Starting phenix.real_space_refine
on Thu Jul  2 17:29:04 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7wfw_32476/07_2026/7wfw_32476.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wfw_32476/07_2026/7wfw_32476.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wfw_32476/07_2026/7wfw_32476.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wfw_32476/07_2026/7wfw_32476.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wfw_32476/07_2026/7wfw_32476.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wfw_32476/07_2026/7wfw_32476.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7wfw_32476/07_2026/7wfw_32476.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7wfw_32476/07_2026/7wfw_32476.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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: 5
    Type Number    sf(0)   Gaussians
     P      13      5.49       5
     S      58      5.16       5
     C    5828      2.51       5
     N    1300      2.21       5
     O    1490      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 102 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8689
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 8064
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 998, 8054
          Classifications: {'peptide': 998}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 968}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
      Conformer: "B"
        Number of residues, atoms: 998, 8054
          Classifications: {'peptide': 998}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 968}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          bond proxies already assigned to first conformer: 8246
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 597
          Unusual residues: {'CLR': 4, 'LPE': 8, 'NAG': 4, 'PCW': 3}
          Classifications: {'peptide': 2, 'undetermined': 19}
          Link IDs: {'TRANS': 1, None: 19}
            Not linked:
              pdbres="NAG A2001 "
              pdbres="NAG A2002 "
            Not linked:
              pdbres="NAG A2002 "
              pdbres="NAG A2003 "
            Not linked:
              pdbres="NAG A2003 "
              pdbres="NAG A2004 "
            Not linked:
              pdbres="NAG A2004 "
              pdbres="CLR A2005 "
            Not linked:
              pdbres="CLR A2005 "
              pdbres="PCW A2006 "
            ... (remaining 14 not shown)
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 109
          Unresolved non-hydrogen chiralities: 4
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS A1631 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A1631 " occ=0.50
  Time building chain proxies: 3.17, per 1000 atoms: 0.36
  Number of scatterers: 8689
  At special positions: 0
  Unit cell: (129.9, 101.755, 100.672, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      58     16.00
     P      13     15.00
     O    1490      8.00
     N    1300      7.00
     C    5828      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 276 " - pdb=" SG  CYS A 319 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 310 " - pdb=" SG  CYS A 325 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 857 " - pdb=" SG  CYS A 866 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1310 " - pdb=" SG  CYS A1332 " distance=2.00
    Simple disulfide: pdb=" SG  CYS A1678 " - pdb=" SG  CYS A1692 " distance=2.02

  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
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG A2001 " - " ASN A 819 "
      " NAG A2002 " - " ASN A 312 "
      " NAG A2003 " - " ASN A1328 "
      " NAG A2004 " - " ASN A1312 "
      " NAG B   1 " - " ASN A1336 "
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 558.6 milliseconds
  

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1890

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 2 sheets defined
      75.7% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 232 through 245
      removed outlier: 3.514A  pdb=" N   ALA A 238 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 269
      removed outlier: 3.650A  pdb=" N   ILE A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 354
    Processing helix  chain 'A' and resid 357 through 369
      removed outlier: 3.859A  pdb=" N   LEU A 361 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 372
      No H-bonds generated for 'chain 'A' and resid 370 through 372'
    Processing helix  chain 'A' and resid 373 through 383
      removed outlier: 3.946A  pdb=" N   PHE A 377 " --> pdb=" O   TYR A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 407
      removed outlier: 3.853A  pdb=" N   ILE A 392 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ALA A 394 " --> pdb=" O   ASN A 390 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   THR A 397 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   MET A 398 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 659
    Processing helix  chain 'A' and resid 666 through 683
      removed outlier: 3.644A  pdb=" N   THR A 670 " --> pdb=" O   PHE A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 717
      removed outlier: 3.621A  pdb=" N   GLU A 694 " --> pdb=" O   SER A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 726
    Processing helix  chain 'A' and resid 727 through 746
      removed outlier: 4.059A  pdb=" N   ILE A 731 " --> pdb=" O   LYS A 727 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   PHE A 732 " --> pdb=" O   LYS A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 757
      removed outlier: 3.742A  pdb=" N   ARG A 756 " --> pdb=" O   LEU A 752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 766
      removed outlier: 3.538A  pdb=" N   LEU A 761 " --> pdb=" O   PHE A 758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 784
    Processing helix  chain 'A' and resid 787 through 816
      removed outlier: 3.711A  pdb=" N   THR A 791 " --> pdb=" O   LEU A 787 " (cutoff:3.500A)
      removed outlier: 5.254A  pdb=" N   GLU A 811 " --> pdb=" O   GLN A 807 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   ASN A 812 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   TYR A 813 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 820
    Processing helix  chain 'A' and resid 834 through 848
    Processing helix  chain 'A' and resid 850 through 861
      removed outlier: 4.002A  pdb=" N   MET A 854 " --> pdb=" O   TRP A 850 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ALA A 856 " --> pdb=" O   GLU A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 894
      removed outlier: 3.571A  pdb=" N   CYS A 866 " --> pdb=" O   GLN A 862 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   LEU A 882 " --> pdb=" O   ASN A 878 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER A 892 " --> pdb=" O   LEU A 888 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   PHE A 893 " --> pdb=" O   LEU A 889 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1137 through 1150
      removed outlier: 3.847A  pdb=" N   GLU A1150 " --> pdb=" O   TYR A1146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1151 through 1168
    Processing helix  chain 'A' and resid 1173 through 1179
      removed outlier: 4.114A  pdb=" N   ASP A1177 " --> pdb=" O   TYR A1174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1181 through 1209
    Processing helix  chain 'A' and resid 1209 through 1216
      removed outlier: 4.098A  pdb=" N   PHE A1214 " --> pdb=" O   PHE A1210 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   THR A1215 " --> pdb=" O   LYS A1211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1218 through 1238
      removed outlier: 3.824A  pdb=" N   ASP A1222 " --> pdb=" O   TRP A1218 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   THR A1234 " --> pdb=" O   LEU A1230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1243 through 1251
      removed outlier: 3.735A  pdb=" N   THR A1251 " --> pdb=" O   LYS A1247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1252 through 1258
      Proline residue:  A1257  - end of helix
    Processing helix  chain 'A' and resid 1259 through 1264
      removed outlier: 4.530A  pdb=" N   ARG A1263 " --> pdb=" O   ARG A1259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1276
    Processing helix  chain 'A' and resid 1277 through 1304
      removed outlier: 3.516A  pdb=" N   PHE A1295 " --> pdb=" O   PHE A1291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1328 through 1333
      removed outlier: 3.555A  pdb=" N   CYS A1332 " --> pdb=" O   ASN A1328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1352 through 1365
    Processing helix  chain 'A' and resid 1368 through 1378
      removed outlier: 3.839A  pdb=" N   ILE A1372 " --> pdb=" O   GLY A1368 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA A1375 " --> pdb=" O   ASP A1371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1391 through 1393
      No H-bonds generated for 'chain 'A' and resid 1391 through 1393'
    Processing helix  chain 'A' and resid 1394 through 1428
      removed outlier: 3.731A  pdb=" N   PHE A1398 " --> pdb=" O   MET A1394 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU A1428 " --> pdb=" O   GLN A1424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1436 through 1450
      removed outlier: 3.655A  pdb=" N   LYS A1440 " --> pdb=" O   THR A1436 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LYS A1441 " --> pdb=" O   GLU A1437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1463 through 1474
      removed outlier: 3.871A  pdb=" N   PHE A1470 " --> pdb=" O   GLN A1466 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR A1474 " --> pdb=" O   PHE A1470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1475 through 1495
      removed outlier: 4.261A  pdb=" N   ASP A1479 " --> pdb=" O   ARG A1475 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL A1495 " --> pdb=" O   ILE A1491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1501 through 1530
      removed outlier: 3.902A  pdb=" N   THR A1505 " --> pdb=" O   SER A1501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1532 through 1537
      removed outlier: 3.593A  pdb=" N   ASN A1537 " --> pdb=" O   TYR A1533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1538 through 1561
    Processing helix  chain 'A' and resid 1569 through 1576
      removed outlier: 3.618A  pdb=" N   ARG A1573 " --> pdb=" O   PRO A1569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1579 through 1585
      removed outlier: 3.651A  pdb=" N   ILE A1583 " --> pdb=" O   ARG A1579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1586 through 1589
      removed outlier: 4.244A  pdb=" N   ALA A1589 " --> pdb=" O   LEU A1586 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1586 through 1589'
    Processing helix  chain 'A' and resid 1590 through 1629
      Proline residue:  A1605  - end of helix
    Processing helix  chain 'A' and resid 1646 through 1659
      removed outlier: 4.355A  pdb=" N   THR A1659 " --> pdb=" O   PHE A1655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1662 through 1668
    Processing helix  chain 'A' and resid 1694 through 1725
      removed outlier: 3.869A  pdb=" N   ILE A1700 " --> pdb=" O   ALA A1696 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   THR A1703 " --> pdb=" O   ILE A1699 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE A1706 " --> pdb=" O   PHE A1702 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ASN A1715 " --> pdb=" O   LEU A1711 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA A1719 " --> pdb=" O   ASN A1715 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL A1720 " --> pdb=" O   MET A1716 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE A1725 " --> pdb=" O   ILE A1721 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 274 through 278
      removed outlier: 3.677A  pdb=" N   LEU A 326 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A 277 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE A 324 " --> pdb=" O   VAL A 277 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1318 through 1320

    512 hydrogen bonds defined for protein.
    1494 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: 1.51

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1562
        1.33 -     1.45: 2264
        1.45 -     1.58: 4944
        1.58 -     1.70: 28
        1.70 -     1.82: 96
  Bond restraints: 8894
  Sorted by residual:
  bond pdb=" C   PRO A1630 "
       pdb=" N  AHIS A1631 "
    ideal  model  delta    sigma   weight residual
    1.332  1.471 -0.139 1.52e-02 4.33e+03 8.34e+01
  bond pdb=" C38 P5S A2020 "
       pdb=" O37 P5S A2020 "
    ideal  model  delta    sigma   weight residual
    1.331  1.463 -0.132 2.00e-02 2.50e+03 4.34e+01
  bond pdb=" C17 P5S A2020 "
       pdb=" O19 P5S A2020 "
    ideal  model  delta    sigma   weight residual
    1.328  1.457 -0.129 2.00e-02 2.50e+03 4.18e+01
  bond pdb=" C11 PCW A2011 "
       pdb=" O3  PCW A2011 "
    ideal  model  delta    sigma   weight residual
    1.326  1.455 -0.129 2.00e-02 2.50e+03 4.13e+01
  bond pdb=" C11 PCW A2007 "
       pdb=" O3  PCW A2007 "
    ideal  model  delta    sigma   weight residual
    1.326  1.453 -0.127 2.00e-02 2.50e+03 4.02e+01
  ... (remaining 8889 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 11146
        2.41 -     4.83: 656
        4.83 -     7.24: 165
        7.24 -     9.65: 35
        9.65 -    12.07: 12
  Bond angle restraints: 12014
  Sorted by residual:
  angle pdb=" N   ILE A 381 "
        pdb=" CA  ILE A 381 "
        pdb=" C   ILE A 381 "
      ideal   model   delta    sigma   weight residual
     111.81  102.26    9.55 8.60e-01 1.35e+00 1.23e+02
  angle pdb=" N   GLY A 810 "
        pdb=" CA  GLY A 810 "
        pdb=" C   GLY A 810 "
      ideal   model   delta    sigma   weight residual
     112.73  124.35  -11.62 1.20e+00 6.94e-01 9.38e+01
  angle pdb=" N   ARG A 817 "
        pdb=" CA  ARG A 817 "
        pdb=" C   ARG A 817 "
      ideal   model   delta    sigma   weight residual
     112.38  124.01  -11.63 1.22e+00 6.72e-01 9.09e+01
  angle pdb=" N   LYS A1329 "
        pdb=" CA  LYS A1329 "
        pdb=" C   LYS A1329 "
      ideal   model   delta    sigma   weight residual
     112.23  103.25    8.98 1.26e+00 6.30e-01 5.08e+01
  angle pdb=" N   LEU A 809 "
        pdb=" CA  LEU A 809 "
        pdb=" C   LEU A 809 "
      ideal   model   delta    sigma   weight residual
     111.36  118.96   -7.60 1.09e+00 8.42e-01 4.86e+01
  ... (remaining 12009 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.50: 4916
       32.50 -    65.00: 273
       65.00 -    97.50: 18
       97.50 -   129.99: 3
      129.99 -   162.49: 3
  Dihedral angle restraints: 5213
    sinusoidal: 2294
      harmonic: 2919
  Sorted by residual:
  dihedral pdb=" CB  CYS A 857 "
           pdb=" SG  CYS A 857 "
           pdb=" SG  CYS A 866 "
           pdb=" CB  CYS A 866 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -173.35   87.35     1      1.00e+01 1.00e-02 9.16e+01
  dihedral pdb=" CB  CYS A1310 "
           pdb=" SG  CYS A1310 "
           pdb=" SG  CYS A1332 "
           pdb=" CB  CYS A1332 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.16  -80.16     1      1.00e+01 1.00e-02 7.96e+01
  dihedral pdb=" CA  PRO A 332 "
           pdb=" C   PRO A 332 "
           pdb=" N   ASP A 333 "
           pdb=" CA  ASP A 333 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.22  -25.78     0      5.00e+00 4.00e-02 2.66e+01
  ... (remaining 5210 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.145: 1309
       0.145 -    0.290: 48
       0.290 -    0.434: 3
       0.434 -    0.579: 1
       0.579 -    0.724: 2
  Chirality restraints: 1363
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.32   -0.08 2.00e-02 2.50e+03 1.66e+01
  chirality pdb=" C1  NAG A2001 "
            pdb=" ND2 ASN A 819 "
            pdb=" C2  NAG A2001 "
            pdb=" O5  NAG A2001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.68   -0.72 2.00e-01 2.50e+01 1.31e+01
  chirality pdb=" C1  NAG A2004 "
            pdb=" ND2 ASN A1312 "
            pdb=" C2  NAG A2004 "
            pdb=" O5  NAG A2004 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.74   -0.66 2.00e-01 2.50e+01 1.09e+01
  ... (remaining 1360 not shown)

  Planarity restraints: 1399
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A2001 "    0.313 2.00e-02 2.50e+03   2.75e-01 9.48e+02
        pdb=" C7  NAG A2001 "   -0.070 2.00e-02 2.50e+03
        pdb=" C8  NAG A2001 "    0.082 2.00e-02 2.50e+03
        pdb=" N2  NAG A2001 "   -0.492 2.00e-02 2.50e+03
        pdb=" O7  NAG A2001 "    0.166 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A2004 "   -0.282 2.00e-02 2.50e+03   2.38e-01 7.08e+02
        pdb=" C7  NAG A2004 "    0.081 2.00e-02 2.50e+03
        pdb=" C8  NAG A2004 "   -0.185 2.00e-02 2.50e+03
        pdb=" N2  NAG A2004 "    0.404 2.00e-02 2.50e+03
        pdb=" O7  NAG A2004 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   1 "    0.272 2.00e-02 2.50e+03   2.28e-01 6.48e+02
        pdb=" C7  NAG B   1 "   -0.072 2.00e-02 2.50e+03
        pdb=" C8  NAG B   1 "    0.181 2.00e-02 2.50e+03
        pdb=" N2  NAG B   1 "   -0.383 2.00e-02 2.50e+03
        pdb=" O7  NAG B   1 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1396 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 1014
        2.73 -     3.28: 8931
        3.28 -     3.82: 13457
        3.82 -     4.36: 16821
        4.36 -     4.90: 28511
  Nonbonded interactions: 68734
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A1537 "
            pdb=" N   GLY A1538 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" N   GLU A1502 "
            pdb=" OE1 GLU A1502 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" O   THR A1659 "
            pdb=" OG  SER A1660 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" OH  TYR A1443 "
            pdb=" OE2 GLU A1723 "
     model   vdw
     2.397 3.040
  nonbonded pdb=" OD2 ASP A1543 "
            pdb=" NH2 ARG A1588 "
     model   vdw
     2.407 3.120
  ... (remaining 68729 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.500
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     11.200
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
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      :  0.013   0.139   8905  Z= 0.585
  Angle     :  1.545  51.577  12042  Z= 0.769
  Chirality :  0.073   0.724   1363
  Planarity :  0.015   0.275   1394
  Dihedral  : 19.078 162.492   3308
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 21.66
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.38 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.16 %
    Favored  : 96.73 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -2.32 (0.24), residues: 993
  helix: -0.93 (0.18), residues: 685
  sheet: -2.91 (1.00), residues: 22
  loop : -2.65 (0.33), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.002   ARG A 814 
 TYR   0.023   0.003   TYR A 362 
 PHE   0.027   0.004   PHE A 659 
 TRP   0.088   0.005   TRP A1369 
 HIS   0.018   0.003   HIS A 833 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01254 /  0.58 ( 8894)
  covalent geometry    : angle       1.41106 /  0.73 (12014)
  SS BOND              : bond        0.01342 /  0.70 (    5)
  SS BOND              : angle      11.91178 /  5.97 (   10)
  hydrogen bonds       : bond        0.15822 / 10.51 (  512)
  hydrogen bonds       : angle       7.24038 /  5.07 ( 1494)
  link_BETA1-4         : bond        0.00018 /  0.01 (    1)
  link_BETA1-4         : angle       0.02522 /  0.01 (    3)
  link_NAG-ASN         : bond        0.07447 /  3.79 (    5)
  link_NAG-ASN         : angle      15.10713 /  9.58 (   15)

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A  689 MET cc_start: 0.7771 (mtt) cc_final: 0.7510 (mtt)
REVERT: A 1397 TYR cc_start: 0.7246 (t80) cc_final: 0.6163 (t80)
REVERT: A 1579 ARG cc_start: 0.6253 (mtt180) cc_final: 0.5808 (mtt180)
REVERT: A 1705 TYR cc_start: 0.7089 (t80) cc_final: 0.6532 (t80)
REVERT: A 1712 ILE cc_start: 0.6777 (mm) cc_final: 0.6564 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0836
  time to fit residues: 16.1329
Evaluate side-chains
  121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 274 ASN
A 300 ASN
A 331 ASN
A 355 GLN
** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 730 ASN
** A 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 853 ASN
A1301 ASN
A1431 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.197564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.162295 restraints weight = 17837.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.4036 rms_B_bonded: 2.23
r_work: 0.3868 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3888
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3888 r_free = 0.3888    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3888 r_free = 0.3888    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3888
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.114   8905  Z= 0.164
  Angle     :  0.747  10.359  12042  Z= 0.371
  Chirality :  0.045   0.452   1363
  Planarity :  0.005   0.054   1394
  Dihedral  : 16.546 168.599   1439
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 10.95 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -0.69 (0.26), residues: 993
  helix:  0.31 (0.19), residues: 701
  sheet:  None (None), residues: 0
  loop : -2.27 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 814 
 TYR   0.028   0.002   TYR A1717 
 PHE   0.029   0.002   PHE A1514 
 TRP   0.038   0.002   TRP A 850 
 HIS   0.010   0.002   HIS A 833 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.16 ( 8894)
  covalent geometry    : angle       0.72894 /  0.37 (12014)
  SS BOND              : bond        0.00701 /  0.35 (    5)
  SS BOND              : angle       3.68506 /  1.35 (   10)
  hydrogen bonds       : bond        0.04672 /  3.13 (  512)
  hydrogen bonds       : angle       4.98619 /  3.51 ( 1494)
  link_BETA1-4         : bond        0.00489 /  0.26 (    1)
  link_BETA1-4         : angle       1.31933 /  0.76 (    3)
  link_NAG-ASN         : bond        0.00289 /  0.15 (    5)
  link_NAG-ASN         : angle       3.55730 /  2.13 (   15)

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 130
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: A  379 LEU cc_start: 0.7272 (tp) cc_final: 0.7067 (tp)
REVERT: A 1397 TYR cc_start: 0.7481 (t80) cc_final: 0.6880 (t80)
REVERT: A 1527 MET cc_start: 0.8078 (mtm) cc_final: 0.7606 (mtm)
REVERT: A 1579 ARG cc_start: 0.6275 (mtt180) cc_final: 0.5612 (mtt180)
  outliers start: 8
  outliers final: 3
  residues processed: 134
  average time/residue: 0.0784
  time to fit residues: 14.7379
Evaluate side-chains
  118 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 115
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue 1435 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 93 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 71 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 73 optimal weight:   20.0000
   chunk 56 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 355 GLN
** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 891 ASN
A1301 ASN
A1444 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.206545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.174149 restraints weight = 23573.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.4214 rms_B_bonded: 3.56
r_work: 0.3949 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3968
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3968 r_free = 0.3968    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3968 r_free = 0.3968    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (8 function evaluations)
r_final: 0.3968
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   8905  Z= 0.143
  Angle     :  0.677  12.716  12042  Z= 0.334
  Chirality :  0.042   0.375   1363
  Planarity :  0.004   0.052   1394
  Dihedral  : 15.618 178.293   1439
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 13.77 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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 (0.27), residues: 993
  helix:  0.83 (0.20), residues: 691
  sheet:  None (None), residues: 0
  loop : -2.05 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 814 
 TYR   0.028   0.002   TYR A1705 
 PHE   0.025   0.001   PHE A 707 
 TRP   0.021   0.002   TRP A1369 
 HIS   0.007   0.001   HIS A 833 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.14 ( 8894)
  covalent geometry    : angle       0.65634 /  0.33 (12014)
  SS BOND              : bond        0.00719 /  0.44 (    5)
  SS BOND              : angle       3.21696 /  1.48 (   10)
  hydrogen bonds       : bond        0.04303 /  2.88 (  512)
  hydrogen bonds       : angle       4.68021 /  3.28 ( 1494)
  link_BETA1-4         : bond        0.00357 /  0.19 (    1)
  link_BETA1-4         : angle       0.94394 /  0.53 (    3)
  link_NAG-ASN         : bond        0.00388 /  0.19 (    5)
  link_NAG-ASN         : angle       3.92414 /  2.47 (   15)

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  383 LEU cc_start: 0.7019 (mt) cc_final: 0.6652 (mt)
REVERT: A 1388 TRP cc_start: 0.7647 (t-100) cc_final: 0.7357 (t-100)
REVERT: A 1397 TYR cc_start: 0.7789 (t80) cc_final: 0.7397 (t80)
REVERT: A 1527 MET cc_start: 0.8117 (mtm) cc_final: 0.7700 (mtm)
REVERT: A 1579 ARG cc_start: 0.6416 (mtt180) cc_final: 0.5706 (mtt180)
  outliers start: 8
  outliers final: 3
  residues processed: 129
  average time/residue: 0.0708
  time to fit residues: 13.1126
Evaluate side-chains
  121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 118
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue 1157 PHE
Chi-restraints excluded: chain A residue 1285 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 7 optimal weight:    0.5980
   chunk 26 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    1.5188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN
A 390 ASN
** A 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 891 ASN
** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1391 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.194366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.159881 restraints weight = 22065.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.4012 rms_B_bonded: 3.26
r_work: 0.3789 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3807
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3807 r_free = 0.3807    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3807 r_free = 0.3807    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (10 function evaluations)
r_final: 0.3807
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.092   8905  Z= 0.181
  Angle     :  0.705  11.852  12042  Z= 0.346
  Chirality :  0.043   0.462   1363
  Planarity :  0.004   0.049   1394
  Dihedral  : 15.086 167.229   1439
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 16.59 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -0.08 (0.27), residues: 993
  helix:  0.85 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -2.19 (0.33), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1380 
 TYR   0.032   0.002   TYR A1705 
 PHE   0.024   0.002   PHE A 707 
 TRP   0.054   0.002   TRP A 850 
 HIS   0.006   0.001   HIS A 833 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00441 /  0.18 ( 8894)
  covalent geometry    : angle       0.68450 /  0.34 (12014)
  SS BOND              : bond        0.00639 /  0.34 (    5)
  SS BOND              : angle       3.62127 /  1.46 (   10)
  hydrogen bonds       : bond        0.04494 /  3.01 (  512)
  hydrogen bonds       : angle       4.73575 /  3.32 ( 1494)
  link_BETA1-4         : bond        0.00358 /  0.19 (    1)
  link_BETA1-4         : angle       0.87340 /  0.49 (    3)
  link_NAG-ASN         : bond        0.00536 /  0.29 (    5)
  link_NAG-ASN         : angle       3.86114 /  2.38 (   15)

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  383 LEU cc_start: 0.7110 (mt) cc_final: 0.6818 (mt)
REVERT: A  398 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6324 (mtm)
REVERT: A 1397 TYR cc_start: 0.7641 (t80) cc_final: 0.7133 (t80)
REVERT: A 1527 MET cc_start: 0.8090 (mtm) cc_final: 0.7677 (mtm)
REVERT: A 1579 ARG cc_start: 0.6530 (mtt180) cc_final: 0.5733 (mtt180)
  outliers start: 9
  outliers final: 6
  residues processed: 129
  average time/residue: 0.0815
  time to fit residues: 15.1501
Evaluate side-chains
  127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 120
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  729 TRP
Chi-restraints excluded: chain A residue  891 ASN
Chi-restraints excluded: chain A residue 1285 LEU
Chi-restraints excluded: chain A residue 1638 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 71 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 79 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0050
   chunk 95 optimal weight:    0.9990
   overall best weight:    0.6996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 279 ASN
A 833 HIS
A1444 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.206591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.173769 restraints weight = 21706.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.4214 rms_B_bonded: 2.78
r_work: 0.3976 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3989
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3989 r_free = 0.3989    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3989 r_free = 0.3989    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3989
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8905  Z= 0.130
  Angle     :  0.639  10.737  12042  Z= 0.313
  Chirality :  0.041   0.392   1363
  Planarity :  0.004   0.047   1394
  Dihedral  : 14.390 156.287   1439
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 18.17 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.22 (0.27), residues: 993
  helix:  1.07 (0.20), residues: 695
  sheet:  None (None), residues: 0
  loop : -2.08 (0.33), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 814 
 TYR   0.029   0.002   TYR A1705 
 PHE   0.026   0.001   PHE A 707 
 TRP   0.034   0.002   TRP A 850 
 HIS   0.004   0.001   HIS A 833 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 ( 8894)
  covalent geometry    : angle       0.62455 /  0.31 (12014)
  SS BOND              : bond        0.00460 /  0.24 (    5)
  SS BOND              : angle       2.75763 /  1.18 (   10)
  hydrogen bonds       : bond        0.04010 /  2.67 (  512)
  hydrogen bonds       : angle       4.48801 /  3.14 ( 1494)
  link_BETA1-4         : bond        0.00336 /  0.18 (    1)
  link_BETA1-4         : angle       0.70856 /  0.40 (    3)
  link_NAG-ASN         : bond        0.00481 /  0.25 (    5)
  link_NAG-ASN         : angle       3.19645 /  1.97 (   15)

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 127
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  383 LEU cc_start: 0.6897 (mt) cc_final: 0.6673 (mt)
REVERT: A  398 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6413 (mtm)
REVERT: A 1388 TRP cc_start: 0.7640 (t-100) cc_final: 0.7407 (t-100)
REVERT: A 1397 TYR cc_start: 0.7688 (t80) cc_final: 0.7340 (t80)
REVERT: A 1527 MET cc_start: 0.8051 (mtm) cc_final: 0.7693 (mtm)
REVERT: A 1579 ARG cc_start: 0.6492 (mtt180) cc_final: 0.5737 (mtt180)
  outliers start: 5
  outliers final: 3
  residues processed: 130
  average time/residue: 0.0704
  time to fit residues: 13.1450
Evaluate side-chains
  127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 123
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  729 TRP
Chi-restraints excluded: chain A residue 1285 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0000
   chunk 16 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    1.3790

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 279 ASN
A 891 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.194606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.161020 restraints weight = 16014.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.4013 rms_B_bonded: 1.91
r_work: 0.3867 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3730 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3754
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3754 r_free = 0.3754    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3754 r_free = 0.3754    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3754
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   8905  Z= 0.166
  Angle     :  0.670  11.921  12042  Z= 0.329
  Chirality :  0.042   0.426   1363
  Planarity :  0.004   0.046   1394
  Dihedral  : 14.130 152.395   1439
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 18.17 %
    Favored  : 80.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.27), residues: 993
  helix:  1.08 (0.20), residues: 686
  sheet: -3.97 (1.04), residues: 10
  loop : -1.99 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1380 
 TYR   0.026   0.002   TYR A1705 
 PHE   0.023   0.002   PHE A1401 
 TRP   0.026   0.002   TRP A 850 
 HIS   0.004   0.001   HIS A 833 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00400 /  0.17 ( 8894)
  covalent geometry    : angle       0.65478 /  0.33 (12014)
  SS BOND              : bond        0.00543 /  0.29 (    5)
  SS BOND              : angle       2.78922 /  1.17 (   10)
  hydrogen bonds       : bond        0.04331 /  2.89 (  512)
  hydrogen bonds       : angle       4.60437 /  3.22 ( 1494)
  link_BETA1-4         : bond        0.00317 /  0.17 (    1)
  link_BETA1-4         : angle       0.66105 /  0.38 (    3)
  link_NAG-ASN         : bond        0.00469 /  0.26 (    5)
  link_NAG-ASN         : angle       3.44304 /  2.10 (   15)

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  383 LEU cc_start: 0.7083 (mt) cc_final: 0.6818 (mt)
REVERT: A  398 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6440 (mtm)
REVERT: A  765 LYS cc_start: 0.8050 (tptp) cc_final: 0.7624 (tptp)
REVERT: A 1397 TYR cc_start: 0.7671 (t80) cc_final: 0.7159 (t80)
REVERT: A 1527 MET cc_start: 0.7824 (mtm) cc_final: 0.7326 (mtm)
REVERT: A 1579 ARG cc_start: 0.6634 (mtt180) cc_final: 0.5723 (mtt180)
REVERT: A 1641 MET cc_start: 0.8368 (ttm) cc_final: 0.8154 (ttm)
  outliers start: 10
  outliers final: 7
  residues processed: 129
  average time/residue: 0.0761
  time to fit residues: 13.9929
Evaluate side-chains
  133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 125
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  729 TRP
Chi-restraints excluded: chain A residue  891 ASN
Chi-restraints excluded: chain A residue 1285 LEU
Chi-restraints excluded: chain A residue 1434 PHE
Chi-restraints excluded: chain A residue 1638 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   overall best weight:    1.1182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 891 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.195824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.162235 restraints weight = 12136.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.4043 rms_B_bonded: 1.70
r_work: 0.3915 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3800 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3817
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3817 r_free = 0.3817    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3817 r_free = 0.3817    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3817
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.2635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8905  Z= 0.147
  Angle     :  0.650  11.270  12042  Z= 0.319
  Chirality :  0.041   0.395   1363
  Planarity :  0.004   0.045   1394
  Dihedral  : 13.871 148.847   1439
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 19.07 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.27 (0.27), residues: 993
  helix:  1.14 (0.20), residues: 688
  sheet: -4.02 (1.00), residues: 10
  loop : -1.99 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 762 
 TYR   0.027   0.002   TYR A1717 
 PHE   0.026   0.001   PHE A 707 
 TRP   0.021   0.001   TRP A 850 
 HIS   0.004   0.001   HIS A 833 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.15 ( 8894)
  covalent geometry    : angle       0.63614 /  0.32 (12014)
  SS BOND              : bond        0.00494 /  0.27 (    5)
  SS BOND              : angle       2.53236 /  1.11 (   10)
  hydrogen bonds       : bond        0.04119 /  2.75 (  512)
  hydrogen bonds       : angle       4.52217 /  3.17 ( 1494)
  link_BETA1-4         : bond        0.00226 /  0.12 (    1)
  link_BETA1-4         : angle       0.57821 /  0.34 (    3)
  link_NAG-ASN         : bond        0.00463 /  0.24 (    5)
  link_NAG-ASN         : angle       3.21011 /  1.97 (   15)

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: A  383 LEU cc_start: 0.6962 (mt) cc_final: 0.6676 (mt)
REVERT: A  398 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6361 (mtm)
REVERT: A  765 LYS cc_start: 0.7999 (tptp) cc_final: 0.7615 (tptp)
REVERT: A 1397 TYR cc_start: 0.7753 (t80) cc_final: 0.7263 (t80)
REVERT: A 1527 MET cc_start: 0.7744 (mtm) cc_final: 0.7311 (mtm)
REVERT: A 1579 ARG cc_start: 0.6510 (mtt180) cc_final: 0.5608 (mtt180)
REVERT: A 1641 MET cc_start: 0.8349 (ttm) cc_final: 0.8128 (ttm)
  outliers start: 8
  outliers final: 6
  residues processed: 133
  average time/residue: 0.0673
  time to fit residues: 12.8478
Evaluate side-chains
  133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 126
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  729 TRP
Chi-restraints excluded: chain A residue  888 LEU
Chi-restraints excluded: chain A residue  891 ASN
Chi-restraints excluded: chain A residue 1285 LEU
Chi-restraints excluded: chain A residue 1434 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0870
   chunk 77 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0970
   chunk 73 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0570
   overall best weight:    0.3274

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 331 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.209694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.177448 restraints weight = 10115.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.4251 rms_B_bonded: 1.76
r_work: 0.4102 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3983 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3998
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3998 r_free = 0.3998    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3998 r_free = 0.3998    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3998
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8905  Z= 0.113
  Angle     :  0.620  11.181  12042  Z= 0.298
  Chirality :  0.039   0.332   1363
  Planarity :  0.004   0.043   1394
  Dihedral  : 13.175 138.921   1439
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 20.32 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.63 (0.27), residues: 993
  helix:  1.37 (0.20), residues: 689
  sheet:  None (None), residues: 0
  loop : -1.84 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 762 
 TYR   0.033   0.002   TYR A1717 
 PHE   0.026   0.001   PHE A 707 
 TRP   0.023   0.001   TRP A 850 
 HIS   0.004   0.001   HIS A 833 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 ( 8894)
  covalent geometry    : angle       0.60653 /  0.29 (12014)
  SS BOND              : bond        0.00226 /  0.12 (    5)
  SS BOND              : angle       2.09897 /  0.96 (   10)
  hydrogen bonds       : bond        0.03644 /  2.41 (  512)
  hydrogen bonds       : angle       4.27297 /  3.00 ( 1494)
  link_BETA1-4         : bond        0.00219 /  0.12 (    1)
  link_BETA1-4         : angle       0.63862 /  0.37 (    3)
  link_NAG-ASN         : bond        0.00705 /  0.35 (    5)
  link_NAG-ASN         : angle       3.30857 /  1.76 (   15)

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 135
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  383 LEU cc_start: 0.6648 (mt) cc_final: 0.6387 (mt)
REVERT: A  398 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6378 (mtm)
REVERT: A  765 LYS cc_start: 0.7999 (tptp) cc_final: 0.7735 (tptp)
REVERT: A  787 LEU cc_start: 0.7229 (mp) cc_final: 0.6980 (tt)
REVERT: A 1388 TRP cc_start: 0.7630 (t-100) cc_final: 0.7421 (t-100)
REVERT: A 1397 TYR cc_start: 0.7725 (t80) cc_final: 0.7436 (t80)
REVERT: A 1579 ARG cc_start: 0.6420 (mtt180) cc_final: 0.5387 (mtt180)
REVERT: A 1641 MET cc_start: 0.8276 (ttm) cc_final: 0.8057 (ttm)
  outliers start: 3
  outliers final: 2
  residues processed: 136
  average time/residue: 0.0764
  time to fit residues: 14.8476
Evaluate side-chains
  132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 129
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  729 TRP
Chi-restraints excluded: chain A residue 1434 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 30 optimal weight:    0.2980
   overall best weight:    1.2184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 331 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.195788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.160734 restraints weight = 16442.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.4022 rms_B_bonded: 2.05
r_work: 0.3869 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3887
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3887 r_free = 0.3887    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3887 r_free = 0.3887    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3887
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   8905  Z= 0.154
  Angle     :  0.676  14.298  12042  Z= 0.328
  Chirality :  0.041   0.386   1363
  Planarity :  0.004   0.042   1394
  Dihedral  : 13.176 138.040   1439
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 20.20 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.49 (0.27), residues: 993
  helix:  1.28 (0.20), residues: 687
  sheet: -3.79 (1.05), residues: 10
  loop : -1.81 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 762 
 TYR   0.030   0.002   TYR A1717 
 PHE   0.025   0.002   PHE A 707 
 TRP   0.021   0.002   TRP A 850 
 HIS   0.003   0.001   HIS A 833 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.15 ( 8894)
  covalent geometry    : angle       0.66155 /  0.32 (12014)
  SS BOND              : bond        0.00492 /  0.27 (    5)
  SS BOND              : angle       2.25422 /  0.96 (   10)
  hydrogen bonds       : bond        0.04081 /  2.72 (  512)
  hydrogen bonds       : angle       4.47634 /  3.14 ( 1494)
  link_BETA1-4         : bond        0.00250 /  0.13 (    1)
  link_BETA1-4         : angle       0.64774 /  0.38 (    3)
  link_NAG-ASN         : bond        0.00520 /  0.27 (    5)
  link_NAG-ASN         : angle       3.65873 /  2.05 (   15)

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A  383 LEU cc_start: 0.6916 (mt) cc_final: 0.6655 (mt)
REVERT: A  398 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6234 (mtm)
REVERT: A  765 LYS cc_start: 0.7980 (tptp) cc_final: 0.7695 (tptp)
REVERT: A  787 LEU cc_start: 0.7279 (mp) cc_final: 0.6916 (tt)
REVERT: A 1397 TYR cc_start: 0.7654 (t80) cc_final: 0.7175 (t80)
REVERT: A 1527 MET cc_start: 0.7417 (mtp) cc_final: 0.7152 (mtm)
REVERT: A 1579 ARG cc_start: 0.6231 (mtt180) cc_final: 0.5259 (mtt180)
  outliers start: 9
  outliers final: 5
  residues processed: 133
  average time/residue: 0.0782
  time to fit residues: 14.9962
Evaluate side-chains
  132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 126
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 SER
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  729 TRP
Chi-restraints excluded: chain A residue  888 LEU
Chi-restraints excluded: chain A residue 1332 CYS
Chi-restraints excluded: chain A residue 1638 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 74 optimal weight:    0.1980
   chunk 11 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 95 optimal weight:    0.1980
   overall best weight:    0.8784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.197279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.163397 restraints weight = 18184.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.4061 rms_B_bonded: 2.23
r_work: 0.3872 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3881 r_free = 0.3881    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3881 r_free = 0.3881    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3881
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8905  Z= 0.133
  Angle     :  0.661  14.084  12042  Z= 0.318
  Chirality :  0.040   0.369   1363
  Planarity :  0.004   0.042   1394
  Dihedral  : 12.949 134.768   1439
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 20.65 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.56 (0.27), residues: 993
  helix:  1.32 (0.20), residues: 689
  sheet: -3.73 (1.12), residues: 10
  loop : -1.76 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 762 
 TYR   0.031   0.002   TYR A1717 
 PHE   0.038   0.001   PHE A1514 
 TRP   0.030   0.001   TRP A 850 
 HIS   0.003   0.001   HIS A 833 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.13 ( 8894)
  covalent geometry    : angle       0.64791 /  0.31 (12014)
  SS BOND              : bond        0.00423 /  0.23 (    5)
  SS BOND              : angle       2.17115 /  0.95 (   10)
  hydrogen bonds       : bond        0.03912 /  2.59 (  512)
  hydrogen bonds       : angle       4.40890 /  3.09 ( 1494)
  link_BETA1-4         : bond        0.00241 /  0.13 (    1)
  link_BETA1-4         : angle       0.61274 /  0.36 (    3)
  link_NAG-ASN         : bond        0.00550 /  0.28 (    5)
  link_NAG-ASN         : angle       3.43796 /  1.94 (   15)

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 131
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A  383 LEU cc_start: 0.6753 (mt) cc_final: 0.6470 (mt)
REVERT: A  398 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6270 (mtm)
REVERT: A  765 LYS cc_start: 0.8024 (tptp) cc_final: 0.7760 (tptp)
REVERT: A  874 MET cc_start: 0.6419 (ttt) cc_final: 0.5761 (ttm)
REVERT: A 1147 ARG cc_start: 0.8323 (ptp90) cc_final: 0.7910 (ptp90)
REVERT: A 1397 TYR cc_start: 0.7645 (t80) cc_final: 0.7247 (t80)
REVERT: A 1527 MET cc_start: 0.7417 (mtp) cc_final: 0.7126 (mtm)
REVERT: A 1579 ARG cc_start: 0.6376 (mtt180) cc_final: 0.5308 (mtt180)
  outliers start: 4
  outliers final: 3
  residues processed: 133
  average time/residue: 0.0771
  time to fit residues: 14.9379
Evaluate side-chains
  133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 129
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 SER
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  729 TRP
Chi-restraints excluded: chain A residue  888 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.9582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.205487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.174280 restraints weight = 12621.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.4211 rms_B_bonded: 1.48
r_work: 0.4026 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3914 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3927
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3927 r_free = 0.3927    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3927 r_free = 0.3927    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.3927
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8905  Z= 0.138
  Angle     :  0.671  14.169  12042  Z= 0.322
  Chirality :  0.041   0.371   1363
  Planarity :  0.004   0.042   1394
  Dihedral  : 12.807 131.592   1439
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 20.65 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.56 (0.27), residues: 993
  helix:  1.30 (0.20), residues: 690
  sheet: -3.74 (1.07), residues: 10
  loop : -1.72 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 762 
 TYR   0.031   0.002   TYR A1717 
 PHE   0.025   0.001   PHE A 707 
 TRP   0.027   0.001   TRP A 850 
 HIS   0.004   0.001   HIS A 833 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.14 ( 8894)
  covalent geometry    : angle       0.65778 /  0.32 (12014)
  SS BOND              : bond        0.00442 /  0.24 (    5)
  SS BOND              : angle       2.14852 /  0.94 (   10)
  hydrogen bonds       : bond        0.03945 /  2.62 (  512)
  hydrogen bonds       : angle       4.42412 /  3.10 ( 1494)
  link_BETA1-4         : bond        0.00234 /  0.12 (    1)
  link_BETA1-4         : angle       0.60296 /  0.35 (    3)
  link_NAG-ASN         : bond        0.00527 /  0.27 (    5)
  link_NAG-ASN         : angle       3.41278 /  1.92 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2206.16 seconds
wall clock time: 38 minutes 19.91 seconds (2299.91 seconds total)