Starting phenix.real_space_refine
on Mon Jul 28 11:21:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uz0_20949/07_2025/6uz0_20949.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uz0_20949/07_2025/6uz0_20949.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uz0_20949/07_2025/6uz0_20949.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uz0_20949/07_2025/6uz0_20949.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uz0_20949/07_2025/6uz0_20949.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uz0_20949/07_2025/6uz0_20949.cif"
  }
  resolution = 3.24
  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=  -0.010 sd=   1.805
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: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     S      68      5.16       5
     C    6383      2.51       5
     N    1440      2.21       5
     O    1655      1.98       5
     F       6      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 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: 9557
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 8970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1138, 8970
          Classifications: {'peptide': 1138}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 1105}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 193
          Unresolved non-hydrogen angles: 234
          Unresolved non-hydrogen dihedrals: 166
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 106
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      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: "D"
      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: 492
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 492
          Unusual residues: {'6OU': 11, '9Z9': 5, 'K4D': 1, 'NAG': 2}
          Classifications: {'undetermined': 19}
          Link IDs: {None: 18}
          Unresolved non-hydrogen bonds: 302
          Unresolved non-hydrogen angles: 344
          Unresolved non-hydrogen dihedrals: 329
          Unresolved non-hydrogen chiralities: 12
          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: 6.73, per 1000 atoms: 0.70
  Number of scatterers: 9557
  At special positions: 0
  Unit cell: (136.224, 126.72, 108.768, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      68     16.00
     P       5     15.00
     F       6      9.00
     O    1655      8.00
     N    1440      7.00
     C    6383      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 281 " - pdb=" SG  CYS A 336 " distance=2.63
    Simple disulfide: pdb=" SG  CYS A 327 " - pdb=" SG  CYS A 342 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 909 " - pdb=" SG  CYS A 918 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=4, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A3003 " - " ASN A 319 "
      " NAG A3009 " - " ASN A 284 "
      " NAG B   1 " - " ASN A1382 "
      " NAG C   1 " - " ASN A 329 "
      " NAG D   1 " - " ASN A1390 "
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.35
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2144

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 1 sheets defined
      79.3% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 119 through 131
    Processing helix  chain 'A' and resid 131 through 150
      removed outlier: 4.177A  pdb=" N   SER A 135 " --> pdb=" O   HIS A 131 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   MET A 136 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 181
      removed outlier: 4.254A  pdb=" N   VAL A 161 " --> pdb=" O   TRP A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 192
      removed outlier: 3.875A  pdb=" N   ASP A 192 " --> pdb=" O   THR A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 211
      removed outlier: 3.769A  pdb=" N   TRP A 196 " --> pdb=" O   ASP A 192 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   LEU A 197 " --> pdb=" O   PRO A 193 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ASP A 198 " --> pdb=" O   TRP A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 228
      removed outlier: 3.672A  pdb=" N   ARG A 220 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   THR A 221 " --> pdb=" O   ALA A 218 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ARG A 223 " --> pdb=" O   ARG A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 234
    Processing helix  chain 'A' and resid 236 through 251
      removed outlier: 3.808A  pdb=" N   GLN A 246 " --> pdb=" O   GLY A 242 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   SER A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 3.748A  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 275 through 279
      removed outlier: 3.514A  pdb=" N   HIS A 279 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 310
      removed outlier: 3.954A  pdb=" N   ASN A 310 " --> pdb=" O   ASP A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 372
      removed outlier: 3.832A  pdb=" N   ALA A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 386
      removed outlier: 4.084A  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 430
    Processing helix  chain 'A' and resid 700 through 715
    Processing helix  chain 'A' and resid 720 through 737
    Processing helix  chain 'A' and resid 743 through 770
    Processing helix  chain 'A' and resid 773 through 780
      removed outlier: 3.877A  pdb=" N   TYR A 777 " --> pdb=" O   ASP A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 798
    Processing helix  chain 'A' and resid 806 through 822
      removed outlier: 4.365A  pdb=" N   ARG A 809 " --> pdb=" O   SER A 806 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   PHE A 811 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LEU A 813 " --> pdb=" O   SER A 810 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A 819 " --> pdb=" O   VAL A 816 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LYS A 821 " --> pdb=" O   LYS A 818 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   SER A 822 " --> pdb=" O   LEU A 819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 823 through 837
      removed outlier: 3.841A  pdb=" N   VAL A 837 " --> pdb=" O   ILE A 833 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 869
      removed outlier: 6.327A  pdb=" N   LYS A 864 " --> pdb=" O   GLN A 860 " (cutoff:3.500A)
      removed outlier: 5.557A  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 887 through 900
    Processing helix  chain 'A' and resid 902 through 913
      removed outlier: 4.446A  pdb=" N   ASP A 908 " --> pdb=" O   GLU A 904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 914 through 944
    Processing helix  chain 'A' and resid 1191 through 1205
    Processing helix  chain 'A' and resid 1206 through 1226
    Processing helix  chain 'A' and resid 1228 through 1232
      removed outlier: 3.887A  pdb=" N   LEU A1231 " --> pdb=" O   ASP A1228 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   GLU A1232 " --> pdb=" O   ILE A1229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1228 through 1232'
    Processing helix  chain 'A' and resid 1234 through 1270
      removed outlier: 4.270A  pdb=" N   VAL A1239 " --> pdb=" O   LYS A1235 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   PHE A1265 " --> pdb=" O   VAL A1261 " (cutoff:3.500A)
      removed outlier: 8.625A  pdb=" N   LYS A1266 " --> pdb=" O   ALA A1262 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LYS A1267 " --> pdb=" O   TYR A1263 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   PHE A1269 " --> pdb=" O   PHE A1265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1271 through 1293
    Processing helix  chain 'A' and resid 1304 through 1313
      Proline residue:  A1312  - end of helix
    Processing helix  chain 'A' and resid 1314 through 1319
      removed outlier: 4.141A  pdb=" N   ARG A1318 " --> pdb=" O   ARG A1314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1319 through 1331
      removed outlier: 3.534A  pdb=" N   VAL A1324 " --> pdb=" O   GLU A1320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1332 through 1358
    Processing helix  chain 'A' and resid 1382 through 1390
      removed outlier: 3.849A  pdb=" N   SER A1388 " --> pdb=" O   SER A1384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1407 through 1420
    Processing helix  chain 'A' and resid 1422 through 1431
      removed outlier: 4.166A  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 1461
      removed outlier: 3.770A  pdb=" N   PHE A1452 " --> pdb=" O   MET A1448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1462 through 1483
    Processing helix  chain 'A' and resid 1490 through 1503
    Processing helix  chain 'A' and resid 1517 through 1529
      removed outlier: 3.683A  pdb=" N   LYS A1529 " --> pdb=" O   ASP A1525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1529 through 1549
      removed outlier: 3.939A  pdb=" N   ASP A1533 " --> pdb=" O   LYS A1529 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   VAL A1534 " --> pdb=" O   GLN A1530 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL A1549 " --> pdb=" O   VAL A1545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1555 through 1582
    Processing helix  chain 'A' and resid 1586 through 1591
      removed outlier: 4.788A  pdb=" N   ASN A1591 " --> pdb=" O   TYR A1587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1591 through 1612
    Processing helix  chain 'A' and resid 1613 through 1618
      removed outlier: 3.865A  pdb=" N   TYR A1617 " --> pdb=" O   ILE A1613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1622 through 1630
      removed outlier: 3.658A  pdb=" N   VAL A1626 " --> pdb=" O   THR A1622 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ILE A1627 " --> pdb=" O   LEU A1623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1631 through 1636
      removed outlier: 4.143A  pdb=" N   ILE A1635 " --> pdb=" O   ARG A1631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1637 through 1640
    Processing helix  chain 'A' and resid 1643 through 1681
      Proline residue:  A1657  - end of helix
    Processing helix  chain 'A' and resid 1698 through 1711
      removed outlier: 3.574A  pdb=" N   SER A1702 " --> pdb=" O   THR A1698 " (cutoff:3.500A)
      removed outlier: 3.923A  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: 4.010A  pdb=" N   ASN A1724 " --> pdb=" O   SER A1720 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1746 through 1780
    Processing sheet with id=AA1, first strand: chain 'A' and resid 280 through 283
      removed outlier: 3.884A  pdb=" N   LYS A 280 " --> pdb=" O   LEU A 343 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LEU A 343 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)

    625 hydrogen bonds defined for protein.
    1809 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: 3.26

  Time building geometry restraints manager: 3.56 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 1420
        1.27 -     1.41: 2563
        1.41 -     1.55: 5613
        1.55 -     1.68: 67
        1.68 -     1.82: 125
  Bond restraints: 9788
  Sorted by residual:
  bond pdb=" C06 9Z9 A3010 "
       pdb=" C07 9Z9 A3010 "
    ideal  model  delta    sigma   weight residual
    1.520  1.135  0.385 2.00e-02 2.50e+03 3.70e+02
  bond pdb=" C06 9Z9 A3014 "
       pdb=" C07 9Z9 A3014 "
    ideal  model  delta    sigma   weight residual
    1.520  1.138  0.382 2.00e-02 2.50e+03 3.65e+02
  bond pdb=" C06 9Z9 A3012 "
       pdb=" C07 9Z9 A3012 "
    ideal  model  delta    sigma   weight residual
    1.520  1.140  0.380 2.00e-02 2.50e+03 3.60e+02
  bond pdb=" C06 9Z9 A3011 "
       pdb=" C07 9Z9 A3011 "
    ideal  model  delta    sigma   weight residual
    1.520  1.140  0.380 2.00e-02 2.50e+03 3.60e+02
  bond pdb=" C06 9Z9 A3013 "
       pdb=" C07 9Z9 A3013 "
    ideal  model  delta    sigma   weight residual
    1.520  1.145  0.375 2.00e-02 2.50e+03 3.52e+02
  ... (remaining 9783 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.64: 13211
        7.64 -    15.27: 60
       15.27 -    22.91: 4
       22.91 -    30.55: 0
       30.55 -    38.18: 1
  Bond angle restraints: 13276
  Sorted by residual:
  angle pdb=" N   GLN A1368 "
        pdb=" CA  GLN A1368 "
        pdb=" C   GLN A1368 "
      ideal   model   delta    sigma   weight residual
     111.28  123.02  -11.74 1.09e+00 8.42e-01 1.16e+02
  angle pdb=" N   TYR A 308 "
        pdb=" CA  TYR A 308 "
        pdb=" C   TYR A 308 "
      ideal   model   delta    sigma   weight residual
     111.07  121.60  -10.53 1.07e+00 8.73e-01 9.68e+01
  angle pdb=" N   ARG A1318 "
        pdb=" CA  ARG A1318 "
        pdb=" C   ARG A1318 "
      ideal   model   delta    sigma   weight residual
     111.36  121.68  -10.32 1.09e+00 8.42e-01 8.97e+01
  angle pdb=" N   ARG A1364 "
        pdb=" CA  ARG A1364 "
        pdb=" C   ARG A1364 "
      ideal   model   delta    sigma   weight residual
     111.36  121.61  -10.25 1.09e+00 8.42e-01 8.85e+01
  angle pdb=" C   LEU A1373 "
        pdb=" N   PRO A1374 "
        pdb=" CD  PRO A1374 "
      ideal   model   delta    sigma   weight residual
     125.00   86.82   38.18 4.10e+00 5.95e-02 8.67e+01
  ... (remaining 13271 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.35: 5922
       35.35 -    70.70: 235
       70.70 -   106.05: 21
      106.05 -   141.40: 16
      141.40 -   176.75: 5
  Dihedral angle restraints: 6199
    sinusoidal: 2883
      harmonic: 3316
  Sorted by residual:
  dihedral pdb=" C   TYR A 308 "
           pdb=" N   TYR A 308 "
           pdb=" CA  TYR A 308 "
           pdb=" CB  TYR A 308 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -145.41   22.81     0      2.50e+00 1.60e-01 8.32e+01
  dihedral pdb=" N   TYR A 308 "
           pdb=" C   TYR A 308 "
           pdb=" CA  TYR A 308 "
           pdb=" CB  TYR A 308 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  144.35  -21.55     0      2.50e+00 1.60e-01 7.43e+01
  dihedral pdb=" CB  CYS A 909 "
           pdb=" SG  CYS A 909 "
           pdb=" SG  CYS A 918 "
           pdb=" CB  CYS A 918 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  152.64  -59.64     1      1.00e+01 1.00e-02 4.75e+01
  ... (remaining 6196 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.923: 1554
       0.923 -    1.846: 5
       1.846 -    2.769: 1
       2.769 -    3.693: 0
       3.693 -    4.616: 1
  Chirality restraints: 1561
  Sorted by residual:
  chirality pdb=" C1  BMA C   3 "
            pdb=" O4  NAG C   2 "
            pdb=" C2  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40    2.22   -4.62 2.00e-02 2.50e+03 5.33e+04
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.81    0.41 2.00e-02 2.50e+03 4.13e+02
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 329 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.15   -2.25 2.00e-01 2.50e+01 1.26e+02
  ... (remaining 1558 not shown)

  Planarity restraints: 1566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.340 2.00e-02 2.50e+03   2.94e-01 1.08e+03
        pdb=" C7  NAG D   2 "    0.078 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "   -0.063 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.519 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "   -0.195 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A3009 "   -0.227 2.00e-02 2.50e+03   1.93e-01 4.66e+02
        pdb=" C7  NAG A3009 "    0.047 2.00e-02 2.50e+03
        pdb=" C8  NAG A3009 "    0.036 2.00e-02 2.50e+03
        pdb=" N2  NAG A3009 "    0.318 2.00e-02 2.50e+03
        pdb=" O7  NAG A3009 "   -0.174 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "    0.195 2.00e-02 2.50e+03   1.62e-01 3.28e+02
        pdb=" C7  NAG C   1 "   -0.053 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "    0.141 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "   -0.264 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1563 not shown)

  Histogram of nonbonded interaction distances:
        0.58 -     1.45: 2
        1.45 -     2.31: 31
        2.31 -     3.17: 9076
        3.17 -     4.04: 23201
        4.04 -     4.90: 43299
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 75609
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 284 "
            pdb=" C8  NAG A3009 "
     model   vdw
     0.584 3.460
  nonbonded pdb=" ND2 ASN A1724 "
            pdb=" SG  CYS A1730 "
     model   vdw
     1.420 3.480
  nonbonded pdb=" O   ARG A1364 "
            pdb=" NE2 GLN A1439 "
     model   vdw
     1.461 3.120
  nonbonded pdb=" CG  ASN A 284 "
            pdb=" C8  NAG A3009 "
     model   vdw
     1.790 3.690
  nonbonded pdb=" O   ARG A 283 "
            pdb=" O   ASN A 284 "
     model   vdw
     1.849 3.040
  ... (remaining 75604 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 'B'
  selection = chain 'D'
}

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:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     26.870
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
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      :  0.023   0.603   9804  Z= 1.223
  Angle     :  1.557  43.125  13309  Z= 0.730
  Chirality :  0.179   4.616   1561
  Planarity :  0.013   0.294   1561
  Dihedral  : 20.233 176.748   4046
  Min Nonbonded Distance : 0.584

Molprobity Statistics.
  All-atom Clashscore : 27.88
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  7.55 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  :  9.75 %
    Favored  : 87.53 %
  Cbeta Deviations :  0.47 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.09 %
    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: -2.63 (0.23), residues: 1126
  helix: -1.10 (0.17), residues: 794
  sheet:  None (None), residues: 0
  loop : -3.10 (0.30), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A1423 
 HIS   0.008   0.002   HIS A 883 
 PHE   0.020   0.002   PHE A 394 
 TYR   0.031   0.002   TYR A 379 
 ARG   0.005   0.001   ARG A 123 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.14304 (    5)
  link_NAG-ASN         : angle      13.60546 (   15)
  link_BETA1-4         : bond        0.03206 (    4)
  link_BETA1-4         : angle      16.08000 (   12)
  hydrogen bonds       : bond        0.12463 (  625)
  hydrogen bonds       : angle       6.22990 ( 1809)
  SS BOND              : bond        0.34831 (    3)
  SS BOND              : angle      14.06779 (    6)
  covalent geometry    : bond        0.02196 ( 9788)
  covalent geometry    : angle       1.37752 (13276)
  Misc. bond           : bond        0.19233 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 267
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.7521 (mttt) cc_final: 0.7150 (tttt)
REVERT: A  196 TRP cc_start: 0.7924 (m-10) cc_final: 0.6902 (m100)
REVERT: A  250 LYS cc_start: 0.8226 (mmmm) cc_final: 0.7945 (mmmt)
REVERT: A  705 MET cc_start: 0.6063 (mmp) cc_final: 0.5273 (mmp)
REVERT: A  754 ASN cc_start: 0.7961 (t0) cc_final: 0.7496 (t0)
REVERT: A  777 TYR cc_start: 0.6127 (m-80) cc_final: 0.5619 (m-80)
REVERT: A  905 THR cc_start: 0.8066 (t) cc_final: 0.7281 (m)
REVERT: A 1218 LEU cc_start: 0.8148 (mm) cc_final: 0.7948 (mp)
REVERT: A 1219 LEU cc_start: 0.7781 (mt) cc_final: 0.7496 (tp)
REVERT: A 1500 MET cc_start: 0.7025 (ttm) cc_final: 0.6743 (ttp)
REVERT: A 1769 TYR cc_start: 0.6516 (OUTLIER) cc_final: 0.6041 (t80)
REVERT: A 1777 PHE cc_start: 0.5581 (OUTLIER) cc_final: 0.5327 (t80)
  outliers start: 26
  outliers final: 14
  residues processed: 286
  average time/residue: 0.2162
  time to fit residues: 86.0298
Evaluate side-chains
  225 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 209
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  284 ASN
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue 1367 ASN
Chi-restraints excluded: chain A residue 1376 ASN
Chi-restraints excluded: chain A residue 1470 VAL
Chi-restraints excluded: chain A residue 1473 ASP
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1769 TYR
Chi-restraints excluded: chain A residue 1772 ILE
Chi-restraints excluded: chain A residue 1774 LEU
Chi-restraints excluded: chain A residue 1777 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    6.9990
   chunk 85 optimal weight:    5.9990
   chunk 47 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 88 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 65 optimal weight:   20.0000
   chunk 102 optimal weight:    0.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 303 ASN
A 407 ASN
A 420 GLN
A 421 ASN
A 865 ASN
** A1206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1368 GLN
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1445 ASN
A1493 GLN
A1543 ASN
A1701 ASN
** A1724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.201388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.164408 restraints weight = 11254.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 1.80
r_work: 0.3756 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3638 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.131   9804  Z= 0.251
  Angle     :  0.851  12.657  13309  Z= 0.410
  Chirality :  0.047   0.328   1561
  Planarity :  0.006   0.110   1561
  Dihedral  : 19.042 178.946   2102
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  6.84 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 15.62 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.23 %
    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: -1.55 (0.24), residues: 1126
  helix: -0.32 (0.17), residues: 804
  sheet:  None (None), residues: 0
  loop : -2.66 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 302 
 HIS   0.011   0.002   HIS A 279 
 PHE   0.021   0.002   PHE A1618 
 TYR   0.026   0.002   TYR A 379 
 ARG   0.006   0.001   ARG A1305 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00489 (    5)
  link_NAG-ASN         : angle       3.09009 (   15)
  link_BETA1-4         : bond        0.01511 (    4)
  link_BETA1-4         : angle       5.83745 (   12)
  hydrogen bonds       : bond        0.04832 (  625)
  hydrogen bonds       : angle       5.20878 ( 1809)
  SS BOND              : bond        0.01687 (    3)
  SS BOND              : angle       5.34952 (    6)
  covalent geometry    : bond        0.00601 ( 9788)
  covalent geometry    : angle       0.81942 (13276)
  Misc. bond           : bond        0.00159 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 230
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6482 (ptm-80)
REVERT: A  196 TRP cc_start: 0.8075 (m-10) cc_final: 0.6989 (m100)
REVERT: A  250 LYS cc_start: 0.8275 (mmmm) cc_final: 0.8068 (mmmt)
REVERT: A  356 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8159 (m-80)
REVERT: A  385 SER cc_start: 0.7987 (OUTLIER) cc_final: 0.7754 (p)
REVERT: A  422 GLN cc_start: 0.8268 (tt0) cc_final: 0.7938 (tm-30)
REVERT: A  733 LEU cc_start: 0.8645 (mp) cc_final: 0.8422 (mp)
REVERT: A  777 TYR cc_start: 0.6158 (m-80) cc_final: 0.5308 (m-80)
REVERT: A  817 PHE cc_start: 0.6864 (m-80) cc_final: 0.6465 (m-80)
REVERT: A  905 THR cc_start: 0.8222 (t) cc_final: 0.7288 (m)
REVERT: A 1218 LEU cc_start: 0.8041 (mm) cc_final: 0.7831 (mp)
REVERT: A 1219 LEU cc_start: 0.7694 (mt) cc_final: 0.7394 (tp)
REVERT: A 1367 ASN cc_start: 0.6158 (OUTLIER) cc_final: 0.5902 (t0)
REVERT: A 1445 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8442 (t0)
REVERT: A 1500 MET cc_start: 0.6655 (ttm) cc_final: 0.6269 (ttp)
REVERT: A 1729 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.6743 (m-80)
REVERT: A 1777 PHE cc_start: 0.6335 (OUTLIER) cc_final: 0.5498 (t80)
  outliers start: 51
  outliers final: 29
  residues processed: 259
  average time/residue: 0.1925
  time to fit residues: 72.2580
Evaluate side-chains
  238 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 202
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  134 PHE
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  785 PHE
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue 1204 VAL
Chi-restraints excluded: chain A residue 1214 ILE
Chi-restraints excluded: chain A residue 1279 LEU
Chi-restraints excluded: chain A residue 1317 SER
Chi-restraints excluded: chain A residue 1367 ASN
Chi-restraints excluded: chain A residue 1376 ASN
Chi-restraints excluded: chain A residue 1379 ILE
Chi-restraints excluded: chain A residue 1388 SER
Chi-restraints excluded: chain A residue 1400 VAL
Chi-restraints excluded: chain A residue 1445 ASN
Chi-restraints excluded: chain A residue 1473 ASP
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1541 CYS
Chi-restraints excluded: chain A residue 1564 LYS
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1763 LEU
Chi-restraints excluded: chain A residue 1777 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   chunk 60 optimal weight:    6.9990
   chunk 73 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9990
   chunk 98 optimal weight:    9.9990
   chunk 104 optimal weight:    0.8980
   chunk 87 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 930 ASN
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1733 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.204242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.166937 restraints weight = 11264.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 1.81
r_work: 0.3762 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3644 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.103   9804  Z= 0.188
  Angle     :  0.760  12.355  13309  Z= 0.367
  Chirality :  0.043   0.198   1561
  Planarity :  0.005   0.088   1561
  Dihedral  : 17.928 178.298   2092
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.31 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 17.40 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.23 %
    Twisted General : 0.09 %

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: -1.11 (0.24), residues: 1126
  helix:  0.03 (0.18), residues: 813
  sheet:  None (None), residues: 0
  loop : -2.67 (0.32), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A1442 
 HIS   0.008   0.002   HIS A 279 
 PHE   0.022   0.002   PHE A 785 
 TYR   0.022   0.002   TYR A 379 
 ARG   0.002   0.000   ARG A1305 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00444 (    5)
  link_NAG-ASN         : angle       2.49061 (   15)
  link_BETA1-4         : bond        0.01792 (    4)
  link_BETA1-4         : angle       4.85636 (   12)
  hydrogen bonds       : bond        0.04505 (  625)
  hydrogen bonds       : angle       4.95462 ( 1809)
  SS BOND              : bond        0.01031 (    3)
  SS BOND              : angle       3.70871 (    6)
  covalent geometry    : bond        0.00438 ( 9788)
  covalent geometry    : angle       0.73756 (13276)
  Misc. bond           : bond        0.00286 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 224
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6598 (ptm160)
REVERT: A  159 LYS cc_start: 0.7578 (mttt) cc_final: 0.7101 (ttmt)
REVERT: A  196 TRP cc_start: 0.7935 (m-10) cc_final: 0.6962 (m100)
REVERT: A  250 LYS cc_start: 0.8285 (mmmm) cc_final: 0.7986 (mmtt)
REVERT: A  356 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8128 (m-80)
REVERT: A  366 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7488 (mp)
REVERT: A  385 SER cc_start: 0.7858 (OUTLIER) cc_final: 0.7656 (p)
REVERT: A  422 GLN cc_start: 0.8289 (tt0) cc_final: 0.7932 (tm-30)
REVERT: A  713 PHE cc_start: 0.6718 (m-80) cc_final: 0.6476 (t80)
REVERT: A  733 LEU cc_start: 0.8677 (mp) cc_final: 0.8400 (mp)
REVERT: A  777 TYR cc_start: 0.6011 (m-80) cc_final: 0.5200 (m-80)
REVERT: A  905 THR cc_start: 0.8212 (t) cc_final: 0.7308 (m)
REVERT: A 1218 LEU cc_start: 0.8053 (mm) cc_final: 0.7809 (mp)
REVERT: A 1219 LEU cc_start: 0.7655 (mt) cc_final: 0.7380 (tp)
REVERT: A 1227 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7683 (mt-10)
REVERT: A 1500 MET cc_start: 0.6676 (ttm) cc_final: 0.6181 (ttp)
REVERT: A 1653 MET cc_start: 0.8294 (ptm) cc_final: 0.7937 (ppp)
REVERT: A 1729 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.6787 (m-80)
REVERT: A 1777 PHE cc_start: 0.6184 (OUTLIER) cc_final: 0.5364 (t80)
  outliers start: 52
  outliers final: 39
  residues processed: 256
  average time/residue: 0.1841
  time to fit residues: 68.7642
Evaluate side-chains
  244 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 199
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  134 PHE
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain A residue  716 MET
Chi-restraints excluded: chain A residue  725 THR
Chi-restraints excluded: chain A residue  734 PHE
Chi-restraints excluded: chain A residue  785 PHE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  924 LEU
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue 1204 VAL
Chi-restraints excluded: chain A residue 1313 LEU
Chi-restraints excluded: chain A residue 1317 SER
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1358 PHE
Chi-restraints excluded: chain A residue 1366 ILE
Chi-restraints excluded: chain A residue 1376 ASN
Chi-restraints excluded: chain A residue 1379 ILE
Chi-restraints excluded: chain A residue 1388 SER
Chi-restraints excluded: chain A residue 1406 ASN
Chi-restraints excluded: chain A residue 1473 ASP
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1541 CYS
Chi-restraints excluded: chain A residue 1654 MET
Chi-restraints excluded: chain A residue 1655 SER
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1763 LEU
Chi-restraints excluded: chain A residue 1777 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 31 optimal weight:    9.9990
   chunk 55 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0270
   chunk 26 optimal weight:    4.9990
   chunk 109 optimal weight:    4.9990
   chunk 73 optimal weight:   20.0000
   chunk 57 optimal weight:    8.9990
   overall best weight:    2.5844

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

Flipped N/Q/H residues before XYZ refinement:
A 731 ASN
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.204284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.166950 restraints weight = 11197.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 1.84
r_work: 0.3738 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3620 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.091   9804  Z= 0.187
  Angle     :  0.732  12.505  13309  Z= 0.356
  Chirality :  0.043   0.202   1561
  Planarity :  0.004   0.069   1561
  Dihedral  : 16.972 179.171   2090
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.28 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 18.87 %
    Favored  : 74.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.23 %
    Twisted General : 0.09 %

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: -0.87 (0.25), residues: 1126
  helix:  0.21 (0.18), residues: 815
  sheet:  None (None), residues: 0
  loop : -2.61 (0.32), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A1442 
 HIS   0.008   0.001   HIS A 279 
 PHE   0.021   0.002   PHE A 785 
 TYR   0.023   0.002   TYR A 379 
 ARG   0.003   0.000   ARG A 223 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00414 (    5)
  link_NAG-ASN         : angle       2.37589 (   15)
  link_BETA1-4         : bond        0.01610 (    4)
  link_BETA1-4         : angle       4.61195 (   12)
  hydrogen bonds       : bond        0.04299 (  625)
  hydrogen bonds       : angle       4.84519 ( 1809)
  SS BOND              : bond        0.00524 (    3)
  SS BOND              : angle       3.87045 (    6)
  covalent geometry    : bond        0.00437 ( 9788)
  covalent geometry    : angle       0.71088 (13276)
  Misc. bond           : bond        0.00253 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 216
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6714 (ptm160)
REVERT: A  196 TRP cc_start: 0.7948 (m-10) cc_final: 0.7017 (m100)
REVERT: A  250 LYS cc_start: 0.8273 (mmmm) cc_final: 0.8050 (mmtt)
REVERT: A  356 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8121 (m-80)
REVERT: A  366 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7467 (mp)
REVERT: A  422 GLN cc_start: 0.8233 (tt0) cc_final: 0.7853 (tm-30)
REVERT: A  733 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8399 (mp)
REVERT: A  777 TYR cc_start: 0.5971 (m-80) cc_final: 0.5153 (m-80)
REVERT: A  905 THR cc_start: 0.8169 (t) cc_final: 0.7291 (m)
REVERT: A 1218 LEU cc_start: 0.8107 (mm) cc_final: 0.7853 (mp)
REVERT: A 1219 LEU cc_start: 0.7681 (mt) cc_final: 0.7352 (tp)
REVERT: A 1729 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6826 (m-80)
REVERT: A 1763 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7759 (mp)
REVERT: A 1777 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5336 (t80)
  outliers start: 61
  outliers final: 38
  residues processed: 256
  average time/residue: 0.1881
  time to fit residues: 70.8067
Evaluate side-chains
  245 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 200
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  134 PHE
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain A residue  716 MET
Chi-restraints excluded: chain A residue  725 THR
Chi-restraints excluded: chain A residue  733 LEU
Chi-restraints excluded: chain A residue  734 PHE
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  785 PHE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  924 LEU
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue 1204 VAL
Chi-restraints excluded: chain A residue 1313 LEU
Chi-restraints excluded: chain A residue 1317 SER
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1340 LEU
Chi-restraints excluded: chain A residue 1358 PHE
Chi-restraints excluded: chain A residue 1366 ILE
Chi-restraints excluded: chain A residue 1376 ASN
Chi-restraints excluded: chain A residue 1388 SER
Chi-restraints excluded: chain A residue 1406 ASN
Chi-restraints excluded: chain A residue 1473 ASP
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1541 CYS
Chi-restraints excluded: chain A residue 1654 MET
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1763 LEU
Chi-restraints excluded: chain A residue 1777 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 7 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9990
   chunk 54 optimal weight:    9.9990
   chunk 9 optimal weight:   40.0000
   chunk 4 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 20 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.207657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.171032 restraints weight = 11085.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.4019 rms_B_bonded: 1.83
r_work: 0.3866 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3751 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   9804  Z= 0.147
  Angle     :  0.689  10.689  13309  Z= 0.333
  Chirality :  0.041   0.197   1561
  Planarity :  0.004   0.061   1561
  Dihedral  : 16.085 179.701   2090
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.22 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 20.75 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.23 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.25), residues: 1126
  helix:  0.44 (0.18), residues: 812
  sheet:  None (None), residues: 0
  loop : -2.59 (0.32), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1442 
 HIS   0.006   0.001   HIS A 279 
 PHE   0.024   0.002   PHE A 785 
 TYR   0.017   0.002   TYR A 169 
 ARG   0.005   0.000   ARG A1305 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00426 (    5)
  link_NAG-ASN         : angle       2.09873 (   15)
  link_BETA1-4         : bond        0.01635 (    4)
  link_BETA1-4         : angle       4.36210 (   12)
  hydrogen bonds       : bond        0.04040 (  625)
  hydrogen bonds       : angle       4.64737 ( 1809)
  SS BOND              : bond        0.00632 (    3)
  SS BOND              : angle       3.09828 (    6)
  covalent geometry    : bond        0.00328 ( 9788)
  covalent geometry    : angle       0.66996 (13276)
  Misc. bond           : bond        0.00152 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 221
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6653 (ptm-80)
REVERT: A  159 LYS cc_start: 0.7626 (mttt) cc_final: 0.7190 (ttmt)
REVERT: A  196 TRP cc_start: 0.7928 (m-10) cc_final: 0.6981 (m100)
REVERT: A  356 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8025 (m-80)
REVERT: A  366 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7508 (mp)
REVERT: A  422 GLN cc_start: 0.8173 (tt0) cc_final: 0.7785 (tm-30)
REVERT: A  713 PHE cc_start: 0.6662 (m-80) cc_final: 0.6402 (t80)
REVERT: A  734 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7843 (m-80)
REVERT: A  777 TYR cc_start: 0.5957 (m-80) cc_final: 0.5131 (m-80)
REVERT: A  860 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6452 (mt0)
REVERT: A 1219 LEU cc_start: 0.7737 (mt) cc_final: 0.7419 (tp)
REVERT: A 1227 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7036 (mt-10)
REVERT: A 1376 ASN cc_start: 0.2971 (OUTLIER) cc_final: 0.2722 (t0)
REVERT: A 1500 MET cc_start: 0.7070 (ttp) cc_final: 0.6566 (ttp)
REVERT: A 1653 MET cc_start: 0.8182 (ptm) cc_final: 0.7865 (ppp)
REVERT: A 1729 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6773 (m-80)
REVERT: A 1763 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7873 (mp)
REVERT: A 1767 ASN cc_start: 0.8000 (m-40) cc_final: 0.7335 (m-40)
REVERT: A 1777 PHE cc_start: 0.6166 (OUTLIER) cc_final: 0.5219 (t80)
  outliers start: 54
  outliers final: 29
  residues processed: 256
  average time/residue: 0.1917
  time to fit residues: 70.9178
Evaluate side-chains
  246 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 208
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  716 MET
Chi-restraints excluded: chain A residue  725 THR
Chi-restraints excluded: chain A residue  734 PHE
Chi-restraints excluded: chain A residue  785 PHE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  860 GLN
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue 1204 VAL
Chi-restraints excluded: chain A residue 1313 LEU
Chi-restraints excluded: chain A residue 1317 SER
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1340 LEU
Chi-restraints excluded: chain A residue 1358 PHE
Chi-restraints excluded: chain A residue 1376 ASN
Chi-restraints excluded: chain A residue 1388 SER
Chi-restraints excluded: chain A residue 1406 ASN
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1541 CYS
Chi-restraints excluded: chain A residue 1602 ILE
Chi-restraints excluded: chain A residue 1654 MET
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1763 LEU
Chi-restraints excluded: chain A residue 1777 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 40 optimal weight:    9.9990
   chunk 42 optimal weight:    7.9990
   chunk 105 optimal weight:    4.9990
   chunk 112 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 9 optimal weight:   30.0000
   chunk 50 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A1406 ASN
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1701 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.209272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.173017 restraints weight = 11180.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.4033 rms_B_bonded: 1.86
r_work: 0.3880 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3762 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   9804  Z= 0.137
  Angle     :  0.677  10.093  13309  Z= 0.329
  Chirality :  0.040   0.202   1561
  Planarity :  0.004   0.055   1561
  Dihedral  : 15.067 179.911   2087
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.39 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 21.59 %
    Favored  : 73.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.23 %
    Twisted General : 0.09 %

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: -0.38 (0.25), residues: 1126
  helix:  0.60 (0.18), residues: 814
  sheet:  None (None), residues: 0
  loop : -2.52 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP A1442 
 HIS   0.005   0.001   HIS A 279 
 PHE   0.022   0.001   PHE A 785 
 TYR   0.015   0.001   TYR A 379 
 ARG   0.003   0.000   ARG A1305 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00403 (    5)
  link_NAG-ASN         : angle       1.99839 (   15)
  link_BETA1-4         : bond        0.01564 (    4)
  link_BETA1-4         : angle       4.12091 (   12)
  hydrogen bonds       : bond        0.03895 (  625)
  hydrogen bonds       : angle       4.56382 ( 1809)
  SS BOND              : bond        0.00558 (    3)
  SS BOND              : angle       2.75758 (    6)
  covalent geometry    : bond        0.00301 ( 9788)
  covalent geometry    : angle       0.66051 (13276)
  Misc. bond           : bond        0.00385 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 228
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6598 (ptm-80)
REVERT: A  159 LYS cc_start: 0.7623 (mttt) cc_final: 0.7165 (ttmt)
REVERT: A  196 TRP cc_start: 0.7875 (m-10) cc_final: 0.6920 (m100)
REVERT: A  395 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7797 (ptt)
REVERT: A  422 GLN cc_start: 0.8155 (tt0) cc_final: 0.7748 (tm-30)
REVERT: A  713 PHE cc_start: 0.6752 (m-80) cc_final: 0.6469 (t80)
REVERT: A  777 TYR cc_start: 0.5880 (m-80) cc_final: 0.5036 (m-80)
REVERT: A  905 THR cc_start: 0.8198 (t) cc_final: 0.7328 (m)
REVERT: A 1219 LEU cc_start: 0.7664 (mt) cc_final: 0.7353 (tp)
REVERT: A 1227 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7341 (mt-10)
REVERT: A 1248 PHE cc_start: 0.8208 (m-10) cc_final: 0.7944 (m-10)
REVERT: A 1376 ASN cc_start: 0.2461 (OUTLIER) cc_final: 0.2012 (t0)
REVERT: A 1500 MET cc_start: 0.7199 (ttp) cc_final: 0.6726 (ttp)
REVERT: A 1597 ASP cc_start: 0.8179 (m-30) cc_final: 0.7917 (m-30)
REVERT: A 1653 MET cc_start: 0.8253 (ptm) cc_final: 0.7619 (ppp)
REVERT: A 1729 TYR cc_start: 0.7135 (OUTLIER) cc_final: 0.6807 (m-80)
REVERT: A 1767 ASN cc_start: 0.7988 (m-40) cc_final: 0.7751 (m-40)
REVERT: A 1777 PHE cc_start: 0.6081 (OUTLIER) cc_final: 0.5087 (t80)
  outliers start: 48
  outliers final: 28
  residues processed: 260
  average time/residue: 0.2207
  time to fit residues: 83.5282
Evaluate side-chains
  245 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 212
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain A residue  725 THR
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  785 PHE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue 1204 VAL
Chi-restraints excluded: chain A residue 1313 LEU
Chi-restraints excluded: chain A residue 1317 SER
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1358 PHE
Chi-restraints excluded: chain A residue 1376 ASN
Chi-restraints excluded: chain A residue 1406 ASN
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1490 THR
Chi-restraints excluded: chain A residue 1541 CYS
Chi-restraints excluded: chain A residue 1602 ILE
Chi-restraints excluded: chain A residue 1654 MET
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1777 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 106 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   chunk 35 optimal weight:    8.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.209445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.173003 restraints weight = 11286.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.4006 rms_B_bonded: 1.87
r_work: 0.3851 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3730 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   9804  Z= 0.139
  Angle     :  0.679  11.302  13309  Z= 0.327
  Chirality :  0.040   0.205   1561
  Planarity :  0.004   0.061   1561
  Dihedral  : 14.554 179.462   2087
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.75 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 22.12 %
    Favored  : 73.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.23 %
    Twisted General : 0.09 %

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: -0.31 (0.25), residues: 1126
  helix:  0.65 (0.18), residues: 815
  sheet:  None (None), residues: 0
  loop : -2.49 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP A1442 
 HIS   0.005   0.001   HIS A 279 
 PHE   0.034   0.002   PHE A1753 
 TYR   0.017   0.001   TYR A 379 
 ARG   0.003   0.000   ARG A1305 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00379 (    5)
  link_NAG-ASN         : angle       1.91626 (   15)
  link_BETA1-4         : bond        0.01532 (    4)
  link_BETA1-4         : angle       3.95134 (   12)
  hydrogen bonds       : bond        0.03880 (  625)
  hydrogen bonds       : angle       4.53230 ( 1809)
  SS BOND              : bond        0.00400 (    3)
  SS BOND              : angle       2.70128 (    6)
  covalent geometry    : bond        0.00309 ( 9788)
  covalent geometry    : angle       0.66374 (13276)
  Misc. bond           : bond        0.00184 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 212
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6569 (ptm-80)
REVERT: A  159 LYS cc_start: 0.7626 (mttt) cc_final: 0.7161 (ttmt)
REVERT: A  172 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7808 (mm-30)
REVERT: A  196 TRP cc_start: 0.7847 (m-10) cc_final: 0.6884 (m100)
REVERT: A  395 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7811 (ptt)
REVERT: A  422 GLN cc_start: 0.8147 (tt0) cc_final: 0.7779 (tm-30)
REVERT: A  713 PHE cc_start: 0.6732 (m-80) cc_final: 0.6474 (t80)
REVERT: A  905 THR cc_start: 0.8175 (t) cc_final: 0.7319 (m)
REVERT: A 1219 LEU cc_start: 0.7658 (mt) cc_final: 0.7371 (tp)
REVERT: A 1227 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7266 (tt0)
REVERT: A 1248 PHE cc_start: 0.8203 (m-10) cc_final: 0.7896 (m-10)
REVERT: A 1376 ASN cc_start: 0.2472 (OUTLIER) cc_final: 0.2028 (t0)
REVERT: A 1500 MET cc_start: 0.7200 (ttp) cc_final: 0.6807 (ttp)
REVERT: A 1585 ARG cc_start: 0.7562 (ppt170) cc_final: 0.7357 (ppt170)
REVERT: A 1597 ASP cc_start: 0.8002 (m-30) cc_final: 0.7775 (m-30)
REVERT: A 1729 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6872 (m-80)
REVERT: A 1767 ASN cc_start: 0.7939 (m-40) cc_final: 0.7540 (m-40)
REVERT: A 1777 PHE cc_start: 0.6055 (OUTLIER) cc_final: 0.5048 (t80)
  outliers start: 43
  outliers final: 30
  residues processed: 241
  average time/residue: 0.2398
  time to fit residues: 84.3814
Evaluate side-chains
  242 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 207
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  785 PHE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue 1204 VAL
Chi-restraints excluded: chain A residue 1313 LEU
Chi-restraints excluded: chain A residue 1317 SER
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1358 PHE
Chi-restraints excluded: chain A residue 1376 ASN
Chi-restraints excluded: chain A residue 1406 ASN
Chi-restraints excluded: chain A residue 1466 LEU
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1490 THR
Chi-restraints excluded: chain A residue 1541 CYS
Chi-restraints excluded: chain A residue 1602 ILE
Chi-restraints excluded: chain A residue 1612 ASP
Chi-restraints excluded: chain A residue 1654 MET
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1777 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 83 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 98 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 420 GLN
** A 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.208311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.171193 restraints weight = 11368.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 1.77
r_work: 0.3844 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3726 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.3312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   9804  Z= 0.150
  Angle     :  0.690  10.512  13309  Z= 0.332
  Chirality :  0.041   0.222   1561
  Planarity :  0.004   0.058   1561
  Dihedral  : 14.197 177.004   2087
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.75 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 22.33 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.23 %
    Twisted General : 0.09 %

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: -0.26 (0.25), residues: 1126
  helix:  0.70 (0.18), residues: 807
  sheet:  None (None), residues: 0
  loop : -2.42 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A1442 
 HIS   0.005   0.001   HIS A 279 
 PHE   0.022   0.002   PHE A1522 
 TYR   0.020   0.002   TYR A 379 
 ARG   0.005   0.000   ARG A 812 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00338 (    5)
  link_NAG-ASN         : angle       1.89109 (   15)
  link_BETA1-4         : bond        0.01452 (    4)
  link_BETA1-4         : angle       3.75387 (   12)
  hydrogen bonds       : bond        0.03896 (  625)
  hydrogen bonds       : angle       4.51399 ( 1809)
  SS BOND              : bond        0.00511 (    3)
  SS BOND              : angle       2.69804 (    6)
  covalent geometry    : bond        0.00343 ( 9788)
  covalent geometry    : angle       0.67619 (13276)
  Misc. bond           : bond        0.00202 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 212
  time to evaluate  : 1.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6649 (ptm-80)
REVERT: A  133 LEU cc_start: 0.8030 (tt) cc_final: 0.7723 (tt)
REVERT: A  159 LYS cc_start: 0.7671 (mttt) cc_final: 0.7237 (ttmt)
REVERT: A  196 TRP cc_start: 0.7919 (m-10) cc_final: 0.6970 (m100)
REVERT: A  356 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8109 (m-80)
REVERT: A  395 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7890 (ptt)
REVERT: A  422 GLN cc_start: 0.8145 (tt0) cc_final: 0.7752 (tm-30)
REVERT: A  905 THR cc_start: 0.8266 (t) cc_final: 0.7384 (m)
REVERT: A 1219 LEU cc_start: 0.7745 (mt) cc_final: 0.7514 (tp)
REVERT: A 1227 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7187 (tt0)
REVERT: A 1298 MET cc_start: 0.5962 (pmm) cc_final: 0.5752 (pmm)
REVERT: A 1376 ASN cc_start: 0.2742 (OUTLIER) cc_final: 0.2230 (t0)
REVERT: A 1729 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.6913 (m-80)
REVERT: A 1767 ASN cc_start: 0.7927 (m-40) cc_final: 0.7509 (m-40)
REVERT: A 1777 PHE cc_start: 0.5937 (OUTLIER) cc_final: 0.4942 (t80)
  outliers start: 44
  outliers final: 29
  residues processed: 240
  average time/residue: 0.2336
  time to fit residues: 82.7716
Evaluate side-chains
  239 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 204
  time to evaluate  : 1.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  785 PHE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue 1204 VAL
Chi-restraints excluded: chain A residue 1313 LEU
Chi-restraints excluded: chain A residue 1317 SER
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1358 PHE
Chi-restraints excluded: chain A residue 1376 ASN
Chi-restraints excluded: chain A residue 1388 SER
Chi-restraints excluded: chain A residue 1406 ASN
Chi-restraints excluded: chain A residue 1466 LEU
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1541 CYS
Chi-restraints excluded: chain A residue 1612 ASP
Chi-restraints excluded: chain A residue 1654 MET
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1777 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 44 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 106 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 90 optimal weight:   10.0000
   chunk 88 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1406 ASN
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1680 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.211044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.174270 restraints weight = 11221.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.4024 rms_B_bonded: 1.77
r_work: 0.3870 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3752 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.3448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9804  Z= 0.126
  Angle     :  0.683  11.051  13309  Z= 0.324
  Chirality :  0.040   0.203   1561
  Planarity :  0.004   0.057   1561
  Dihedral  : 13.865 176.096   2087
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.31 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 23.48 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.23 %
    Twisted General : 0.09 %

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: -0.14 (0.25), residues: 1126
  helix:  0.77 (0.18), residues: 807
  sheet:  None (None), residues: 0
  loop : -2.32 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A1442 
 HIS   0.003   0.001   HIS A 279 
 PHE   0.026   0.001   PHE A1522 
 TYR   0.013   0.001   TYR A 379 
 ARG   0.010   0.001   ARG A 812 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00375 (    5)
  link_NAG-ASN         : angle       1.77883 (   15)
  link_BETA1-4         : bond        0.01459 (    4)
  link_BETA1-4         : angle       3.67730 (   12)
  hydrogen bonds       : bond        0.03780 (  625)
  hydrogen bonds       : angle       4.47274 ( 1809)
  SS BOND              : bond        0.00878 (    3)
  SS BOND              : angle       1.15779 (    6)
  covalent geometry    : bond        0.00268 ( 9788)
  covalent geometry    : angle       0.67179 (13276)
  Misc. bond           : bond        0.00181 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 216
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6623 (ptm-80)
REVERT: A  159 LYS cc_start: 0.7668 (mttt) cc_final: 0.7218 (ttmt)
REVERT: A  172 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7717 (mm-30)
REVERT: A  196 TRP cc_start: 0.7897 (m-10) cc_final: 0.6957 (m100)
REVERT: A  356 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7883 (m-80)
REVERT: A  395 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7868 (ptt)
REVERT: A  417 TYR cc_start: 0.7838 (t80) cc_final: 0.7576 (t80)
REVERT: A  422 GLN cc_start: 0.8143 (tt0) cc_final: 0.7719 (tm-30)
REVERT: A  901 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7562 (mt-10)
REVERT: A  905 THR cc_start: 0.8257 (t) cc_final: 0.7384 (m)
REVERT: A 1219 LEU cc_start: 0.7756 (mt) cc_final: 0.7518 (tp)
REVERT: A 1227 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7216 (tt0)
REVERT: A 1248 PHE cc_start: 0.8236 (m-10) cc_final: 0.7917 (m-10)
REVERT: A 1298 MET cc_start: 0.5843 (pmm) cc_final: 0.5603 (pmm)
REVERT: A 1597 ASP cc_start: 0.7869 (m-30) cc_final: 0.7571 (m-30)
REVERT: A 1729 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6895 (m-80)
REVERT: A 1762 PHE cc_start: 0.8608 (t80) cc_final: 0.8325 (t80)
REVERT: A 1767 ASN cc_start: 0.7808 (m-40) cc_final: 0.7495 (m-40)
REVERT: A 1777 PHE cc_start: 0.5989 (OUTLIER) cc_final: 0.5003 (t80)
  outliers start: 41
  outliers final: 28
  residues processed: 243
  average time/residue: 0.1971
  time to fit residues: 70.2618
Evaluate side-chains
  241 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 207
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  785 PHE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  901 GLU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue 1204 VAL
Chi-restraints excluded: chain A residue 1313 LEU
Chi-restraints excluded: chain A residue 1358 PHE
Chi-restraints excluded: chain A residue 1388 SER
Chi-restraints excluded: chain A residue 1406 ASN
Chi-restraints excluded: chain A residue 1466 LEU
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1490 THR
Chi-restraints excluded: chain A residue 1541 CYS
Chi-restraints excluded: chain A residue 1612 ASP
Chi-restraints excluded: chain A residue 1654 MET
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1777 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 35 optimal weight:    4.9990
   chunk 97 optimal weight:   10.0000
   chunk 79 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   chunk 46 optimal weight:    0.6980
   chunk 84 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1701 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.204696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.167760 restraints weight = 11320.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3969 rms_B_bonded: 1.84
r_work: 0.3811 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3693 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.3385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.100   9804  Z= 0.227
  Angle     :  0.782  10.639  13309  Z= 0.377
  Chirality :  0.044   0.211   1561
  Planarity :  0.005   0.058   1561
  Dihedral  : 14.287 170.337   2085
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.46 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 23.27 %
    Favored  : 72.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.23 %
    Twisted General : 0.09 %

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: -0.48 (0.25), residues: 1126
  helix:  0.51 (0.18), residues: 813
  sheet: -2.63 (1.65), residues: 12
  loop : -2.44 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A1442 
 HIS   0.006   0.001   HIS A 279 
 PHE   0.025   0.002   PHE A1522 
 TYR   0.034   0.002   TYR A 379 
 ARG   0.008   0.001   ARG A 812 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00303 (    5)
  link_NAG-ASN         : angle       2.01901 (   15)
  link_BETA1-4         : bond        0.01334 (    4)
  link_BETA1-4         : angle       3.70851 (   12)
  hydrogen bonds       : bond        0.04165 (  625)
  hydrogen bonds       : angle       4.70648 ( 1809)
  SS BOND              : bond        0.01170 (    3)
  SS BOND              : angle       2.79151 (    6)
  covalent geometry    : bond        0.00542 ( 9788)
  covalent geometry    : angle       0.76925 (13276)
  Misc. bond           : bond        0.00542 (    4)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 209
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6707 (ptm160)
REVERT: A  133 LEU cc_start: 0.8066 (tt) cc_final: 0.7788 (tt)
REVERT: A  159 LYS cc_start: 0.7666 (mttt) cc_final: 0.7208 (ttmt)
REVERT: A  172 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7775 (mm-30)
REVERT: A  196 TRP cc_start: 0.7867 (m-10) cc_final: 0.6889 (m100)
REVERT: A  356 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8160 (m-80)
REVERT: A  421 ASN cc_start: 0.7743 (m-40) cc_final: 0.7455 (m-40)
REVERT: A  422 GLN cc_start: 0.8157 (tt0) cc_final: 0.7753 (tm-30)
REVERT: A  745 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6937 (mm-30)
REVERT: A  817 PHE cc_start: 0.6973 (m-80) cc_final: 0.6740 (m-80)
REVERT: A  905 THR cc_start: 0.8254 (t) cc_final: 0.7357 (m)
REVERT: A 1219 LEU cc_start: 0.7857 (mt) cc_final: 0.7563 (tp)
REVERT: A 1227 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7275 (tt0)
REVERT: A 1298 MET cc_start: 0.5710 (pmm) cc_final: 0.5471 (pmm)
REVERT: A 1597 ASP cc_start: 0.7876 (m-30) cc_final: 0.7676 (m-30)
REVERT: A 1637 ARG cc_start: 0.8621 (tpp80) cc_final: 0.8401 (tpp80)
REVERT: A 1680 ASN cc_start: 0.8773 (m110) cc_final: 0.7866 (m-40)
REVERT: A 1729 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.7077 (m-80)
REVERT: A 1762 PHE cc_start: 0.8665 (t80) cc_final: 0.8320 (t80)
REVERT: A 1767 ASN cc_start: 0.7999 (m-40) cc_final: 0.7603 (m-40)
REVERT: A 1777 PHE cc_start: 0.5961 (OUTLIER) cc_final: 0.4980 (t80)
  outliers start: 37
  outliers final: 31
  residues processed: 230
  average time/residue: 0.2131
  time to fit residues: 72.0967
Evaluate side-chains
  242 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 207
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  157 TRP
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  356 PHE
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain A residue  725 THR
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  785 PHE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue 1204 VAL
Chi-restraints excluded: chain A residue 1317 SER
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1358 PHE
Chi-restraints excluded: chain A residue 1406 ASN
Chi-restraints excluded: chain A residue 1466 LEU
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1490 THR
Chi-restraints excluded: chain A residue 1541 CYS
Chi-restraints excluded: chain A residue 1612 ASP
Chi-restraints excluded: chain A residue 1654 MET
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1777 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 101 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0020
   chunk 105 optimal weight:    0.9980
   chunk 40 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 71 optimal weight:    6.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 407 ASN
A 739 HIS
** A 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1376 ASN
A1701 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.211302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.175108 restraints weight = 11310.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.4030 rms_B_bonded: 1.90
r_work: 0.3876 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3757 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9804  Z= 0.131
  Angle     :  0.707  10.769  13309  Z= 0.336
  Chirality :  0.040   0.201   1561
  Planarity :  0.004   0.056   1561
  Dihedral  : 13.655 166.384   2085
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.13 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 24.53 %
    Favored  : 72.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.09 %
    Twisted Proline : 3.23 %
    Twisted General : 0.09 %

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: -0.20 (0.25), residues: 1126
  helix:  0.71 (0.18), residues: 814
  sheet: -2.73 (1.65), residues: 12
  loop : -2.28 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A1442 
 HIS   0.005   0.001   HIS A1586 
 PHE   0.027   0.002   PHE A1522 
 TYR   0.013   0.001   TYR A 379 
 ARG   0.008   0.001   ARG A 812 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00398 (    5)
  link_NAG-ASN         : angle       1.76041 (   15)
  link_BETA1-4         : bond        0.01510 (    4)
  link_BETA1-4         : angle       3.59548 (   12)
  hydrogen bonds       : bond        0.03821 (  625)
  hydrogen bonds       : angle       4.48807 ( 1809)
  SS BOND              : bond        0.01142 (    3)
  SS BOND              : angle       1.56384 (    6)
  covalent geometry    : bond        0.00275 ( 9788)
  covalent geometry    : angle       0.69658 (13276)
  Misc. bond           : bond        0.00328 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7149.81 seconds
wall clock time: 127 minutes 14.11 seconds (7634.11 seconds total)