmm)
REVERT: A  381 LEU cc_start: 0.8856 (tp) cc_final: 0.8631 (tp)
REVERT: A  387 PHE cc_start: 0.8848 (t80) cc_final: 0.8565 (t80)
REVERT: A  759 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8013 (tmm)
REVERT: A  767 MET cc_start: 0.7029 (mtt) cc_final: 0.6627 (mmt)
REVERT: A  807 LEU cc_start: 0.8587 (tp) cc_final: 0.8338 (tp)
REVERT: A  822 ASP cc_start: 0.8373 (t0) cc_final: 0.8038 (t70)
REVERT: A  855 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.7768 (t0)
REVERT: A 1364 ASP cc_start: 0.8123 (m-30) cc_final: 0.7762 (t0)
REVERT: A 1407 MET cc_start: 0.8695 (mmp) cc_final: 0.8368 (mmt)
REVERT: A 1449 ARG cc_start: 0.8936 (ptt90) cc_final: 0.8511 (ptt-90)
REVERT: A 1497 ILE cc_start: 0.9589 (mm) cc_final: 0.9181 (tt)
REVERT: A 1601 MET cc_start: 0.8000 (pmm) cc_final: 0.7629 (tpt)
REVERT: A 1609 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8184 (pp)
REVERT: A 1662 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7496 (mm-30)
REVERT: A 1704 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7595 (t80)
  outliers start: 21
  outliers final: 13
  residues processed: 207
  average time/residue: 0.0679
  time to fit residues: 21.8950
Evaluate side-chains
  203 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 184
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 PHE
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  409 HIS
Chi-restraints excluded: chain A residue  707 PHE
Chi-restraints excluded: chain A residue  717 TRP
Chi-restraints excluded: chain A residue  759 MET
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  811 ILE
Chi-restraints excluded: chain A residue  839 SER
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain A residue  855 ASN
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1208 ASN
Chi-restraints excluded: chain A residue 1323 LEU
Chi-restraints excluded: chain A residue 1609 LEU
Chi-restraints excluded: chain A residue 1704 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 26 optimal weight:    0.0980
   chunk 79 optimal weight:    0.0170
   chunk 35 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 93 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   overall best weight:    0.4818

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

Flipped N/Q/H residues before XYZ refinement:
A 653 ASN
** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.121089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.086339 restraints weight = 29467.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.089540 restraints weight = 13393.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.091488 restraints weight = 8679.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.092601 restraints weight = 6953.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.092974 restraints weight = 6221.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3368
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3368
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.3602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9676  Z= 0.137
  Angle     :  0.814  16.661  13135  Z= 0.391
  Chirality :  0.045   0.322   1537
  Planarity :  0.004   0.045   1580
  Dihedral  :  9.568 128.543   1781
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 22.37 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.25), residues: 1130
  helix:  0.91 (0.19), residues: 786
  sheet:  None (None), residues: 0
  loop : -2.02 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 191 
 TYR   0.010   0.001   TYR A 699 
 PHE   0.031   0.002   PHE A1246 
 TRP   0.010   0.001   TRP A 319 
 HIS   0.004   0.001   HIS A1440 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9669)
  covalent geometry    : angle       0.81325 (13119)
  SS BOND              : bond        0.00099 (    5)
  SS BOND              : angle       0.48693 (   10)
  hydrogen bonds       : bond        0.03741 (  596)
  hydrogen bonds       : angle       4.70310 ( 1725)
  link_NAG-ASN         : bond        0.00404 (    2)
  link_NAG-ASN         : angle       2.05392 (    6)

*********************** 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
  228 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 207
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  124 ILE cc_start: 0.9534 (mt) cc_final: 0.9268 (tp)
REVERT: A  125 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8635 (t80)
REVERT: A  194 SER cc_start: 0.9023 (p) cc_final: 0.8755 (t)
REVERT: A  363 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.7739 (tmm)
REVERT: A  387 PHE cc_start: 0.8795 (t80) cc_final: 0.8335 (t80)
REVERT: A  647 MET cc_start: 0.8323 (mmp) cc_final: 0.8107 (mmm)
REVERT: A  759 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7991 (tmm)
REVERT: A  767 MET cc_start: 0.7028 (mtt) cc_final: 0.6622 (mmt)
REVERT: A  807 LEU cc_start: 0.8545 (tp) cc_final: 0.8255 (tp)
REVERT: A  822 ASP cc_start: 0.8340 (t0) cc_final: 0.7977 (t70)
REVERT: A  855 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.7793 (t0)
REVERT: A 1185 ILE cc_start: 0.9457 (mt) cc_final: 0.9235 (mt)
REVERT: A 1364 ASP cc_start: 0.8087 (m-30) cc_final: 0.7726 (t0)
REVERT: A 1407 MET cc_start: 0.8640 (mmp) cc_final: 0.8318 (mmt)
REVERT: A 1449 ARG cc_start: 0.8942 (ptt90) cc_final: 0.8552 (ptp-170)
REVERT: A 1488 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.6794 (m-80)
REVERT: A 1497 ILE cc_start: 0.9574 (mm) cc_final: 0.9150 (tt)
REVERT: A 1533 GLU cc_start: 0.8750 (pp20) cc_final: 0.8549 (pp20)
REVERT: A 1601 MET cc_start: 0.8072 (pmm) cc_final: 0.7614 (tpt)
REVERT: A 1609 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8192 (pp)
REVERT: A 1662 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7452 (mm-30)
REVERT: A 1704 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7522 (t80)
  outliers start: 21
  outliers final: 12
  residues processed: 216
  average time/residue: 0.0690
  time to fit residues: 23.2694
Evaluate side-chains
  215 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 196
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 PHE
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  409 HIS
Chi-restraints excluded: chain A residue  707 PHE
Chi-restraints excluded: chain A residue  717 TRP
Chi-restraints excluded: chain A residue  759 MET
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  839 SER
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain A residue  855 ASN
Chi-restraints excluded: chain A residue 1208 ASN
Chi-restraints excluded: chain A residue 1323 LEU
Chi-restraints excluded: chain A residue 1488 TYR
Chi-restraints excluded: chain A residue 1609 LEU
Chi-restraints excluded: chain A residue 1684 MET
Chi-restraints excluded: chain A residue 1704 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 112 optimal weight:    0.0980
   chunk 14 optimal weight:    0.0170
   chunk 60 optimal weight:    0.9990
   chunk 7 optimal weight:   10.0000
   chunk 59 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.8022

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
A 820 GLN
A 850 ASN
** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.118989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.082864 restraints weight = 42568.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.086397 restraints weight = 16381.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.088666 restraints weight = 9711.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.089915 restraints weight = 7373.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.090355 restraints weight = 6436.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3314
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3314
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9676  Z= 0.143
  Angle     :  0.823  15.431  13135  Z= 0.397
  Chirality :  0.045   0.270   1537
  Planarity :  0.004   0.051   1580
  Dihedral  :  9.204 106.770   1781
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 22.56 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.25), residues: 1130
  helix:  0.88 (0.19), residues: 787
  sheet:  None (None), residues: 0
  loop : -2.09 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 191 
 TYR   0.020   0.001   TYR A1473 
 PHE   0.031   0.002   PHE A1246 
 TRP   0.009   0.001   TRP A 319 
 HIS   0.004   0.001   HIS A1358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 9669)
  covalent geometry    : angle       0.82272 (13119)
  SS BOND              : bond        0.00099 (    5)
  SS BOND              : angle       0.46998 (   10)
  hydrogen bonds       : bond        0.03743 (  596)
  hydrogen bonds       : angle       4.72953 ( 1725)
  link_NAG-ASN         : bond        0.00366 (    2)
  link_NAG-ASN         : angle       1.96092 (    6)

*********************** 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
  223 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 201
  time to evaluate  : 0.347 
Fit side-chains
TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ILE cc_start: 0.9539 (mt) cc_final: 0.9268 (tp)
REVERT: A  125 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8651 (t80)
REVERT: A  194 SER cc_start: 0.9051 (p) cc_final: 0.8786 (t)
REVERT: A  363 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.7801 (tmm)
REVERT: A  387 PHE cc_start: 0.8792 (t80) cc_final: 0.8347 (t80)
REVERT: A  759 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7987 (tmm)
REVERT: A  767 MET cc_start: 0.7041 (mtt) cc_final: 0.6605 (mmt)
REVERT: A  807 LEU cc_start: 0.8553 (tp) cc_final: 0.8328 (tp)
REVERT: A  822 ASP cc_start: 0.8375 (t0) cc_final: 0.8010 (t70)
REVERT: A  855 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.7825 (t0)
REVERT: A 1185 ILE cc_start: 0.9445 (mt) cc_final: 0.9222 (mt)
REVERT: A 1364 ASP cc_start: 0.8148 (m-30) cc_final: 0.7785 (t0)
REVERT: A 1407 MET cc_start: 0.8710 (mmp) cc_final: 0.8384 (mmt)
REVERT: A 1449 ARG cc_start: 0.8986 (ptt90) cc_final: 0.8588 (ptp-170)
REVERT: A 1488 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6817 (m-80)
REVERT: A 1497 ILE cc_start: 0.9572 (mm) cc_final: 0.9125 (tt)
REVERT: A 1601 MET cc_start: 0.8070 (pmm) cc_final: 0.7568 (tpt)
REVERT: A 1609 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8214 (pp)
REVERT: A 1662 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7463 (mm-30)
REVERT: A 1704 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7546 (t80)
  outliers start: 22
  outliers final: 15
  residues processed: 210
  average time/residue: 0.0654
  time to fit residues: 21.4983
Evaluate side-chains
  222 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 200
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 PHE
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  409 HIS
Chi-restraints excluded: chain A residue  707 PHE
Chi-restraints excluded: chain A residue  717 TRP
Chi-restraints excluded: chain A residue  759 MET
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  839 SER
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain A residue  855 ASN
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1208 ASN
Chi-restraints excluded: chain A residue 1323 LEU
Chi-restraints excluded: chain A residue 1488 TYR
Chi-restraints excluded: chain A residue 1586 ILE
Chi-restraints excluded: chain A residue 1609 LEU
Chi-restraints excluded: chain A residue 1684 MET
Chi-restraints excluded: chain A residue 1704 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 17 optimal weight:    0.1980
   chunk 8 optimal weight:    3.9990
   chunk 41 optimal weight:    0.3980
   chunk 77 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 84 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 653 ASN
A 820 GLN
A 850 ASN
** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.119950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.084560 restraints weight = 33804.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.087891 restraints weight = 14481.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.089917 restraints weight = 9097.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.091159 restraints weight = 7133.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.091595 restraints weight = 6297.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3332
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3332
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.3898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9676  Z= 0.140
  Angle     :  0.833  15.698  13135  Z= 0.399
  Chirality :  0.045   0.297   1537
  Planarity :  0.004   0.066   1580
  Dihedral  :  8.845  83.909   1781
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 23.36 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.25), residues: 1130
  helix:  0.87 (0.19), residues: 787
  sheet:  None (None), residues: 0
  loop : -2.09 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 191 
 TYR   0.011   0.001   TYR A 699 
 PHE   0.033   0.002   PHE A1246 
 TRP   0.023   0.001   TRP A1382 
 HIS   0.004   0.001   HIS A1440 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9669)
  covalent geometry    : angle       0.83200 (13119)
  SS BOND              : bond        0.00102 (    5)
  SS BOND              : angle       0.47671 (   10)
  hydrogen bonds       : bond        0.03735 (  596)
  hydrogen bonds       : angle       4.69108 ( 1725)
  link_NAG-ASN         : bond        0.00374 (    2)
  link_NAG-ASN         : angle       1.88427 (    6)

********************** 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
  221 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 200
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  124 ILE cc_start: 0.9524 (mt) cc_final: 0.9252 (tp)
REVERT: A  125 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8636 (t80)
REVERT: A  194 SER cc_start: 0.9040 (p) cc_final: 0.8780 (t)
REVERT: A  387 PHE cc_start: 0.8815 (t80) cc_final: 0.8346 (t80)
REVERT: A  390 ILE cc_start: 0.8448 (pt) cc_final: 0.8175 (mm)
REVERT: A  759 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7968 (tmm)
REVERT: A  767 MET cc_start: 0.7029 (mtt) cc_final: 0.6605 (mmt)
REVERT: A  807 LEU cc_start: 0.8557 (tp) cc_final: 0.8268 (tp)
REVERT: A  822 ASP cc_start: 0.8354 (t0) cc_final: 0.7982 (t70)
REVERT: A  855 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.7828 (t0)
REVERT: A 1185 ILE cc_start: 0.9443 (mt) cc_final: 0.9222 (mt)
REVERT: A 1364 ASP cc_start: 0.8134 (m-30) cc_final: 0.7773 (t0)
REVERT: A 1449 ARG cc_start: 0.8991 (ptt90) cc_final: 0.8608 (ptp-170)
REVERT: A 1488 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6745 (m-80)
REVERT: A 1497 ILE cc_start: 0.9585 (mm) cc_final: 0.9120 (tt)
REVERT: A 1601 MET cc_start: 0.8066 (pmm) cc_final: 0.7678 (tpt)
REVERT: A 1609 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8124 (pp)
REVERT: A 1662 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7441 (mm-30)
REVERT: A 1704 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7528 (t80)
  outliers start: 21
  outliers final: 15
  residues processed: 208
  average time/residue: 0.0673
  time to fit residues: 21.5177
Evaluate side-chains
  218 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 197
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 PHE
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  409 HIS
Chi-restraints excluded: chain A residue  707 PHE
Chi-restraints excluded: chain A residue  717 TRP
Chi-restraints excluded: chain A residue  759 MET
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  839 SER
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain A residue  855 ASN
Chi-restraints excluded: chain A residue 1208 ASN
Chi-restraints excluded: chain A residue 1323 LEU
Chi-restraints excluded: chain A residue 1488 TYR
Chi-restraints excluded: chain A residue 1586 ILE
Chi-restraints excluded: chain A residue 1609 LEU
Chi-restraints excluded: chain A residue 1684 MET
Chi-restraints excluded: chain A residue 1704 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 66 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   chunk 75 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 23 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
A 820 GLN
A 850 ASN
** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.119300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.084246 restraints weight = 31639.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.087403 restraints weight = 13991.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.089354 restraints weight = 8968.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.090480 restraints weight = 7114.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.090767 restraints weight = 6342.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3315
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3315
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9676  Z= 0.146
  Angle     :  0.840  15.200  13135  Z= 0.408
  Chirality :  0.046   0.268   1537
  Planarity :  0.004   0.063   1580
  Dihedral  :  8.493  84.084   1781
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 23.16 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.25), residues: 1130
  helix:  0.84 (0.19), residues: 786
  sheet:  None (None), residues: 0
  loop : -2.07 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 191 
 TYR   0.019   0.001   TYR A1473 
 PHE   0.034   0.002   PHE A1246 
 TRP   0.035   0.001   TRP A1382 
 HIS   0.004   0.001   HIS A1358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 9669)
  covalent geometry    : angle       0.83693 (13119)
  SS BOND              : bond        0.00342 (    5)
  SS BOND              : angle       2.45032 (   10)
  hydrogen bonds       : bond        0.03726 (  596)
  hydrogen bonds       : angle       4.73731 ( 1725)
  link_NAG-ASN         : bond        0.00348 (    2)
  link_NAG-ASN         : angle       1.87362 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1828.88 seconds
wall clock time: 32 minutes 8.28 seconds (1928.28 seconds total)