Starting phenix.real_space_refine
on Mon Jul 28 07:26:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k18_22621/07_2025/7k18_22621.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k18_22621/07_2025/7k18_22621.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k18_22621/07_2025/7k18_22621.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k18_22621/07_2025/7k18_22621.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k18_22621/07_2025/7k18_22621.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k18_22621/07_2025/7k18_22621.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     S      76      5.16       5
     C    6442      2.51       5
     N    1511      2.21       5
     O    1715      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9749
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 8861
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1128, 8861
          Classifications: {'peptide': 1128}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 1096}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 213
          Unresolved non-hydrogen angles: 259
          Unresolved non-hydrogen dihedrals: 188
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 119
    Chain: "B"
      Number of atoms: 489
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 489
          Classifications: {'peptide': 67}
          Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 62}
    Chain: "C"
      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 dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      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 dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 304
          Unusual residues: {'6OU': 11, 'NAG': 1}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 250
          Unresolved non-hydrogen angles: 276
          Unresolved non-hydrogen dihedrals: 255
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'6OU:plan-1': 9, '6OU:plan-2': 2, '6OU:plan-3': 1}
          Unresolved non-hydrogen planarities: 31
  Time building chain proxies: 6.59, per 1000 atoms: 0.68
  Number of scatterers: 9749
  At special positions: 0
  Unit cell: (133.056, 125.664, 107.712, 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      76     16.00
     P       5     15.00
     O    1715      8.00
     N    1511      7.00
     C    6442      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 281 " - pdb=" SG  CYS A 336 " distance=1.81
    Simple disulfide: pdb=" SG  CYS A 327 " - pdb=" SG  CYS A 342 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 909 " - pdb=" SG  CYS A 918 " distance=2.80
    Simple disulfide: pdb=" SG  CYS A1365 " - pdb=" SG  CYS A1386 " distance=2.74
    Simple disulfide: pdb=" SG  CYS A1730 " - pdb=" SG  CYS A1744 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  12 " - pdb=" SG  CYS B  65 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  16 " - pdb=" SG  CYS B  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  47 " distance=2.32
    Simple disulfide: pdb=" SG  CYS B  27 " - pdb=" SG  CYS B  49 " distance=1.41

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG A2201 " - " ASN A 319 "
      " NAG C   1 " - " ASN A1382 "
      " NAG D   1 " - " ASN A 329 "
      " NAG E   1 " - " ASN A1390 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.99
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2236

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 2 sheets defined
      73.7% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 121 through 130
    Processing helix  chain 'A' and resid 132 through 150
      removed outlier: 3.536A  pdb=" N   MET A 136 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 159
    Processing helix  chain 'A' and resid 160 through 181
    Processing helix  chain 'A' and resid 183 through 190
    Processing helix  chain 'A' and resid 194 through 211
      removed outlier: 3.674A  pdb=" N   ASP A 198 " --> pdb=" O   TRP A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 227
      removed outlier: 3.542A  pdb=" N   ARG A 223 " --> pdb=" O   ARG A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 234
      removed outlier: 3.629A  pdb=" N   SER A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 251
      removed outlier: 3.959A  pdb=" N   LYS A 238 " --> pdb=" O   ILE A 234 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   THR A 239 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLN A 246 " --> pdb=" O   GLY A 242 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   SER A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 274
    Processing helix  chain 'A' and resid 305 through 311
    Processing helix  chain 'A' and resid 312 through 315
    Processing helix  chain 'A' and resid 358 through 372
      removed outlier: 3.718A  pdb=" N   ALA A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 386
      removed outlier: 3.704A  pdb=" N   LEU A 378 " --> pdb=" O   CYS A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 389
      No H-bonds generated for 'chain 'A' and resid 387 through 389'
    Processing helix  chain 'A' and resid 390 through 401
    Processing helix  chain 'A' and resid 401 through 423
    Processing helix  chain 'A' and resid 700 through 716
    Processing helix  chain 'A' and resid 720 through 737
      removed outlier: 3.544A  pdb=" N   LEU A 737 " --> pdb=" O   LEU A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 772
    Processing helix  chain 'A' and resid 775 through 780
    Processing helix  chain 'A' and resid 780 through 797
    Processing helix  chain 'A' and resid 808 through 822
      removed outlier: 3.911A  pdb=" N   PHE A 811 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   LEU A 813 " --> pdb=" O   SER A 810 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LYS A 818 " --> pdb=" O   ARG A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 823 through 836
    Processing helix  chain 'A' and resid 840 through 869
      removed outlier: 5.081A  pdb=" N   LYS A 864 " --> pdb=" O   GLN A 860 " (cutoff:3.500A)
      removed outlier: 5.678A  pdb=" N   ASN A 865 " --> pdb=" O   LEU A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 870 through 873
    Processing helix  chain 'A' and resid 886 through 900
      removed outlier: 3.599A  pdb=" N   ALA A 890 " --> pdb=" O   ASP A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 902 through 913
      removed outlier: 4.158A  pdb=" N   ASP A 908 " --> pdb=" O   GLU A 904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 914 through 945
      removed outlier: 3.637A  pdb=" N   PHE A 945 " --> pdb=" O   LEU A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1191 through 1205
    Processing helix  chain 'A' and resid 1206 through 1226
    Processing helix  chain 'A' and resid 1234 through 1270
      removed outlier: 3.737A  pdb=" N   LYS A1238 " --> pdb=" O   ARG A1234 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A1239 " --> pdb=" O   LYS A1235 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   PHE A1265 " --> pdb=" O   VAL A1261 " (cutoff:3.500A)
      removed outlier: 9.274A  pdb=" N   LYS A1266 " --> pdb=" O   ALA A1262 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   LYS A1267 " --> pdb=" O   TYR A1263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1272 through 1293
    Processing helix  chain 'A' and resid 1301 through 1306
    Processing helix  chain 'A' and resid 1307 through 1318
      Proline residue:  A1312  - end of helix
      removed outlier: 3.698A  pdb=" N   LEU A1316 " --> pdb=" O   LEU A1313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1319 through 1331
      removed outlier: 3.677A  pdb=" N   VAL A1324 " --> pdb=" O   GLU A1320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1332 through 1359
      removed outlier: 4.304A  pdb=" N   ASN A1338 " --> pdb=" O   PRO A1334 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   VAL A1339 " --> pdb=" O   SER A1335 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   PHE A1350 " --> pdb=" O   PHE A1346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1382 through 1387
    Processing helix  chain 'A' and resid 1388 through 1390
      No H-bonds generated for 'chain 'A' and resid 1388 through 1390'
    Processing helix  chain 'A' and resid 1407 through 1419
    Processing helix  chain 'A' and resid 1422 through 1432
      removed outlier: 3.783A  pdb=" N   ILE A1426 " --> pdb=" O   GLY A1422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1445 through 1447
      No H-bonds generated for 'chain 'A' and resid 1445 through 1447'
    Processing helix  chain 'A' and resid 1448 through 1462
      removed outlier: 3.788A  pdb=" N   PHE A1452 " --> pdb=" O   MET A1448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1462 through 1482
      removed outlier: 3.816A  pdb=" N   LYS A1480 " --> pdb=" O   ASN A1476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1490 through 1504
    Processing helix  chain 'A' and resid 1517 through 1528
    Processing helix  chain 'A' and resid 1529 through 1547
      removed outlier: 3.878A  pdb=" N   ASP A1533 " --> pdb=" O   LYS A1529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1555 through 1582
    Processing helix  chain 'A' and resid 1585 through 1589
      removed outlier: 4.364A  pdb=" N   TYR A1588 " --> pdb=" O   ARG A1585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1591 through 1614
      removed outlier: 4.034A  pdb=" N   THR A1608 " --> pdb=" O   SER A1604 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   VAL A1609 " --> pdb=" O   ILE A1605 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LEU A1610 " --> pdb=" O   VAL A1606 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ILE A1613 " --> pdb=" O   VAL A1609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1622 through 1630
      removed outlier: 3.596A  pdb=" N   ILE A1627 " --> pdb=" O   PHE A1624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1631 through 1639
      removed outlier: 4.204A  pdb=" N   ILE A1635 " --> pdb=" O   ARG A1631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1643 through 1681
      removed outlier: 3.605A  pdb=" N   THR A1647 " --> pdb=" O   LYS A1643 " (cutoff:3.500A)
      Proline residue:  A1657  - end of helix
    Processing helix  chain 'A' and resid 1698 through 1711
      removed outlier: 3.974A  pdb=" N   THR A1711 " --> pdb=" O   PHE A1707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1714 through 1724
      Proline residue:  A1721  - end of helix
      removed outlier: 3.987A  pdb=" N   ASN A1724 " --> pdb=" O   SER A1720 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1746 through 1779
    Processing helix  chain 'B' and resid 23 through 31
    Processing sheet with id=AA1, first strand: chain 'A' and resid 280 through 282
    Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 5
      removed outlier: 3.569A  pdb=" N   LEU B  52 " --> pdb=" O   ARG B   2 " (cutoff:3.500A)
      removed outlier: 7.320A  pdb=" N   GLY B   4 " --> pdb=" O   ASN B  50 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   ASN B  50 " --> pdb=" O   GLY B   4 " (cutoff:3.500A)

    622 hydrogen bonds defined for protein.
    1767 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: 3.35

  Time building geometry restraints manager: 3.35 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1473
        1.31 -     1.44: 2779
        1.44 -     1.56: 5577
        1.56 -     1.69: 13
        1.69 -     1.82: 119
  Bond restraints: 9961
  Sorted by residual:
  bond pdb=" C07 6OU A2212 "
       pdb=" C08 6OU A2212 "
    ideal  model  delta    sigma   weight residual
    1.524  1.313  0.211 2.00e-02 2.50e+03 1.11e+02
  bond pdb=" C07 6OU A2211 "
       pdb=" C08 6OU A2211 "
    ideal  model  delta    sigma   weight residual
    1.524  1.318  0.206 2.00e-02 2.50e+03 1.06e+02
  bond pdb=" N   PRO A1374 "
       pdb=" CD  PRO A1374 "
    ideal  model  delta    sigma   weight residual
    1.473  1.585 -0.112 1.40e-02 5.10e+03 6.35e+01
  bond pdb=" N   PRO A1732 "
       pdb=" CD  PRO A1732 "
    ideal  model  delta    sigma   weight residual
    1.473  1.533 -0.060 1.40e-02 5.10e+03 1.84e+01
  bond pdb=" C16 6OU A2202 "
       pdb=" O18 6OU A2202 "
    ideal  model  delta    sigma   weight residual
    1.327  1.401 -0.074 2.00e-02 2.50e+03 1.37e+01
  ... (remaining 9956 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.21: 13150
        3.21 -     6.42: 249
        6.42 -     9.63: 47
        9.63 -    12.85: 9
       12.85 -    16.06: 6
  Bond angle restraints: 13461
  Sorted by residual:
  angle pdb=" N   LYS A1302 "
        pdb=" CA  LYS A1302 "
        pdb=" C   LYS A1302 "
      ideal   model   delta    sigma   weight residual
     113.12  102.04   11.08 1.25e+00 6.40e-01 7.85e+01
  angle pdb=" N   ILE A1366 "
        pdb=" CA  ILE A1366 "
        pdb=" C   ILE A1366 "
      ideal   model   delta    sigma   weight residual
     108.58  120.32  -11.74 1.44e+00 4.82e-01 6.64e+01
  angle pdb=" N   CYS A1365 "
        pdb=" CA  CYS A1365 "
        pdb=" C   CYS A1365 "
      ideal   model   delta    sigma   weight residual
     108.24  122.39  -14.15 1.81e+00 3.05e-01 6.11e+01
  angle pdb=" C   CYS A1365 "
        pdb=" CA  CYS A1365 "
        pdb=" CB  CYS A1365 "
      ideal   model   delta    sigma   weight residual
     112.05  101.56   10.49 1.52e+00 4.33e-01 4.76e+01
  angle pdb=" N   ILE A1366 "
        pdb=" CA  ILE A1366 "
        pdb=" CB  ILE A1366 "
      ideal   model   delta    sigma   weight residual
     110.72  103.66    7.06 1.09e+00 8.42e-01 4.20e+01
  ... (remaining 13456 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.37: 5670
       34.37 -    68.75: 284
       68.75 -   103.12: 28
      103.12 -   137.50: 11
      137.50 -   171.87: 6
  Dihedral angle restraints: 5999
    sinusoidal: 2534
      harmonic: 3465
  Sorted by residual:
  dihedral pdb=" CB  CYS A1730 "
           pdb=" SG  CYS A1730 "
           pdb=" SG  CYS A1744 "
           pdb=" CB  CYS A1744 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.61   71.61     1      1.00e+01 1.00e-02 6.57e+01
  dihedral pdb=" CB  CYS A1365 "
           pdb=" SG  CYS A1365 "
           pdb=" SG  CYS A1386 "
           pdb=" CB  CYS A1386 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -17.68  -68.32     1      1.00e+01 1.00e-02 6.05e+01
  dihedral pdb=" CB  CYS B  16 "
           pdb=" SG  CYS B  16 "
           pdb=" SG  CYS B  37 "
           pdb=" CB  CYS B  37 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.04   56.04     1      1.00e+01 1.00e-02 4.24e+01
  ... (remaining 5996 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 1495
       0.093 -    0.185: 55
       0.185 -    0.278: 6
       0.278 -    0.371: 5
       0.371 -    0.464: 1
  Chirality restraints: 1562
  Sorted by residual:
  chirality pdb=" CA  ILE A1301 "
            pdb=" N   ILE A1301 "
            pdb=" C   ILE A1301 "
            pdb=" CB  ILE A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.90   -0.46 2.00e-01 2.50e+01 5.37e+00
  chirality pdb=" CA  GLU B  29 "
            pdb=" N   GLU B  29 "
            pdb=" C   GLU B  29 "
            pdb=" CB  GLU B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.22e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 329 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.74    0.34 2.00e-01 2.50e+01 2.93e+00
  ... (remaining 1559 not shown)

  Planarity restraints: 1634
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 319 "   -0.077 2.00e-02 2.50e+03   2.41e-01 7.28e+02
        pdb=" CG  ASN A 319 "   -0.059 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 319 "    0.246 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 319 "   -0.383 2.00e-02 2.50e+03
        pdb=" C1  NAG A2201 "    0.273 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 329 "   -0.083 2.00e-02 2.50e+03   1.63e-01 3.34e+02
        pdb=" CG  ASN A 329 "    0.045 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 329 "   -0.080 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 329 "    0.295 2.00e-02 2.50e+03
        pdb=" C1  NAG D   1 "   -0.177 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A1731 "    0.072 5.00e-02 4.00e+02   1.10e-01 1.95e+01
        pdb=" N   PRO A1732 "   -0.191 5.00e-02 4.00e+02
        pdb=" CA  PRO A1732 "    0.064 5.00e-02 4.00e+02
        pdb=" CD  PRO A1732 "    0.055 5.00e-02 4.00e+02
  ... (remaining 1631 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 92
        2.53 -     3.12: 8067
        3.12 -     3.71: 15218
        3.71 -     4.31: 20984
        4.31 -     4.90: 33877
  Nonbonded interactions: 78238
  Sorted by model distance:
  nonbonded pdb=" O   CYS B  27 "
            pdb=" N   GLY B  32 "
     model   vdw
     1.936 3.120
  nonbonded pdb=" OD1 ASN A 329 "
            pdb=" O7  NAG D   1 "
     model   vdw
     1.953 3.040
  nonbonded pdb=" O   LEU A1752 "
            pdb=" OG1 THR A1756 "
     model   vdw
     2.050 3.040
  nonbonded pdb=" O   LEU A1344 "
            pdb=" OH  TYR A1411 "
     model   vdw
     2.071 3.040
  nonbonded pdb=" O   LEU A 270 "
            pdb=" CG  MET A 274 "
     model   vdw
     2.094 3.440
  ... (remaining 78233 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}

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=1.00 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:             1.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     26.860
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
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      :  0.015   0.771   9979  Z= 0.733
  Angle     :  1.337  39.290  13503  Z= 0.631
  Chirality :  0.049   0.464   1562
  Planarity :  0.006   0.110   1630
  Dihedral  : 20.820 171.870   3736
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 21.56
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  7.87 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 21.08 %
    Favored  : 75.50 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.42 (0.21), residues: 1181
  helix: -1.78 (0.15), residues: 799
  sheet: -3.29 (1.22), residues: 14
  loop : -3.05 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1715 
 HIS   0.006   0.001   HIS A 889 
 PHE   0.013   0.001   PHE A1694 
 TYR   0.015   0.002   TYR A 379 
 ARG   0.003   0.000   ARG A1308 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.14302 (    4)
  link_NAG-ASN         : angle      12.14944 (   12)
  link_BETA1-4         : bond        0.00760 (    4)
  link_BETA1-4         : angle       4.46076 (   12)
  hydrogen bonds       : bond        0.10761 (  622)
  hydrogen bonds       : angle       6.29344 ( 1767)
  SS BOND              : bond        0.42408 (    9)
  SS BOND              : angle      18.24794 (   18)
  covalent geometry    : bond        0.00646 ( 9961)
  covalent geometry    : angle       1.09438 (13461)
  Misc. bond           : bond        0.00305 (    1)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 286
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.7867 (mmmt) cc_final: 0.7640 (ttpt)
REVERT: A  177 ILE cc_start: 0.7823 (mt) cc_final: 0.7286 (tp)
REVERT: A  199 PHE cc_start: 0.7463 (t80) cc_final: 0.7168 (t80)
REVERT: A  219 LEU cc_start: 0.6530 (pt) cc_final: 0.6140 (tp)
REVERT: A  341 ARG cc_start: 0.7987 (ptm160) cc_final: 0.7428 (mpt-90)
REVERT: A  705 MET cc_start: 0.4544 (mmp) cc_final: 0.4129 (tpp)
REVERT: A  754 ASN cc_start: 0.6963 (m-40) cc_final: 0.5649 (m-40)
REVERT: A  783 ASN cc_start: 0.8057 (m110) cc_final: 0.7826 (m-40)
REVERT: A 1298 MET cc_start: 0.2243 (OUTLIER) cc_final: 0.1060 (ptm)
REVERT: A 1337 MET cc_start: 0.6682 (mmm) cc_final: 0.6115 (mmm)
REVERT: A 1438 GLU cc_start: 0.5554 (pt0) cc_final: 0.5229 (tt0)
REVERT: B   15 HIS cc_start: 0.5127 (m90) cc_final: 0.4644 (p-80)
  outliers start: 34
  outliers final: 19
  residues processed: 315
  average time/residue: 0.2045
  time to fit residues: 90.9946
Evaluate side-chains
  251 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 231
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  904 GLU
Chi-restraints excluded: chain A residue  913 SER
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue 1298 MET
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1494 LYS
Chi-restraints excluded: chain A residue 1546 THR
Chi-restraints excluded: chain A residue 1551 THR
Chi-restraints excluded: chain A residue 1608 THR
Chi-restraints excluded: chain A residue 1612 ASP
Chi-restraints excluded: chain A residue 1613 ILE
Chi-restraints excluded: chain A residue 1645 ILE
Chi-restraints excluded: chain A residue 1708 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:   10.0000
   chunk 89 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0060
   chunk 92 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 107 optimal weight:    0.0670
   overall best weight:    0.5134

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 151 GLN
A 195 ASN
** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 ASN
A 865 ASN
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1206 HIS
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1543 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.187721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.137929 restraints weight = 14513.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 2.43
r_work: 0.3654 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9979  Z= 0.147
  Angle     :  0.704   9.257  13503  Z= 0.355
  Chirality :  0.043   0.295   1562
  Planarity :  0.005   0.069   1630
  Dihedral  : 19.055 178.131   1725
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 24.10 %
    Favored  : 71.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.24), residues: 1181
  helix: -0.36 (0.17), residues: 808
  sheet:  None (None), residues: 0
  loop : -2.46 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1715 
 HIS   0.003   0.001   HIS B  15 
 PHE   0.019   0.002   PHE A1455 
 TYR   0.030   0.002   TYR A 379 
 ARG   0.003   0.001   ARG A1364 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00792 (    4)
  link_NAG-ASN         : angle       4.10194 (   12)
  link_BETA1-4         : bond        0.00702 (    4)
  link_BETA1-4         : angle       3.35795 (   12)
  hydrogen bonds       : bond        0.04278 (  622)
  hydrogen bonds       : angle       5.27157 ( 1767)
  SS BOND              : bond        0.00456 (    9)
  SS BOND              : angle       2.96021 (   18)
  covalent geometry    : bond        0.00309 ( 9961)
  covalent geometry    : angle       0.67888 (13461)
  Misc. bond           : bond        0.00042 (    1)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 257
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8567 (mmmt) cc_final: 0.7840 (ttpt)
REVERT: A  177 ILE cc_start: 0.8218 (mt) cc_final: 0.7631 (tp)
REVERT: A  199 PHE cc_start: 0.8283 (t80) cc_final: 0.8072 (t80)
REVERT: A  219 LEU cc_start: 0.7649 (pt) cc_final: 0.6908 (tp)
REVERT: A  223 ARG cc_start: 0.7436 (mmm-85) cc_final: 0.6782 (ttm-80)
REVERT: A  226 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7586 (mtt-85)
REVERT: A  341 ARG cc_start: 0.8480 (ptm160) cc_final: 0.7203 (mmm-85)
REVERT: A  705 MET cc_start: 0.5301 (mmp) cc_final: 0.4251 (tpp)
REVERT: A  750 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7832 (mm)
REVERT: A  817 PHE cc_start: 0.7841 (m-80) cc_final: 0.7518 (m-80)
REVERT: A 1193 TRP cc_start: 0.7227 (t-100) cc_final: 0.6817 (t-100)
REVERT: A 1234 ARG cc_start: 0.7035 (ptp-170) cc_final: 0.6830 (ptp-170)
REVERT: A 1241 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7968 (mm)
REVERT: A 1298 MET cc_start: 0.2938 (ttm) cc_final: 0.1079 (ptm)
REVERT: A 1337 MET cc_start: 0.7904 (mmm) cc_final: 0.7353 (mmm)
REVERT: A 1438 GLU cc_start: 0.6105 (pt0) cc_final: 0.5556 (tt0)
REVERT: A 1441 GLN cc_start: 0.4126 (mp10) cc_final: 0.3728 (mp10)
REVERT: A 1493 GLN cc_start: 0.6825 (mm-40) cc_final: 0.6231 (mp10)
REVERT: A 1618 PHE cc_start: 0.5727 (OUTLIER) cc_final: 0.5368 (m-80)
  outliers start: 45
  outliers final: 22
  residues processed: 286
  average time/residue: 0.2225
  time to fit residues: 91.9249
Evaluate side-chains
  252 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 227
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  904 GLU
Chi-restraints excluded: chain A residue  924 LEU
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue 1236 THR
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain A residue 1318 ARG
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1609 VAL
Chi-restraints excluded: chain A residue 1612 ASP
Chi-restraints excluded: chain A residue 1618 PHE
Chi-restraints excluded: chain A residue 1667 PHE
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1708 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0060
   chunk 6 optimal weight:    6.9990
   chunk 112 optimal weight:   20.0000
   chunk 26 optimal weight:    2.9990
   chunk 9 optimal weight:   20.0000
   chunk 31 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 107 optimal weight:    0.9990
   chunk 104 optimal weight:    0.8980
   overall best weight:    1.7802

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 731 ASN
A 754 ASN
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1474 ASN
A1478 GLN
A1543 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.185229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.134678 restraints weight = 14709.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3795 rms_B_bonded: 2.46
r_work: 0.3645 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   9979  Z= 0.186
  Angle     :  0.700  10.543  13503  Z= 0.352
  Chirality :  0.043   0.210   1562
  Planarity :  0.004   0.062   1630
  Dihedral  : 17.717 179.208   1700
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 25.70 %
    Favored  : 68.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.24), residues: 1181
  helix:  0.05 (0.17), residues: 806
  sheet: -3.72 (1.35), residues: 14
  loop : -2.43 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1260 
 HIS   0.004   0.001   HIS A 889 
 PHE   0.027   0.002   PHE A1753 
 TYR   0.031   0.002   TYR A 777 
 ARG   0.005   0.000   ARG A1631 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00671 (    4)
  link_NAG-ASN         : angle       3.89147 (   12)
  link_BETA1-4         : bond        0.00844 (    4)
  link_BETA1-4         : angle       3.70086 (   12)
  hydrogen bonds       : bond        0.04163 (  622)
  hydrogen bonds       : angle       5.22488 ( 1767)
  SS BOND              : bond        0.00516 (    9)
  SS BOND              : angle       2.10406 (   18)
  covalent geometry    : bond        0.00423 ( 9961)
  covalent geometry    : angle       0.67866 (13461)
  Misc. bond           : bond        0.00074 (    1)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 237
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8607 (mmmt) cc_final: 0.7963 (ttpt)
REVERT: A  199 PHE cc_start: 0.8273 (t80) cc_final: 0.8000 (t80)
REVERT: A  223 ARG cc_start: 0.7379 (mmm-85) cc_final: 0.6991 (ttm-80)
REVERT: A  226 ARG cc_start: 0.8014 (mtt180) cc_final: 0.7770 (mtt-85)
REVERT: A  309 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7123 (tp)
REVERT: A  341 ARG cc_start: 0.8443 (ptm160) cc_final: 0.7184 (mpt180)
REVERT: A  705 MET cc_start: 0.5431 (mmp) cc_final: 0.4373 (tpp)
REVERT: A  795 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7403 (tmm)
REVERT: A  817 PHE cc_start: 0.8135 (m-80) cc_final: 0.7810 (m-80)
REVERT: A 1234 ARG cc_start: 0.7222 (ptp-170) cc_final: 0.6829 (ptp-170)
REVERT: A 1241 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7931 (mm)
REVERT: A 1298 MET cc_start: 0.2765 (ttm) cc_final: 0.0899 (ptm)
REVERT: A 1337 MET cc_start: 0.7991 (mmm) cc_final: 0.7447 (mmm)
REVERT: A 1424 MET cc_start: 0.8312 (mmm) cc_final: 0.7740 (mmm)
REVERT: A 1434 ARG cc_start: 0.6352 (mmm-85) cc_final: 0.5825 (mmm-85)
REVERT: A 1438 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.4248 (tt0)
REVERT: A 1441 GLN cc_start: 0.4237 (mp10) cc_final: 0.3858 (mm-40)
REVERT: A 1493 GLN cc_start: 0.6668 (mm-40) cc_final: 0.6347 (mp10)
REVERT: A 1618 PHE cc_start: 0.5723 (OUTLIER) cc_final: 0.5360 (m-80)
  outliers start: 60
  outliers final: 36
  residues processed: 278
  average time/residue: 0.1943
  time to fit residues: 78.0475
Evaluate side-chains
  259 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 218
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  795 MET
Chi-restraints excluded: chain A residue  796 GLU
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  818 LYS
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  904 GLU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  920 LEU
Chi-restraints excluded: chain A residue  924 LEU
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue 1236 THR
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain A residue 1243 TYR
Chi-restraints excluded: chain A residue 1318 ARG
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1384 SER
Chi-restraints excluded: chain A residue 1438 GLU
Chi-restraints excluded: chain A residue 1609 VAL
Chi-restraints excluded: chain A residue 1618 PHE
Chi-restraints excluded: chain A residue 1626 VAL
Chi-restraints excluded: chain A residue 1645 ILE
Chi-restraints excluded: chain A residue 1667 PHE
Chi-restraints excluded: chain A residue 1678 MET
Chi-restraints excluded: chain A residue 1684 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 31 optimal weight:    0.2980
   chunk 76 optimal weight:    0.7980
   chunk 46 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 110 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 108 optimal weight:    5.9990
   chunk 83 optimal weight:    0.0040
   chunk 10 optimal weight:    6.9990
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1465 ASN
A1474 ASN
A1724 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.189008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.139319 restraints weight = 14503.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 2.45
r_work: 0.3669 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9979  Z= 0.131
  Angle     :  0.657   7.845  13503  Z= 0.325
  Chirality :  0.042   0.243   1562
  Planarity :  0.004   0.056   1630
  Dihedral  : 16.368 177.328   1693
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  5.72 %
    Allowed  : 25.30 %
    Favored  : 68.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.25), residues: 1181
  helix:  0.48 (0.18), residues: 804
  sheet: -3.42 (0.98), residues: 26
  loop : -2.33 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1260 
 HIS   0.002   0.001   HIS A 739 
 PHE   0.025   0.001   PHE A1455 
 TYR   0.028   0.002   TYR A 777 
 ARG   0.005   0.000   ARG A1631 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00802 (    4)
  link_NAG-ASN         : angle       3.54183 (   12)
  link_BETA1-4         : bond        0.00852 (    4)
  link_BETA1-4         : angle       3.53995 (   12)
  hydrogen bonds       : bond        0.03885 (  622)
  hydrogen bonds       : angle       5.00290 ( 1767)
  SS BOND              : bond        0.00483 (    9)
  SS BOND              : angle       1.67866 (   18)
  covalent geometry    : bond        0.00280 ( 9961)
  covalent geometry    : angle       0.63761 (13461)
  Misc. bond           : bond        0.00051 (    1)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 242
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8543 (mmmt) cc_final: 0.7843 (ttpt)
REVERT: A  199 PHE cc_start: 0.8290 (t80) cc_final: 0.8024 (t80)
REVERT: A  223 ARG cc_start: 0.7274 (mmm-85) cc_final: 0.6936 (ttm-80)
REVERT: A  341 ARG cc_start: 0.8348 (ptm160) cc_final: 0.7075 (mmt-90)
REVERT: A  705 MET cc_start: 0.5254 (mmp) cc_final: 0.4325 (tpp)
REVERT: A  716 MET cc_start: 0.3749 (ptt) cc_final: 0.3201 (ppp)
REVERT: A  795 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7291 (tmm)
REVERT: A  812 ARG cc_start: 0.7637 (mtp-110) cc_final: 0.7046 (mtp85)
REVERT: A  817 PHE cc_start: 0.8062 (m-80) cc_final: 0.7811 (m-80)
REVERT: A 1234 ARG cc_start: 0.7241 (ptp-170) cc_final: 0.6774 (ptp-170)
REVERT: A 1241 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7944 (mm)
REVERT: A 1298 MET cc_start: 0.2533 (OUTLIER) cc_final: 0.0807 (ptm)
REVERT: A 1337 MET cc_start: 0.7930 (mmm) cc_final: 0.7386 (mmm)
REVERT: A 1434 ARG cc_start: 0.6517 (mmm-85) cc_final: 0.6222 (mmm-85)
REVERT: A 1493 GLN cc_start: 0.6575 (mm-40) cc_final: 0.6187 (mp10)
REVERT: A 1618 PHE cc_start: 0.5755 (OUTLIER) cc_final: 0.5368 (m-80)
REVERT: A 1649 LEU cc_start: 0.8059 (mt) cc_final: 0.7608 (mt)
REVERT: A 1724 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7411 (p0)
REVERT: B   15 HIS cc_start: 0.5750 (m90) cc_final: 0.5217 (p90)
  outliers start: 57
  outliers final: 33
  residues processed: 281
  average time/residue: 0.2050
  time to fit residues: 83.2441
Evaluate side-chains
  264 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 226
  time to evaluate  : 1.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  735 MET
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  795 MET
Chi-restraints excluded: chain A residue  796 GLU
Chi-restraints excluded: chain A residue  818 LYS
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  904 GLU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  924 LEU
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue 1236 THR
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain A residue 1243 TYR
Chi-restraints excluded: chain A residue 1298 MET
Chi-restraints excluded: chain A residue 1318 ARG
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1384 SER
Chi-restraints excluded: chain A residue 1438 GLU
Chi-restraints excluded: chain A residue 1618 PHE
Chi-restraints excluded: chain A residue 1626 VAL
Chi-restraints excluded: chain A residue 1645 ILE
Chi-restraints excluded: chain A residue 1667 PHE
Chi-restraints excluded: chain A residue 1678 MET
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1724 ASN
Chi-restraints excluded: chain B residue   48 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 115 optimal weight:   20.0000
   chunk 114 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 104 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1441 GLN
A1724 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.183889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.134076 restraints weight = 14603.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 2.37
r_work: 0.3595 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.088   9979  Z= 0.241
  Angle     :  0.758  12.653  13503  Z= 0.372
  Chirality :  0.045   0.220   1562
  Planarity :  0.004   0.061   1630
  Dihedral  : 16.153 179.723   1693
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.45 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 26.91 %
    Favored  : 67.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.25), residues: 1181
  helix:  0.37 (0.18), residues: 809
  sheet: -3.55 (1.00), residues: 26
  loop : -2.24 (0.36), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A1260 
 HIS   0.006   0.001   HIS A 889 
 PHE   0.015   0.002   PHE A1278 
 TYR   0.028   0.002   TYR A 777 
 ARG   0.005   0.001   ARG A 226 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00750 (    4)
  link_NAG-ASN         : angle       3.53806 (   12)
  link_BETA1-4         : bond        0.00797 (    4)
  link_BETA1-4         : angle       3.79156 (   12)
  hydrogen bonds       : bond        0.04133 (  622)
  hydrogen bonds       : angle       5.19041 ( 1767)
  SS BOND              : bond        0.00437 (    9)
  SS BOND              : angle       2.78516 (   18)
  covalent geometry    : bond        0.00561 ( 9961)
  covalent geometry    : angle       0.73590 (13461)
  Misc. bond           : bond        0.00098 (    1)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 231
  time to evaluate  : 4.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8573 (mmmt) cc_final: 0.7749 (ttpt)
REVERT: A  199 PHE cc_start: 0.8318 (t80) cc_final: 0.8071 (t80)
REVERT: A  705 MET cc_start: 0.5421 (mmp) cc_final: 0.4397 (tpp)
REVERT: A  795 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7337 (tmm)
REVERT: A  817 PHE cc_start: 0.8207 (m-80) cc_final: 0.7899 (m-80)
REVERT: A 1234 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6918 (ptp-170)
REVERT: A 1241 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7945 (mm)
REVERT: A 1273 TRP cc_start: 0.7463 (m-90) cc_final: 0.7156 (m-90)
REVERT: A 1298 MET cc_start: 0.2505 (OUTLIER) cc_final: 0.0678 (ptm)
REVERT: A 1493 GLN cc_start: 0.6613 (mm-40) cc_final: 0.6189 (mp10)
REVERT: A 1593 TRP cc_start: 0.6671 (m100) cc_final: 0.5805 (m-10)
REVERT: A 1618 PHE cc_start: 0.5774 (OUTLIER) cc_final: 0.5387 (m-80)
REVERT: B   15 HIS cc_start: 0.5741 (m90) cc_final: 0.5264 (p90)
  outliers start: 58
  outliers final: 41
  residues processed: 268
  average time/residue: 0.3146
  time to fit residues: 128.5540
Evaluate side-chains
  261 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 215
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  735 MET
Chi-restraints excluded: chain A residue  789 ILE
Chi-restraints excluded: chain A residue  795 MET
Chi-restraints excluded: chain A residue  796 GLU
Chi-restraints excluded: chain A residue  818 LYS
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  904 GLU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  920 LEU
Chi-restraints excluded: chain A residue  924 LEU
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue 1234 ARG
Chi-restraints excluded: chain A residue 1236 THR
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain A residue 1243 TYR
Chi-restraints excluded: chain A residue 1298 MET
Chi-restraints excluded: chain A residue 1318 ARG
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1384 SER
Chi-restraints excluded: chain A residue 1438 GLU
Chi-restraints excluded: chain A residue 1490 THR
Chi-restraints excluded: chain A residue 1554 GLN
Chi-restraints excluded: chain A residue 1609 VAL
Chi-restraints excluded: chain A residue 1618 PHE
Chi-restraints excluded: chain A residue 1626 VAL
Chi-restraints excluded: chain A residue 1645 ILE
Chi-restraints excluded: chain A residue 1667 PHE
Chi-restraints excluded: chain A residue 1678 MET
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1746 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 115 optimal weight:   20.0000
   chunk 3 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9990
   chunk 93 optimal weight:    9.9990
   chunk 31 optimal weight:   20.0000
   chunk 43 optimal weight:    0.7980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1474 ASN
A1478 GLN
A1724 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.186796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.146935 restraints weight = 14676.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3954 rms_B_bonded: 3.07
r_work: 0.3623 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   9979  Z= 0.156
  Angle     :  0.696  10.351  13503  Z= 0.339
  Chirality :  0.043   0.241   1562
  Planarity :  0.004   0.056   1630
  Dihedral  : 15.194 179.439   1693
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  : 28.71 %
    Favored  : 65.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.25), residues: 1181
  helix:  0.64 (0.18), residues: 805
  sheet: -3.51 (1.01), residues: 26
  loop : -2.16 (0.36), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A1260 
 HIS   0.003   0.001   HIS A 889 
 PHE   0.028   0.001   PHE A1455 
 TYR   0.026   0.002   TYR A 777 
 ARG   0.005   0.000   ARG A1631 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00722 (    4)
  link_NAG-ASN         : angle       3.35962 (   12)
  link_BETA1-4         : bond        0.00856 (    4)
  link_BETA1-4         : angle       3.63889 (   12)
  hydrogen bonds       : bond        0.03892 (  622)
  hydrogen bonds       : angle       5.04024 ( 1767)
  SS BOND              : bond        0.00349 (    9)
  SS BOND              : angle       2.09579 (   18)
  covalent geometry    : bond        0.00349 ( 9961)
  covalent geometry    : angle       0.67674 (13461)
  Misc. bond           : bond        0.00077 (    1)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 232
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8523 (mmmt) cc_final: 0.7674 (ttpt)
REVERT: A  199 PHE cc_start: 0.8300 (t80) cc_final: 0.8062 (t80)
REVERT: A  383 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8563 (mp)
REVERT: A  705 MET cc_start: 0.5422 (mmp) cc_final: 0.4424 (tpp)
REVERT: A  795 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7262 (tmm)
REVERT: A  817 PHE cc_start: 0.8167 (m-80) cc_final: 0.7916 (m-80)
REVERT: A 1234 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6876 (ptp-170)
REVERT: A 1241 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8018 (mm)
REVERT: A 1273 TRP cc_start: 0.7418 (m-90) cc_final: 0.7130 (m-90)
REVERT: A 1298 MET cc_start: 0.2602 (OUTLIER) cc_final: 0.0770 (ptm)
REVERT: A 1493 GLN cc_start: 0.6565 (mm-40) cc_final: 0.6244 (mp10)
REVERT: A 1552 ASP cc_start: 0.6365 (p0) cc_final: 0.6158 (p0)
REVERT: A 1593 TRP cc_start: 0.6714 (m100) cc_final: 0.5913 (m-10)
REVERT: A 1618 PHE cc_start: 0.5759 (OUTLIER) cc_final: 0.5369 (m-80)
REVERT: B   15 HIS cc_start: 0.5733 (m90) cc_final: 0.5291 (p90)
  outliers start: 55
  outliers final: 37
  residues processed: 267
  average time/residue: 0.1914
  time to fit residues: 76.6747
Evaluate side-chains
  262 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 219
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  361 TRP
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  795 MET
Chi-restraints excluded: chain A residue  796 GLU
Chi-restraints excluded: chain A residue  818 LYS
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  904 GLU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  924 LEU
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue 1213 ILE
Chi-restraints excluded: chain A residue 1234 ARG
Chi-restraints excluded: chain A residue 1236 THR
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain A residue 1243 TYR
Chi-restraints excluded: chain A residue 1298 MET
Chi-restraints excluded: chain A residue 1318 ARG
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1384 SER
Chi-restraints excluded: chain A residue 1438 GLU
Chi-restraints excluded: chain A residue 1490 THR
Chi-restraints excluded: chain A residue 1608 THR
Chi-restraints excluded: chain A residue 1609 VAL
Chi-restraints excluded: chain A residue 1618 PHE
Chi-restraints excluded: chain A residue 1626 VAL
Chi-restraints excluded: chain A residue 1645 ILE
Chi-restraints excluded: chain A residue 1667 PHE
Chi-restraints excluded: chain A residue 1678 MET
Chi-restraints excluded: chain A residue 1684 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 116 optimal weight:    7.9990
   chunk 112 optimal weight:   30.0000
   chunk 17 optimal weight:   20.0000
   chunk 61 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1474 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.183806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.133848 restraints weight = 14676.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 2.39
r_work: 0.3632 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.090   9979  Z= 0.216
  Angle     :  0.763  11.010  13503  Z= 0.369
  Chirality :  0.045   0.209   1562
  Planarity :  0.004   0.059   1630
  Dihedral  : 14.892 175.836   1693
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.54 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 28.61 %
    Favored  : 65.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.25), residues: 1181
  helix:  0.50 (0.18), residues: 809
  sheet: -3.57 (0.98), residues: 26
  loop : -2.18 (0.36), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A1260 
 HIS   0.006   0.001   HIS A 889 
 PHE   0.021   0.002   PHE A1455 
 TYR   0.028   0.002   TYR A 777 
 ARG   0.007   0.000   ARG A1631 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00589 (    4)
  link_NAG-ASN         : angle       3.50003 (   12)
  link_BETA1-4         : bond        0.00883 (    4)
  link_BETA1-4         : angle       3.82035 (   12)
  hydrogen bonds       : bond        0.04113 (  622)
  hydrogen bonds       : angle       5.15844 ( 1767)
  SS BOND              : bond        0.00479 (    9)
  SS BOND              : angle       2.27940 (   18)
  covalent geometry    : bond        0.00502 ( 9961)
  covalent geometry    : angle       0.74346 (13461)
  Misc. bond           : bond        0.00094 (    1)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 232
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8533 (mmmt) cc_final: 0.7719 (ttpt)
REVERT: A  199 PHE cc_start: 0.8278 (t80) cc_final: 0.8028 (t80)
REVERT: A  383 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8649 (mp)
REVERT: A  705 MET cc_start: 0.5455 (mmp) cc_final: 0.4415 (tpp)
REVERT: A  795 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7337 (tmm)
REVERT: A  817 PHE cc_start: 0.8167 (m-80) cc_final: 0.7903 (m-80)
REVERT: A 1193 TRP cc_start: 0.7236 (t-100) cc_final: 0.6675 (t-100)
REVERT: A 1234 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6966 (ptp-170)
REVERT: A 1241 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8004 (mm)
REVERT: A 1273 TRP cc_start: 0.7469 (m-90) cc_final: 0.7155 (m-90)
REVERT: A 1298 MET cc_start: 0.3009 (OUTLIER) cc_final: 0.0984 (ptm)
REVERT: A 1493 GLN cc_start: 0.6486 (mm-40) cc_final: 0.6243 (mp10)
REVERT: A 1593 TRP cc_start: 0.6769 (m100) cc_final: 0.5951 (m-10)
REVERT: A 1618 PHE cc_start: 0.5695 (OUTLIER) cc_final: 0.5318 (m-80)
REVERT: B   15 HIS cc_start: 0.5825 (m90) cc_final: 0.5365 (p90)
  outliers start: 60
  outliers final: 40
  residues processed: 270
  average time/residue: 0.1841
  time to fit residues: 72.5811
Evaluate side-chains
  267 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 221
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  361 TRP
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  795 MET
Chi-restraints excluded: chain A residue  796 GLU
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  904 GLU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  920 LEU
Chi-restraints excluded: chain A residue  924 LEU
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue 1234 ARG
Chi-restraints excluded: chain A residue 1236 THR
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain A residue 1243 TYR
Chi-restraints excluded: chain A residue 1298 MET
Chi-restraints excluded: chain A residue 1318 ARG
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1384 SER
Chi-restraints excluded: chain A residue 1438 GLU
Chi-restraints excluded: chain A residue 1474 ASN
Chi-restraints excluded: chain A residue 1608 THR
Chi-restraints excluded: chain A residue 1609 VAL
Chi-restraints excluded: chain A residue 1618 PHE
Chi-restraints excluded: chain A residue 1626 VAL
Chi-restraints excluded: chain A residue 1645 ILE
Chi-restraints excluded: chain A residue 1678 MET
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1746 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9990
   chunk 103 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 101 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1474 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.187829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.137696 restraints weight = 14762.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 2.46
r_work: 0.3652 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   9979  Z= 0.141
  Angle     :  0.717  10.016  13503  Z= 0.346
  Chirality :  0.043   0.226   1562
  Planarity :  0.004   0.056   1630
  Dihedral  : 14.145 175.662   1693
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  5.72 %
    Allowed  : 29.72 %
    Favored  : 64.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.25), residues: 1181
  helix:  0.69 (0.18), residues: 807
  sheet: -3.53 (0.99), residues: 26
  loop : -2.09 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1260 
 HIS   0.002   0.001   HIS A 889 
 PHE   0.029   0.001   PHE A1455 
 TYR   0.026   0.002   TYR A 777 
 ARG   0.009   0.000   ARG A1631 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00697 (    4)
  link_NAG-ASN         : angle       3.21019 (   12)
  link_BETA1-4         : bond        0.00975 (    4)
  link_BETA1-4         : angle       3.72184 (   12)
  hydrogen bonds       : bond        0.03916 (  622)
  hydrogen bonds       : angle       4.99313 ( 1767)
  SS BOND              : bond        0.00338 (    9)
  SS BOND              : angle       2.07434 (   18)
  covalent geometry    : bond        0.00312 ( 9961)
  covalent geometry    : angle       0.69849 (13461)
  Misc. bond           : bond        0.00070 (    1)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 230
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8521 (mmmt) cc_final: 0.7684 (ttpt)
REVERT: A  199 PHE cc_start: 0.8281 (t80) cc_final: 0.8037 (t80)
REVERT: A  315 TYR cc_start: 0.6081 (m-10) cc_final: 0.5811 (m-10)
REVERT: A  383 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8604 (mt)
REVERT: A  705 MET cc_start: 0.5294 (mmp) cc_final: 0.4447 (tpp)
REVERT: A  795 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7244 (tmm)
REVERT: A  817 PHE cc_start: 0.8094 (m-80) cc_final: 0.7894 (m-80)
REVERT: A 1234 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6907 (ptp-170)
REVERT: A 1241 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7992 (mm)
REVERT: A 1245 ASP cc_start: 0.8273 (t0) cc_final: 0.8050 (t0)
REVERT: A 1248 PHE cc_start: 0.8485 (m-10) cc_final: 0.7960 (m-80)
REVERT: A 1273 TRP cc_start: 0.7429 (m-90) cc_final: 0.7118 (m-90)
REVERT: A 1298 MET cc_start: 0.2980 (OUTLIER) cc_final: 0.1054 (ptm)
REVERT: A 1489 MET cc_start: 0.6563 (mmt) cc_final: 0.6236 (mmt)
REVERT: A 1493 GLN cc_start: 0.6400 (mm-40) cc_final: 0.6192 (mp10)
REVERT: A 1593 TRP cc_start: 0.6748 (m100) cc_final: 0.5900 (m-10)
REVERT: A 1618 PHE cc_start: 0.5678 (OUTLIER) cc_final: 0.5317 (m-80)
REVERT: A 1634 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7791 (ttm-80)
REVERT: B   15 HIS cc_start: 0.5823 (m90) cc_final: 0.5418 (p-80)
  outliers start: 57
  outliers final: 39
  residues processed: 265
  average time/residue: 0.1778
  time to fit residues: 69.8478
Evaluate side-chains
  267 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 222
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  361 TRP
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  795 MET
Chi-restraints excluded: chain A residue  796 GLU
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  904 GLU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  920 LEU
Chi-restraints excluded: chain A residue  924 LEU
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue 1213 ILE
Chi-restraints excluded: chain A residue 1234 ARG
Chi-restraints excluded: chain A residue 1236 THR
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain A residue 1243 TYR
Chi-restraints excluded: chain A residue 1298 MET
Chi-restraints excluded: chain A residue 1318 ARG
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1384 SER
Chi-restraints excluded: chain A residue 1438 GLU
Chi-restraints excluded: chain A residue 1490 THR
Chi-restraints excluded: chain A residue 1609 VAL
Chi-restraints excluded: chain A residue 1618 PHE
Chi-restraints excluded: chain A residue 1626 VAL
Chi-restraints excluded: chain A residue 1645 ILE
Chi-restraints excluded: chain A residue 1667 PHE
Chi-restraints excluded: chain A residue 1678 MET
Chi-restraints excluded: chain A residue 1684 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 88 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 17 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9980
   chunk 97 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1381 ASN
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1441 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.186754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.136538 restraints weight = 14599.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 2.43
r_work: 0.3660 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.098   9979  Z= 0.167
  Angle     :  0.755  14.226  13503  Z= 0.363
  Chirality :  0.044   0.218   1562
  Planarity :  0.004   0.054   1630
  Dihedral  : 13.859 173.496   1693
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 30.52 %
    Favored  : 64.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.25), residues: 1181
  helix:  0.65 (0.18), residues: 806
  sheet: -3.45 (1.00), residues: 26
  loop : -2.07 (0.36), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A1260 
 HIS   0.003   0.001   HIS A 889 
 PHE   0.024   0.002   PHE A1455 
 TYR   0.027   0.002   TYR A 777 
 ARG   0.009   0.000   ARG A1631 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00664 (    4)
  link_NAG-ASN         : angle       3.27628 (   12)
  link_BETA1-4         : bond        0.01018 (    4)
  link_BETA1-4         : angle       3.79279 (   12)
  hydrogen bonds       : bond        0.03949 (  622)
  hydrogen bonds       : angle       5.06855 ( 1767)
  SS BOND              : bond        0.00274 (    9)
  SS BOND              : angle       2.37504 (   18)
  covalent geometry    : bond        0.00386 ( 9961)
  covalent geometry    : angle       0.73635 (13461)
  Misc. bond           : bond        0.00072 (    1)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 225
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8509 (mmmt) cc_final: 0.7697 (ttpt)
REVERT: A  199 PHE cc_start: 0.8259 (t80) cc_final: 0.8013 (t80)
REVERT: A  315 TYR cc_start: 0.6063 (m-10) cc_final: 0.5811 (m-10)
REVERT: A  383 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8553 (mp)
REVERT: A  705 MET cc_start: 0.5291 (mmp) cc_final: 0.4448 (tpp)
REVERT: A  795 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7194 (tmm)
REVERT: A  817 PHE cc_start: 0.8133 (m-80) cc_final: 0.7922 (m-80)
REVERT: A 1234 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6947 (ptp-170)
REVERT: A 1241 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8000 (mm)
REVERT: A 1245 ASP cc_start: 0.8270 (t0) cc_final: 0.8031 (t0)
REVERT: A 1248 PHE cc_start: 0.8557 (m-10) cc_final: 0.8007 (m-80)
REVERT: A 1273 TRP cc_start: 0.7461 (m-90) cc_final: 0.7135 (m-90)
REVERT: A 1298 MET cc_start: 0.3125 (OUTLIER) cc_final: 0.0998 (ptm)
REVERT: A 1493 GLN cc_start: 0.6441 (mm-40) cc_final: 0.6164 (mp10)
REVERT: A 1593 TRP cc_start: 0.6769 (m100) cc_final: 0.5953 (m-10)
REVERT: A 1649 LEU cc_start: 0.8075 (mt) cc_final: 0.7568 (mt)
REVERT: B   15 HIS cc_start: 0.5850 (m90) cc_final: 0.5338 (p90)
  outliers start: 54
  outliers final: 43
  residues processed: 258
  average time/residue: 0.1750
  time to fit residues: 66.8539
Evaluate side-chains
  269 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 221
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  361 TRP
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  735 MET
Chi-restraints excluded: chain A residue  795 MET
Chi-restraints excluded: chain A residue  796 GLU
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  904 GLU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  920 LEU
Chi-restraints excluded: chain A residue  924 LEU
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue 1213 ILE
Chi-restraints excluded: chain A residue 1234 ARG
Chi-restraints excluded: chain A residue 1236 THR
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain A residue 1243 TYR
Chi-restraints excluded: chain A residue 1298 MET
Chi-restraints excluded: chain A residue 1318 ARG
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1384 SER
Chi-restraints excluded: chain A residue 1438 GLU
Chi-restraints excluded: chain A residue 1490 THR
Chi-restraints excluded: chain A residue 1609 VAL
Chi-restraints excluded: chain A residue 1612 ASP
Chi-restraints excluded: chain A residue 1626 VAL
Chi-restraints excluded: chain A residue 1645 ILE
Chi-restraints excluded: chain A residue 1667 PHE
Chi-restraints excluded: chain A residue 1678 MET
Chi-restraints excluded: chain A residue 1684 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 112 optimal weight:   40.0000
   chunk 13 optimal weight:    0.8980
   chunk 36 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 69 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 82 optimal weight:    0.2980
   chunk 56 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1441 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.187898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.137703 restraints weight = 14791.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 2.47
r_work: 0.3644 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.3315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9979  Z= 0.147
  Angle     :  0.759  15.708  13503  Z= 0.357
  Chirality :  0.044   0.207   1562
  Planarity :  0.004   0.056   1630
  Dihedral  : 13.383 171.298   1693
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 30.72 %
    Favored  : 64.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.25), residues: 1181
  helix:  0.77 (0.18), residues: 796
  sheet: -3.39 (1.00), residues: 26
  loop : -1.90 (0.36), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A1260 
 HIS   0.003   0.001   HIS A 889 
 PHE   0.027   0.001   PHE A1488 
 TYR   0.025   0.002   TYR A 777 
 ARG   0.011   0.001   ARG A1631 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00721 (    4)
  link_NAG-ASN         : angle       2.97633 (   12)
  link_BETA1-4         : bond        0.00863 (    4)
  link_BETA1-4         : angle       3.79686 (   12)
  hydrogen bonds       : bond        0.03886 (  622)
  hydrogen bonds       : angle       4.98152 ( 1767)
  SS BOND              : bond        0.00333 (    9)
  SS BOND              : angle       1.77795 (   18)
  covalent geometry    : bond        0.00327 ( 9961)
  covalent geometry    : angle       0.74324 (13461)
  Misc. bond           : bond        0.00065 (    1)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 230
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8518 (mmmt) cc_final: 0.7698 (ttpt)
REVERT: A  199 PHE cc_start: 0.8270 (t80) cc_final: 0.8047 (t80)
REVERT: A  383 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8607 (mt)
REVERT: A  705 MET cc_start: 0.5247 (mmp) cc_final: 0.4457 (tpp)
REVERT: A  795 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7239 (tmm)
REVERT: A  817 PHE cc_start: 0.8108 (m-80) cc_final: 0.7882 (m-80)
REVERT: A 1234 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6975 (ptp-170)
REVERT: A 1241 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8023 (mm)
REVERT: A 1245 ASP cc_start: 0.8313 (t0) cc_final: 0.8061 (t0)
REVERT: A 1248 PHE cc_start: 0.8530 (m-10) cc_final: 0.7936 (m-80)
REVERT: A 1273 TRP cc_start: 0.7427 (m-90) cc_final: 0.7112 (m-90)
REVERT: A 1298 MET cc_start: 0.3100 (OUTLIER) cc_final: 0.1013 (ptm)
REVERT: A 1489 MET cc_start: 0.6578 (mmt) cc_final: 0.6229 (mmt)
REVERT: A 1493 GLN cc_start: 0.6366 (mm-40) cc_final: 0.6147 (mp10)
REVERT: A 1593 TRP cc_start: 0.6781 (m100) cc_final: 0.5997 (m-10)
REVERT: A 1649 LEU cc_start: 0.8010 (mt) cc_final: 0.7523 (mt)
REVERT: B   15 HIS cc_start: 0.5833 (m90) cc_final: 0.5337 (p90)
  outliers start: 46
  outliers final: 41
  residues processed: 258
  average time/residue: 0.1820
  time to fit residues: 69.7935
Evaluate side-chains
  269 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 223
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  361 TRP
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  715 VAL
Chi-restraints excluded: chain A residue  735 MET
Chi-restraints excluded: chain A residue  795 MET
Chi-restraints excluded: chain A residue  796 GLU
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  904 GLU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  920 LEU
Chi-restraints excluded: chain A residue  924 LEU
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue 1213 ILE
Chi-restraints excluded: chain A residue 1234 ARG
Chi-restraints excluded: chain A residue 1236 THR
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain A residue 1243 TYR
Chi-restraints excluded: chain A residue 1298 MET
Chi-restraints excluded: chain A residue 1318 ARG
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1384 SER
Chi-restraints excluded: chain A residue 1438 GLU
Chi-restraints excluded: chain A residue 1490 THR
Chi-restraints excluded: chain A residue 1609 VAL
Chi-restraints excluded: chain A residue 1612 ASP
Chi-restraints excluded: chain A residue 1626 VAL
Chi-restraints excluded: chain A residue 1667 PHE
Chi-restraints excluded: chain A residue 1678 MET
Chi-restraints excluded: chain A residue 1684 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 86 optimal weight:   20.0000
   chunk 66 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 112 optimal weight:   40.0000
   chunk 77 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 113 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   chunk 97 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 114 optimal weight:    0.9980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1441 GLN
A1465 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.187183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.137169 restraints weight = 14612.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 2.42
r_work: 0.3647 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.3386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9979  Z= 0.160
  Angle     :  0.764  14.799  13503  Z= 0.361
  Chirality :  0.044   0.202   1562
  Planarity :  0.004   0.055   1630
  Dihedral  : 13.213 167.183   1693
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 31.12 %
    Favored  : 64.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.25), residues: 1181
  helix:  0.79 (0.18), residues: 797
  sheet: -3.38 (1.01), residues: 26
  loop : -1.84 (0.36), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A1260 
 HIS   0.003   0.001   HIS A 889 
 PHE   0.027   0.001   PHE A1455 
 TYR   0.025   0.002   TYR A 777 
 ARG   0.010   0.000   ARG A1631 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00632 (    4)
  link_NAG-ASN         : angle       2.99178 (   12)
  link_BETA1-4         : bond        0.00962 (    4)
  link_BETA1-4         : angle       3.86393 (   12)
  hydrogen bonds       : bond        0.03920 (  622)
  hydrogen bonds       : angle       5.05576 ( 1767)
  SS BOND              : bond        0.00462 (    9)
  SS BOND              : angle       1.61784 (   18)
  covalent geometry    : bond        0.00363 ( 9961)
  covalent geometry    : angle       0.74884 (13461)
  Misc. bond           : bond        0.00065 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8984.89 seconds
wall clock time: 158 minutes 20.39 seconds (9500.39 seconds total)