Starting phenix.real_space_refine
on Sat May 17 11:14:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8epm_28530/05_2025/8epm_28530.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8epm_28530/05_2025/8epm_28530.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8epm_28530/05_2025/8epm_28530.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8epm_28530/05_2025/8epm_28530.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8epm_28530/05_2025/8epm_28530.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8epm_28530/05_2025/8epm_28530.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     S      84      5.16       5
     C    9990      2.51       5
     N    2519      2.21       5
     O    2863      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 15458
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 7676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 991, 7676
          Classifications: {'peptide': 991}
          Incomplete info: {'truncation_to_alanine': 75}
          Link IDs: {'PTRANS': 28, 'TRANS': 962}
          Chain breaks: 8
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 297
          Unresolved non-hydrogen angles: 394
          Unresolved non-hydrogen dihedrals: 257
          Unresolved non-hydrogen chiralities: 32
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 13, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 175
    Chain: "C"
      Number of atoms: 7570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 948, 7570
          Classifications: {'peptide': 948}
          Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907}
          Chain breaks: 5
    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: "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: "E"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "F"
      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: "G"
      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: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {' CA': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 9.13, per 1000 atoms: 0.59
  Number of scatterers: 15458
  At special positions: 0
  Unit cell: (130.338, 142.592, 149.276, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      2     19.99
     S      84     16.00
     O    2863      8.00
     N    2519      7.00
     C    9990      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 251 " - pdb=" SG  CYS A 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 268 " - pdb=" SG  CYS A 279 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1318 " - pdb=" SG  CYS A1329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1678 " - pdb=" SG  CYS A1694 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 303 " - pdb=" SG  CYS C1044 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 404 " - pdb=" SG  CYS C1071 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 667 " - pdb=" SG  CYS C 697 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 904 " - pdb=" SG  CYS C 974 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 996 " - pdb=" SG  CYS C1026 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 999 " - pdb=" SG  CYS C1024 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " NAG E   3 "
      " NAG E   3 " - " NAG E   4 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG B   1 " - " ASN C 184 "
      " NAG C1201 " - " ASN C  92 "
      " NAG C1202 " - " ASN C 781 "
      " NAG D   1 " - " ASN C 348 "
      " NAG E   1 " - " ASN C 468 "
      " NAG F   1 " - " ASN C 613 "
      " NAG G   1 " - " ASN C 895 "
  Time building additional restraints: 4.35
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3648

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 15 sheets defined
      54.5% alpha, 10.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 107
    Processing helix  chain 'A' and resid 118 through 127
      removed outlier: 3.793A  pdb=" N   ARG A 123 " --> pdb=" O   PRO A 119 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   THR A 127 " --> pdb=" O   ARG A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 144
      removed outlier: 3.975A  pdb=" N   PHE A 131 " --> pdb=" O   THR A 127 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ILE A 134 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   PHE A 135 " --> pdb=" O   PHE A 131 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA A 139 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 175
    Processing helix  chain 'A' and resid 195 through 197
      No H-bonds generated for 'chain 'A' and resid 195 through 197'
    Processing helix  chain 'A' and resid 198 through 204
      removed outlier: 4.117A  pdb=" N   SER A 202 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE A 204 " --> pdb=" O   LEU A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 216
      removed outlier: 3.622A  pdb=" N   GLN A 208 " --> pdb=" O   ILE A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 241
      removed outlier: 3.677A  pdb=" N   GLN A 223 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ILE A 224 " --> pdb=" O   PRO A 220 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LEU A 227 " --> pdb=" O   GLN A 223 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU A 228 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   PHE A 235 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 307
    Processing helix  chain 'A' and resid 310 through 323
      removed outlier: 3.833A  pdb=" N   ALA A 321 " --> pdb=" O   ASN A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 337
      Proline residue:  A 333  - end of helix
    Processing helix  chain 'A' and resid 339 through 356
      removed outlier: 3.707A  pdb=" N   GLU A 353 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS A 356 " --> pdb=" O   GLY A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 494
      removed outlier: 3.678A  pdb=" N   LEU A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR A 490 " --> pdb=" O   VAL A 486 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA A 491 " --> pdb=" O   ALA A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 526
      removed outlier: 3.549A  pdb=" N   PHE A 513 " --> pdb=" O   TYR A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 560
      removed outlier: 3.921A  pdb=" N   ILE A 552 " --> pdb=" O   THR A 548 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   PHE A 560 " --> pdb=" O   VAL A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 577
      removed outlier: 3.586A  pdb=" N   LEU A 574 " --> pdb=" O   LEU A 571 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG A 575 " --> pdb=" O   ARG A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 602
    Processing helix  chain 'A' and resid 603 through 626
    Processing helix  chain 'A' and resid 642 through 656
    Processing helix  chain 'A' and resid 658 through 670
      removed outlier: 3.577A  pdb=" N   VAL A 662 " --> pdb=" O   ASP A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 678
      No H-bonds generated for 'chain 'A' and resid 676 through 678'
    Processing helix  chain 'A' and resid 679 through 708
      removed outlier: 4.100A  pdb=" N   PHE A 683 " --> pdb=" O   SER A 679 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASN A 696 " --> pdb=" O   TYR A 692 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA A 707 " --> pdb=" O   VAL A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1156 through 1172
      removed outlier: 3.571A  pdb=" N   ILE A1163 " --> pdb=" O   ILE A1159 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA A1171 " --> pdb=" O   SER A1167 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ALA A1172 " --> pdb=" O   ILE A1168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1180 through 1208
      removed outlier: 4.333A  pdb=" N   TYR A1188 " --> pdb=" O   LYS A1184 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   PHE A1189 " --> pdb=" O   VAL A1185 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ILE A1206 " --> pdb=" O   VAL A1202 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ASP A1207 " --> pdb=" O   ILE A1203 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLN A1208 " --> pdb=" O   LYS A1204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1222 through 1241
      removed outlier: 3.677A  pdb=" N   ASN A1241 " --> pdb=" O   PHE A1237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1252 through 1259
      removed outlier: 3.920A  pdb=" N   SER A1256 " --> pdb=" O   LYS A1252 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   LEU A1257 " --> pdb=" O   THR A1253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1260 through 1266
      Proline residue:  A1265  - end of helix
    Processing helix  chain 'A' and resid 1267 through 1272
      removed outlier: 3.728A  pdb=" N   ARG A1271 " --> pdb=" O   LYS A1267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1272 through 1312
      removed outlier: 3.720A  pdb=" N   VAL A1278 " --> pdb=" O   LYS A1274 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   ASN A1291 " --> pdb=" O   LYS A1287 " (cutoff:3.500A)
      removed outlier: 5.693A  pdb=" N   ILE A1292 " --> pdb=" O   ASN A1288 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL A1295 " --> pdb=" O   ASN A1291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1336 through 1340
      removed outlier: 3.553A  pdb=" N   ASN A1339 " --> pdb=" O   HIS A1336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1357 through 1371
    Processing helix  chain 'A' and resid 1373 through 1383
      removed outlier: 3.574A  pdb=" N   ASP A1383 " --> pdb=" O   GLN A1379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1396 through 1398
      No H-bonds generated for 'chain 'A' and resid 1396 through 1398'
    Processing helix  chain 'A' and resid 1399 through 1425
      removed outlier: 4.094A  pdb=" N   TYR A1403 " --> pdb=" O   MET A1399 " (cutoff:3.500A)
      Proline residue:  A1411  - end of helix
      removed outlier: 3.922A  pdb=" N   VAL A1415 " --> pdb=" O   PRO A1411 " (cutoff:3.500A)
      removed outlier: 5.203A  pdb=" N   ASN A1416 " --> pdb=" O   PHE A1412 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   VAL A1419 " --> pdb=" O   VAL A1415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1477 through 1496
      removed outlier: 3.571A  pdb=" N   ALA A1489 " --> pdb=" O   MET A1485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1503 through 1533
    Processing helix  chain 'A' and resid 1533 through 1538
      removed outlier: 4.376A  pdb=" N   PHE A1538 " --> pdb=" O   PHE A1534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1540 through 1562
      removed outlier: 3.863A  pdb=" N   ASP A1561 " --> pdb=" O   ILE A1557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1575 through 1580
      removed outlier: 3.936A  pdb=" N   ARG A1579 " --> pdb=" O   LEU A1575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1581 through 1587
      removed outlier: 3.732A  pdb=" N   LYS A1585 " --> pdb=" O   ALA A1581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1591 through 1596
    Processing helix  chain 'A' and resid 1606 through 1609
    Processing helix  chain 'A' and resid 1610 through 1630
    Processing helix  chain 'A' and resid 1648 through 1662
    Processing helix  chain 'A' and resid 1664 through 1672
    Processing helix  chain 'A' and resid 1698 through 1725
    Processing helix  chain 'A' and resid 1725 through 1730
    Processing helix  chain 'C' and resid 29 through 53
    Processing helix  chain 'C' and resid 53 through 65
      removed outlier: 3.624A  pdb=" N   GLN C  65 " --> pdb=" O   TYR C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 110
      removed outlier: 3.699A  pdb=" N   ALA C 110 " --> pdb=" O   LYS C 106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 187
    Processing helix  chain 'C' and resid 188 through 200
      removed outlier: 4.510A  pdb=" N   VAL C 192 " --> pdb=" O   ALA C 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 237 through 240
    Processing helix  chain 'C' and resid 241 through 249
      removed outlier: 3.681A  pdb=" N   ALA C 249 " --> pdb=" O   ILE C 245 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 265
    Processing helix  chain 'C' and resid 266 through 281
      removed outlier: 3.621A  pdb=" N   LYS C 270 " --> pdb=" O   GLY C 266 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 311 through 323
    Processing helix  chain 'C' and resid 332 through 344
    Processing helix  chain 'C' and resid 369 through 376
    Processing helix  chain 'C' and resid 396 through 406
      removed outlier: 4.055A  pdb=" N   ASN C 406 " --> pdb=" O   MET C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 423
      removed outlier: 4.457A  pdb=" N   ARG C 420 " --> pdb=" O   ILE C 416 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   ILE C 421 " --> pdb=" O   GLY C 417 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 425 through 431
      removed outlier: 4.168A  pdb=" N   VAL C 429 " --> pdb=" O   GLU C 425 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 431 through 438
      removed outlier: 3.783A  pdb=" N   GLY C 438 " --> pdb=" O   MET C 434 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 442
      removed outlier: 3.521A  pdb=" N   LYS C 442 " --> pdb=" O   ASP C 439 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 439 through 442'
    Processing helix  chain 'C' and resid 494 through 500
      removed outlier: 3.506A  pdb=" N   LEU C 500 " --> pdb=" O   ASP C 496 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 560 through 565
      removed outlier: 3.678A  pdb=" N   GLU C 565 " --> pdb=" O   PHE C 561 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 568 through 581
      removed outlier: 3.605A  pdb=" N   ASP C 580 " --> pdb=" O   ASN C 576 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLY C 581 " --> pdb=" O   LYS C 577 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 637 through 646
      removed outlier: 3.604A  pdb=" N   GLN C 641 " --> pdb=" O   GLU C 637 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 647 through 654
      Proline residue:  C 650  - end of helix
      removed outlier: 4.481A  pdb=" N   GLU C 654 " --> pdb=" O   ASP C 651 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 678 through 690
    Processing helix  chain 'C' and resid 698 through 719
      removed outlier: 4.073A  pdb=" N   ILE C 702 " --> pdb=" O   ASN C 698 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 720 through 723
    Processing helix  chain 'C' and resid 745 through 752
    Processing helix  chain 'C' and resid 757 through 760
    Processing helix  chain 'C' and resid 761 through 770
    Processing helix  chain 'C' and resid 817 through 827
    Processing helix  chain 'C' and resid 874 through 878
      removed outlier: 3.598A  pdb=" N   ILE C 878 " --> pdb=" O   PHE C 875 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 879 through 889
    Processing sheet with id=AA1, first strand: chain 'A' and resid 249 through 251
      removed outlier: 3.794A  pdb=" N   ALA A 250 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LYS A 280 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1316 through 1318
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1332 through 1335
    Processing sheet with id=AA4, first strand: chain 'C' and resid 69 through 72
    Processing sheet with id=AA5, first strand: chain 'C' and resid 122 through 123
      removed outlier: 6.093A  pdb=" N   VAL C 122 " --> pdb=" O   GLN C 143 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 125 through 126
      removed outlier: 6.835A  pdb=" N   TYR C 125 " --> pdb=" O   VAL C 166 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 126
      removed outlier: 6.835A  pdb=" N   TYR C 125 " --> pdb=" O   VAL C 166 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 150 through 151
    Processing sheet with id=AA9, first strand: chain 'C' and resid 298 through 300
      removed outlier: 6.153A  pdb=" N   ILE C 256 " --> pdb=" O   ALA C 292 " (cutoff:3.500A)
      removed outlier: 7.730A  pdb=" N   PHE C 294 " --> pdb=" O   ILE C 256 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   VAL C 258 " --> pdb=" O   PHE C 294 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   VAL C 384 " --> pdb=" O   TYR C 409 " (cutoff:3.500A)
      removed outlier: 8.268A  pdb=" N   TYR C 411 " --> pdb=" O   VAL C 384 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   THR C 386 " --> pdb=" O   TYR C 411 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   ILE C 413 " --> pdb=" O   THR C 386 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   SER C 388 " --> pdb=" O   ILE C 413 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 521 through 523
      removed outlier: 6.506A  pdb=" N   ALA C 514 " --> pdb=" O   LEU C 522 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TRP C 609 " --> pdb=" O   GLY C 584 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 658 through 659
      removed outlier: 3.770A  pdb=" N   ALA C 731 " --> pdb=" O   LYS C 815 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   MET C 793 " --> pdb=" O   THR C 776 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 800 through 801
    Processing sheet with id=AB4, first strand: chain 'C' and resid 859 through 861
      removed outlier: 7.005A  pdb=" N   ILE C 852 " --> pdb=" O   LEU C 860 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLU C1019 " --> pdb=" O   ILE C1002 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   ILE C1002 " --> pdb=" O   GLU C1019 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 892 through 899
    Processing sheet with id=AB6, first strand: chain 'C' and resid 903 through 904

    813 hydrogen bonds defined for protein.
    2304 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: 5.99

  Time building geometry restraints manager: 5.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4894
        1.34 -     1.46: 3662
        1.46 -     1.58: 7096
        1.58 -     1.70: 1
        1.70 -     1.82: 133
  Bond restraints: 15786
  Sorted by residual:
  bond pdb=" C1  NAG E   3 "
       pdb=" O5  NAG E   3 "
    ideal  model  delta    sigma   weight residual
    1.406  1.489 -0.083 2.00e-02 2.50e+03 1.73e+01
  bond pdb=" C1  NAG G   2 "
       pdb=" O5  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.486 -0.080 2.00e-02 2.50e+03 1.58e+01
  bond pdb=" C1  NAG C1202 "
       pdb=" O5  NAG C1202 "
    ideal  model  delta    sigma   weight residual
    1.406  1.477 -0.071 2.00e-02 2.50e+03 1.27e+01
  bond pdb=" CB  PRO A1680 "
       pdb=" CG  PRO A1680 "
    ideal  model  delta    sigma   weight residual
    1.492  1.598 -0.106 5.00e-02 4.00e+02 4.51e+00
  bond pdb=" C1  NAG D   1 "
       pdb=" C2  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.532  1.565 -0.033 2.00e-02 2.50e+03 2.72e+00
  ... (remaining 15781 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 20906
        1.54 -     3.08: 410
        3.08 -     4.62: 63
        4.62 -     6.16: 22
        6.16 -     7.70: 9
  Bond angle restraints: 21410
  Sorted by residual:
  angle pdb=" N   ILE A 579 "
        pdb=" CA  ILE A 579 "
        pdb=" C   ILE A 579 "
      ideal   model   delta    sigma   weight residual
     113.20  108.68    4.52 9.60e-01 1.09e+00 2.22e+01
  angle pdb=" N   GLN A1589 "
        pdb=" CA  GLN A1589 "
        pdb=" C   GLN A1589 "
      ideal   model   delta    sigma   weight residual
     111.28  106.36    4.92 1.09e+00 8.42e-01 2.04e+01
  angle pdb=" CA  PRO A1680 "
        pdb=" N   PRO A1680 "
        pdb=" CD  PRO A1680 "
      ideal   model   delta    sigma   weight residual
     112.00  105.96    6.04 1.40e+00 5.10e-01 1.86e+01
  angle pdb=" N   PRO A1680 "
        pdb=" CD  PRO A1680 "
        pdb=" CG  PRO A1680 "
      ideal   model   delta    sigma   weight residual
     103.20   97.32    5.88 1.50e+00 4.44e-01 1.54e+01
  angle pdb=" N   LYS A1585 "
        pdb=" CA  LYS A1585 "
        pdb=" C   LYS A1585 "
      ideal   model   delta    sigma   weight residual
     113.41  108.87    4.54 1.22e+00 6.72e-01 1.38e+01
  ... (remaining 21405 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.71: 8777
       24.71 -    49.43: 661
       49.43 -    74.14: 80
       74.14 -    98.85: 36
       98.85 -   123.57: 14
  Dihedral angle restraints: 9568
    sinusoidal: 3919
      harmonic: 5649
  Sorted by residual:
  dihedral pdb=" CB  CYS A 268 "
           pdb=" SG  CYS A 268 "
           pdb=" SG  CYS A 279 "
           pdb=" CB  CYS A 279 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.19   53.19     1      1.00e+01 1.00e-02 3.85e+01
  dihedral pdb=" CB  CYS C 404 "
           pdb=" SG  CYS C 404 "
           pdb=" SG  CYS C1071 "
           pdb=" CB  CYS C1071 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   50.80   42.20     1      1.00e+01 1.00e-02 2.49e+01
  dihedral pdb=" CA  ASP A 263 "
           pdb=" C   ASP A 263 "
           pdb=" N   PRO A 264 "
           pdb=" CA  PRO A 264 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.71   22.29     0      5.00e+00 4.00e-02 1.99e+01
  ... (remaining 9565 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 2243
       0.067 -    0.134: 219
       0.134 -    0.202: 9
       0.202 -    0.269: 1
       0.269 -    0.336: 3
  Chirality restraints: 2475
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN C 348 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.06   -0.34 2.00e-01 2.50e+01 2.83e+00
  chirality pdb=" C4  NAG D   1 "
            pdb=" C3  NAG D   1 "
            pdb=" C5  NAG D   1 "
            pdb=" O4  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.23   -0.30 2.00e-01 2.50e+01 2.21e+00
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN C 184 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.14e+00
  ... (remaining 2472 not shown)

  Planarity restraints: 2709
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A1679 "   -0.053 5.00e-02 4.00e+02   7.66e-02 9.38e+00
        pdb=" N   PRO A1680 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO A1680 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A1680 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 263 "   -0.041 5.00e-02 4.00e+02   6.21e-02 6.16e+00
        pdb=" N   PRO A 264 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A 264 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 264 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP C 674 "   -0.010 2.00e-02 2.50e+03   2.10e-02 4.43e+00
        pdb=" CG  ASP C 674 "    0.036 2.00e-02 2.50e+03
        pdb=" OD1 ASP C 674 "   -0.013 2.00e-02 2.50e+03
        pdb=" OD2 ASP C 674 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 2706 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1494
        2.74 -     3.28: 15429
        3.28 -     3.82: 25492
        3.82 -     4.36: 29347
        4.36 -     4.90: 51372
  Nonbonded interactions: 123134
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 479 "
            pdb=" O   ARG A 578 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   GLU C 182 "
            pdb=" OG1 THR C 186 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O4  NAG D   2 "
            pdb=" O7  NAG D   2 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   ASP C 285 "
            pdb=" NE2 GLN C 309 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" OH  TYR C 450 "
            pdb=" OG1 THR C 461 "
     model   vdw
     2.273 3.040
  ... (remaining 123129 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'
  selection = chain 'F'
  selection = chain 'G'
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.680
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     38.060
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
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      :  0.004   0.106  15810  Z= 0.165
  Angle     :  0.569   9.862  21472  Z= 0.290
  Chirality :  0.042   0.336   2475
  Planarity :  0.003   0.077   2702
  Dihedral  : 18.036 123.568   5890
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.81 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 18.50 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.19), residues: 1909
  helix:  1.07 (0.17), residues: 948
  sheet: -0.21 (0.38), residues: 185
  loop : -1.38 (0.22), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 185 
 HIS   0.002   0.001   HIS A1639 
 PHE   0.020   0.001   PHE C1003 
 TYR   0.015   0.001   TYR A1728 
 ARG   0.002   0.000   ARG A 590 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00572 (    7)
  link_NAG-ASN         : angle       2.84149 (   21)
  link_BETA1-4         : bond        0.00746 (    7)
  link_BETA1-4         : angle       3.32426 (   21)
  hydrogen bonds       : bond        0.19453 (  793)
  hydrogen bonds       : angle       6.41113 ( 2304)
  SS BOND              : bond        0.00161 (   10)
  SS BOND              : angle       1.05700 (   20)
  covalent geometry    : bond        0.00372 (15786)
  covalent geometry    : angle       0.55226 (21410)

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

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

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 205
  time to evaluate  : 1.736 
Fit side-chains
  outliers start: 9
  outliers final: 3
  residues processed: 211
  average time/residue: 0.2800
  time to fit residues: 87.5580
Evaluate side-chains
  203 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 200
  time to evaluate  : 1.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1584 ILE
Chi-restraints excluded: chain A residue 1586 LEU
Chi-restraints excluded: chain C residue  379 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 162 optimal weight:    2.9990
   chunk 146 optimal weight:    0.5980
   chunk 81 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   chunk 98 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 151 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   chunk 175 optimal weight:    7.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 691 ASN
A1288 ASN
A1395 ASN
A1491 ASN
A1725 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.156909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.120804 restraints weight = 20008.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 2.37
r_work: 0.3074 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.0873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  15810  Z= 0.161
  Angle     :  0.599   9.521  21472  Z= 0.297
  Chirality :  0.044   0.334   2475
  Planarity :  0.004   0.036   2702
  Dihedral  : 11.535 114.338   2395
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.34 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.28 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.19), residues: 1909
  helix:  1.30 (0.17), residues: 967
  sheet: -0.23 (0.35), residues: 197
  loop : -1.48 (0.22), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 185 
 HIS   0.003   0.001   HIS A 497 
 PHE   0.011   0.001   PHE C 653 
 TYR   0.013   0.001   TYR C 744 
 ARG   0.003   0.000   ARG A1588 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00709 (    7)
  link_NAG-ASN         : angle       2.89536 (   21)
  link_BETA1-4         : bond        0.00877 (    7)
  link_BETA1-4         : angle       2.85120 (   21)
  hydrogen bonds       : bond        0.04702 (  793)
  hydrogen bonds       : angle       4.53258 ( 2304)
  SS BOND              : bond        0.00135 (   10)
  SS BOND              : angle       1.16788 (   20)
  covalent geometry    : bond        0.00370 (15786)
  covalent geometry    : angle       0.58507 (21410)

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

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

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 217
  time to evaluate  : 1.767 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 ARG cc_start: 0.7192 (ptt90) cc_final: 0.6360 (ptp-170)
REVERT: A 1335 ASP cc_start: 0.8503 (t70) cc_final: 0.8002 (t0)
REVERT: C  309 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8115 (tm-30)
  outliers start: 34
  outliers final: 19
  residues processed: 241
  average time/residue: 0.2615
  time to fit residues: 95.2113
Evaluate side-chains
  220 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 200
  time to evaluate  : 1.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  679 SER
Chi-restraints excluded: chain A residue 1230 VAL
Chi-restraints excluded: chain A residue 1294 ILE
Chi-restraints excluded: chain A residue 1584 ILE
Chi-restraints excluded: chain A residue 1586 LEU
Chi-restraints excluded: chain A residue 1626 MET
Chi-restraints excluded: chain A residue 1670 LEU
Chi-restraints excluded: chain A residue 1701 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue  309 GLN
Chi-restraints excluded: chain C residue  585 GLU
Chi-restraints excluded: chain C residue  587 THR
Chi-restraints excluded: chain C residue  667 CYS
Chi-restraints excluded: chain C residue  741 THR
Chi-restraints excluded: chain C residue 1032 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 170 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 145 optimal weight:    0.4980
   chunk 172 optimal weight:    0.4980
   chunk 157 optimal weight:    0.6980
   chunk 15 optimal weight:    8.9990
   chunk 183 optimal weight:    2.9990
   chunk 108 optimal weight:    4.9990
   chunk 92 optimal weight:    0.7980
   chunk 168 optimal weight:    0.4980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 344 ASN
A1179 ASN
A1309 GLN
A1725 ASN
C  65 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.160070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.123662 restraints weight = 19993.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 2.28
r_work: 0.3107 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.1162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  15810  Z= 0.109
  Angle     :  0.540   9.455  21472  Z= 0.266
  Chirality :  0.042   0.302   2475
  Planarity :  0.003   0.056   2702
  Dihedral  : 10.646 114.637   2393
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.24 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 17.83 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.20), residues: 1909
  helix:  1.53 (0.17), residues: 967
  sheet: -0.24 (0.35), residues: 199
  loop : -1.39 (0.22), residues: 743

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 185 
 HIS   0.002   0.001   HIS A 266 
 PHE   0.012   0.001   PHE A 230 
 TYR   0.017   0.001   TYR C 744 
 ARG   0.003   0.000   ARG A1187 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00666 (    7)
  link_NAG-ASN         : angle       2.58447 (   21)
  link_BETA1-4         : bond        0.00825 (    7)
  link_BETA1-4         : angle       2.54394 (   21)
  hydrogen bonds       : bond        0.03926 (  793)
  hydrogen bonds       : angle       4.16626 ( 2304)
  SS BOND              : bond        0.00184 (   10)
  SS BOND              : angle       0.87201 (   20)
  covalent geometry    : bond        0.00230 (15786)
  covalent geometry    : angle       0.52824 (21410)

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

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

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 227
  time to evaluate  : 1.687 
Fit side-chains
REVERT: A  125 GLU cc_start: 0.8373 (tp30) cc_final: 0.8142 (tp30)
REVERT: A  221 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8208 (mp)
REVERT: A  278 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6841 (pp20)
REVERT: A  293 ASP cc_start: 0.8414 (m-30) cc_final: 0.8191 (m-30)
REVERT: A  304 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8728 (pp30)
REVERT: A  705 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7883 (t0)
REVERT: A  706 LEU cc_start: 0.7714 (mt) cc_final: 0.7423 (mp)
REVERT: A 1335 ASP cc_start: 0.8470 (t70) cc_final: 0.8026 (t0)
  outliers start: 42
  outliers final: 25
  residues processed: 261
  average time/residue: 0.2535
  time to fit residues: 100.8233
Evaluate side-chains
  240 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 211
  time to evaluate  : 1.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  705 ASN
Chi-restraints excluded: chain A residue 1230 VAL
Chi-restraints excluded: chain A residue 1294 ILE
Chi-restraints excluded: chain A residue 1584 ILE
Chi-restraints excluded: chain A residue 1586 LEU
Chi-restraints excluded: chain A residue 1626 MET
Chi-restraints excluded: chain A residue 1675 GLU
Chi-restraints excluded: chain A residue 1701 VAL
Chi-restraints excluded: chain C residue   65 GLN
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  506 LEU
Chi-restraints excluded: chain C residue  585 GLU
Chi-restraints excluded: chain C residue  587 THR
Chi-restraints excluded: chain C residue  667 CYS
Chi-restraints excluded: chain C residue  741 THR
Chi-restraints excluded: chain C residue  848 MET
Chi-restraints excluded: chain C residue 1032 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 136 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 190 optimal weight:    1.9990
   chunk 163 optimal weight:    2.9990
   chunk 165 optimal weight:    5.9990
   chunk 127 optimal weight:    5.9990
   chunk 91 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 144 optimal weight:    0.6980
   chunk 115 optimal weight:    1.9990
   chunk 182 optimal weight:    0.0980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A1309 GLN
C  65 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.157576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.120757 restraints weight = 19993.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.32
r_work: 0.3071 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15810  Z= 0.144
  Angle     :  0.566   9.592  21472  Z= 0.277
  Chirality :  0.043   0.289   2475
  Planarity :  0.003   0.044   2702
  Dihedral  : 10.343 113.918   2393
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.24 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 18.69 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.19), residues: 1909
  helix:  1.58 (0.17), residues: 962
  sheet: -0.34 (0.34), residues: 201
  loop : -1.42 (0.22), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 185 
 HIS   0.002   0.001   HIS A 266 
 PHE   0.014   0.001   PHE C 686 
 TYR   0.012   0.001   TYR C 719 
 ARG   0.002   0.000   ARG A 590 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00592 (    7)
  link_NAG-ASN         : angle       2.67335 (   21)
  link_BETA1-4         : bond        0.00816 (    7)
  link_BETA1-4         : angle       2.66837 (   21)
  hydrogen bonds       : bond        0.03918 (  793)
  hydrogen bonds       : angle       4.11440 ( 2304)
  SS BOND              : bond        0.00137 (   10)
  SS BOND              : angle       1.05442 (   20)
  covalent geometry    : bond        0.00338 (15786)
  covalent geometry    : angle       0.55350 (21410)

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

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

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 214
  time to evaluate  : 1.680 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 ARG cc_start: 0.7188 (ptt90) cc_final: 0.6302 (ptp-170)
REVERT: A  287 ASP cc_start: 0.8241 (t0) cc_final: 0.7810 (t0)
REVERT: A 1193 PHE cc_start: 0.8300 (m-80) cc_final: 0.8082 (m-80)
REVERT: A 1335 ASP cc_start: 0.8471 (t70) cc_final: 0.8045 (t0)
  outliers start: 56
  outliers final: 40
  residues processed: 258
  average time/residue: 0.2550
  time to fit residues: 99.6842
Evaluate side-chains
  240 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 200
  time to evaluate  : 1.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  679 SER
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue 1230 VAL
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1294 ILE
Chi-restraints excluded: chain A residue 1584 ILE
Chi-restraints excluded: chain A residue 1586 LEU
Chi-restraints excluded: chain A residue 1626 MET
Chi-restraints excluded: chain A residue 1670 LEU
Chi-restraints excluded: chain A residue 1675 GLU
Chi-restraints excluded: chain A residue 1697 ASP
Chi-restraints excluded: chain A residue 1701 VAL
Chi-restraints excluded: chain A residue 1719 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  506 LEU
Chi-restraints excluded: chain C residue  515 ILE
Chi-restraints excluded: chain C residue  585 GLU
Chi-restraints excluded: chain C residue  587 THR
Chi-restraints excluded: chain C residue  667 CYS
Chi-restraints excluded: chain C residue  740 ILE
Chi-restraints excluded: chain C residue  741 THR
Chi-restraints excluded: chain C residue  795 SER
Chi-restraints excluded: chain C residue  848 MET
Chi-restraints excluded: chain C residue  871 ILE
Chi-restraints excluded: chain C residue  979 THR
Chi-restraints excluded: chain C residue 1032 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 144 optimal weight:    0.8980
   chunk 185 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 133 optimal weight:    3.9990
   chunk 158 optimal weight:    3.9990
   chunk 150 optimal weight:    2.9990
   chunk 126 optimal weight:    4.9990
   chunk 22 optimal weight:    0.3980
   chunk 166 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 705 ASN
** C  65 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 = 0.3822 r_free = 0.3822 target = 0.159171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.122332 restraints weight = 20211.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.46
r_work: 0.3068 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15810  Z= 0.133
  Angle     :  0.561   9.584  21472  Z= 0.275
  Chirality :  0.043   0.280   2475
  Planarity :  0.003   0.036   2702
  Dihedral  : 10.070 114.939   2393
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.34 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.30 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.19), residues: 1909
  helix:  1.59 (0.17), residues: 962
  sheet: -0.42 (0.35), residues: 203
  loop : -1.41 (0.22), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 185 
 HIS   0.002   0.001   HIS A 497 
 PHE   0.022   0.001   PHE C 686 
 TYR   0.010   0.001   TYR C 217 
 ARG   0.003   0.000   ARG C1001 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00593 (    7)
  link_NAG-ASN         : angle       2.68356 (   21)
  link_BETA1-4         : bond        0.00816 (    7)
  link_BETA1-4         : angle       2.67990 (   21)
  hydrogen bonds       : bond        0.03808 (  793)
  hydrogen bonds       : angle       4.05901 ( 2304)
  SS BOND              : bond        0.00163 (   10)
  SS BOND              : angle       1.10434 (   20)
  covalent geometry    : bond        0.00311 (15786)
  covalent geometry    : angle       0.54850 (21410)

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

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

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 216
  time to evaluate  : 1.767 
Fit side-chains
REVERT: A  190 ARG cc_start: 0.6992 (ptt90) cc_final: 0.6070 (ptp-170)
REVERT: A  278 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6643 (pp20)
REVERT: A  287 ASP cc_start: 0.8195 (t0) cc_final: 0.7831 (t0)
REVERT: A  648 MET cc_start: 0.9200 (mmp) cc_final: 0.8799 (mmp)
REVERT: A  706 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7213 (mp)
REVERT: A 1161 LEU cc_start: 0.8516 (mt) cc_final: 0.8243 (mt)
REVERT: A 1335 ASP cc_start: 0.8374 (t70) cc_final: 0.7896 (t0)
REVERT: C  674 ASP cc_start: 0.7803 (t0) cc_final: 0.7551 (t0)
REVERT: C  675 ASN cc_start: 0.6480 (t0) cc_final: 0.6244 (t0)
REVERT: C  799 GLU cc_start: 0.7843 (mp0) cc_final: 0.7508 (mp0)
  outliers start: 57
  outliers final: 43
  residues processed: 259
  average time/residue: 0.2443
  time to fit residues: 97.7379
Evaluate side-chains
  255 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 210
  time to evaluate  : 1.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  679 SER
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  705 ASN
Chi-restraints excluded: chain A residue  706 LEU
Chi-restraints excluded: chain A residue 1211 ILE
Chi-restraints excluded: chain A residue 1230 VAL
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1294 ILE
Chi-restraints excluded: chain A residue 1505 THR
Chi-restraints excluded: chain A residue 1584 ILE
Chi-restraints excluded: chain A residue 1586 LEU
Chi-restraints excluded: chain A residue 1626 MET
Chi-restraints excluded: chain A residue 1670 LEU
Chi-restraints excluded: chain A residue 1675 GLU
Chi-restraints excluded: chain A residue 1701 VAL
Chi-restraints excluded: chain A residue 1719 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  199 GLU
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  506 LEU
Chi-restraints excluded: chain C residue  585 GLU
Chi-restraints excluded: chain C residue  587 THR
Chi-restraints excluded: chain C residue  667 CYS
Chi-restraints excluded: chain C residue  691 THR
Chi-restraints excluded: chain C residue  740 ILE
Chi-restraints excluded: chain C residue  741 THR
Chi-restraints excluded: chain C residue  795 SER
Chi-restraints excluded: chain C residue  848 MET
Chi-restraints excluded: chain C residue  979 THR
Chi-restraints excluded: chain C residue 1032 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 152 optimal weight:    1.9990
   chunk 182 optimal weight:    0.5980
   chunk 134 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0970
   chunk 127 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 184 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 161 optimal weight:    7.9990
   chunk 114 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C  65 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.160302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.123296 restraints weight = 20125.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.43
r_work: 0.3133 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  15810  Z= 0.109
  Angle     :  0.546   9.566  21472  Z= 0.266
  Chirality :  0.042   0.273   2475
  Planarity :  0.003   0.033   2702
  Dihedral  :  9.810 115.282   2393
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.08 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 19.30 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.20), residues: 1909
  helix:  1.66 (0.17), residues: 964
  sheet: -0.40 (0.35), residues: 204
  loop : -1.39 (0.22), residues: 741

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 185 
 HIS   0.002   0.001   HIS A 266 
 PHE   0.018   0.001   PHE C 686 
 TYR   0.009   0.001   TYR A 277 
 ARG   0.003   0.000   ARG A1187 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00603 (    7)
  link_NAG-ASN         : angle       2.58818 (   21)
  link_BETA1-4         : bond        0.00838 (    7)
  link_BETA1-4         : angle       2.61320 (   21)
  hydrogen bonds       : bond        0.03561 (  793)
  hydrogen bonds       : angle       3.97320 ( 2304)
  SS BOND              : bond        0.00447 (   10)
  SS BOND              : angle       1.00167 (   20)
  covalent geometry    : bond        0.00241 (15786)
  covalent geometry    : angle       0.53365 (21410)

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

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

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 219
  time to evaluate  : 1.787 
Fit side-chains
REVERT: A  190 ARG cc_start: 0.7043 (ptt90) cc_final: 0.6116 (ptp-170)
REVERT: A  278 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6678 (pp20)
REVERT: A  287 ASP cc_start: 0.8190 (t0) cc_final: 0.7756 (t0)
REVERT: A  293 ASP cc_start: 0.8468 (m-30) cc_final: 0.7995 (m-30)
REVERT: A  485 LEU cc_start: 0.8178 (mp) cc_final: 0.7883 (tt)
REVERT: A  648 MET cc_start: 0.9192 (mmp) cc_final: 0.8792 (mmp)
REVERT: A  705 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7770 (m-40)
REVERT: A 1161 LEU cc_start: 0.8552 (mt) cc_final: 0.8345 (mt)
REVERT: A 1335 ASP cc_start: 0.8353 (t70) cc_final: 0.7906 (t0)
REVERT: A 1374 TRP cc_start: 0.9299 (OUTLIER) cc_final: 0.8964 (p-90)
REVERT: C  674 ASP cc_start: 0.7814 (t0) cc_final: 0.7596 (t0)
REVERT: C  675 ASN cc_start: 0.6528 (t0) cc_final: 0.6310 (t0)
REVERT: C  799 GLU cc_start: 0.7803 (mp0) cc_final: 0.7424 (mp0)
  outliers start: 56
  outliers final: 45
  residues processed: 262
  average time/residue: 0.2522
  time to fit residues: 101.0647
Evaluate side-chains
  259 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 211
  time to evaluate  : 1.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  679 SER
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  705 ASN
Chi-restraints excluded: chain A residue  706 LEU
Chi-restraints excluded: chain A residue 1211 ILE
Chi-restraints excluded: chain A residue 1230 VAL
Chi-restraints excluded: chain A residue 1253 THR
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1294 ILE
Chi-restraints excluded: chain A residue 1374 TRP
Chi-restraints excluded: chain A residue 1505 THR
Chi-restraints excluded: chain A residue 1584 ILE
Chi-restraints excluded: chain A residue 1586 LEU
Chi-restraints excluded: chain A residue 1626 MET
Chi-restraints excluded: chain A residue 1648 SER
Chi-restraints excluded: chain A residue 1670 LEU
Chi-restraints excluded: chain A residue 1675 GLU
Chi-restraints excluded: chain A residue 1697 ASP
Chi-restraints excluded: chain A residue 1701 VAL
Chi-restraints excluded: chain A residue 1719 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   65 GLN
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  506 LEU
Chi-restraints excluded: chain C residue  515 ILE
Chi-restraints excluded: chain C residue  585 GLU
Chi-restraints excluded: chain C residue  587 THR
Chi-restraints excluded: chain C residue  667 CYS
Chi-restraints excluded: chain C residue  691 THR
Chi-restraints excluded: chain C residue  740 ILE
Chi-restraints excluded: chain C residue  741 THR
Chi-restraints excluded: chain C residue  795 SER
Chi-restraints excluded: chain C residue  848 MET
Chi-restraints excluded: chain C residue  871 ILE
Chi-restraints excluded: chain C residue  979 THR
Chi-restraints excluded: chain C residue 1032 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 155 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0040
   chunk 99 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 186 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 181 optimal weight:    3.9990
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  65 GLN
C 481 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.160602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.123767 restraints weight = 20101.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.43
r_work: 0.3099 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  15810  Z= 0.111
  Angle     :  0.551   9.572  21472  Z= 0.268
  Chirality :  0.042   0.320   2475
  Planarity :  0.003   0.037   2702
  Dihedral  :  9.590 115.257   2393
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.08 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 19.36 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.20), residues: 1909
  helix:  1.70 (0.17), residues: 964
  sheet: -0.34 (0.35), residues: 203
  loop : -1.37 (0.22), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 185 
 HIS   0.002   0.001   HIS A1639 
 PHE   0.016   0.001   PHE C 686 
 TYR   0.012   0.001   TYR C 629 
 ARG   0.008   0.000   ARG A1258 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00595 (    7)
  link_NAG-ASN         : angle       2.53471 (   21)
  link_BETA1-4         : bond        0.00821 (    7)
  link_BETA1-4         : angle       2.61805 (   21)
  hydrogen bonds       : bond        0.03474 (  793)
  hydrogen bonds       : angle       3.93266 ( 2304)
  SS BOND              : bond        0.00159 (   10)
  SS BOND              : angle       0.93794 (   20)
  covalent geometry    : bond        0.00245 (15786)
  covalent geometry    : angle       0.53951 (21410)

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

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

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 224
  time to evaluate  : 1.634 
Fit side-chains
REVERT: A  190 ARG cc_start: 0.6895 (ptt90) cc_final: 0.6047 (ptp-170)
REVERT: A  278 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6529 (pp20)
REVERT: A  287 ASP cc_start: 0.8266 (t0) cc_final: 0.7787 (t0)
REVERT: A  293 ASP cc_start: 0.8483 (m-30) cc_final: 0.8001 (m-30)
REVERT: A  485 LEU cc_start: 0.8145 (mp) cc_final: 0.7826 (tt)
REVERT: A  648 MET cc_start: 0.9200 (mmp) cc_final: 0.8804 (mmp)
REVERT: A 1335 ASP cc_start: 0.8338 (t70) cc_final: 0.7883 (t0)
REVERT: A 1374 TRP cc_start: 0.9279 (OUTLIER) cc_final: 0.8935 (p-90)
REVERT: C  675 ASN cc_start: 0.6463 (t0) cc_final: 0.6242 (t0)
REVERT: C  770 ASN cc_start: 0.7913 (m110) cc_final: 0.7575 (m110)
REVERT: C  848 MET cc_start: 0.3641 (OUTLIER) cc_final: 0.3148 (ptt)
  outliers start: 62
  outliers final: 48
  residues processed: 271
  average time/residue: 0.2424
  time to fit residues: 101.4484
Evaluate side-chains
  264 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 213
  time to evaluate  : 1.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  633 ASP
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  679 SER
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  706 LEU
Chi-restraints excluded: chain A residue 1211 ILE
Chi-restraints excluded: chain A residue 1230 VAL
Chi-restraints excluded: chain A residue 1253 THR
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1294 ILE
Chi-restraints excluded: chain A residue 1374 TRP
Chi-restraints excluded: chain A residue 1421 LEU
Chi-restraints excluded: chain A residue 1505 THR
Chi-restraints excluded: chain A residue 1584 ILE
Chi-restraints excluded: chain A residue 1586 LEU
Chi-restraints excluded: chain A residue 1626 MET
Chi-restraints excluded: chain A residue 1648 SER
Chi-restraints excluded: chain A residue 1670 LEU
Chi-restraints excluded: chain A residue 1675 GLU
Chi-restraints excluded: chain A residue 1697 ASP
Chi-restraints excluded: chain A residue 1701 VAL
Chi-restraints excluded: chain A residue 1719 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   65 GLN
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  357 ILE
Chi-restraints excluded: chain C residue  506 LEU
Chi-restraints excluded: chain C residue  515 ILE
Chi-restraints excluded: chain C residue  585 GLU
Chi-restraints excluded: chain C residue  587 THR
Chi-restraints excluded: chain C residue  667 CYS
Chi-restraints excluded: chain C residue  691 THR
Chi-restraints excluded: chain C residue  740 ILE
Chi-restraints excluded: chain C residue  741 THR
Chi-restraints excluded: chain C residue  795 SER
Chi-restraints excluded: chain C residue  848 MET
Chi-restraints excluded: chain C residue  871 ILE
Chi-restraints excluded: chain C residue  979 THR
Chi-restraints excluded: chain C residue 1032 ILE
Chi-restraints excluded: chain C residue 1037 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 138 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 31 optimal weight:   30.0000
   chunk 53 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9980
   chunk 173 optimal weight:    5.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  65 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.159998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.123232 restraints weight = 19953.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.41
r_work: 0.3101 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15810  Z= 0.126
  Angle     :  0.569   9.593  21472  Z= 0.279
  Chirality :  0.043   0.262   2475
  Planarity :  0.003   0.039   2702
  Dihedral  :  9.463 115.159   2393
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.34 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 19.91 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.20), residues: 1909
  helix:  1.68 (0.17), residues: 964
  sheet: -0.36 (0.35), residues: 204
  loop : -1.38 (0.22), residues: 741

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 185 
 HIS   0.002   0.001   HIS A 497 
 PHE   0.024   0.001   PHE C 686 
 TYR   0.011   0.001   TYR C 629 
 ARG   0.006   0.000   ARG A1258 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00570 (    7)
  link_NAG-ASN         : angle       2.54842 (   21)
  link_BETA1-4         : bond        0.00812 (    7)
  link_BETA1-4         : angle       2.67146 (   21)
  hydrogen bonds       : bond        0.03540 (  793)
  hydrogen bonds       : angle       3.93645 ( 2304)
  SS BOND              : bond        0.00137 (   10)
  SS BOND              : angle       1.08402 (   20)
  covalent geometry    : bond        0.00289 (15786)
  covalent geometry    : angle       0.55702 (21410)

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

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

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 213
  time to evaluate  : 1.658 
Fit side-chains
REVERT: A  190 ARG cc_start: 0.7078 (ptt90) cc_final: 0.6173 (ptp-170)
REVERT: A  208 GLN cc_start: 0.8335 (tt0) cc_final: 0.7965 (mt0)
REVERT: A  278 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6541 (pp20)
REVERT: A  287 ASP cc_start: 0.8397 (t0) cc_final: 0.7876 (t0)
REVERT: A  293 ASP cc_start: 0.8532 (m-30) cc_final: 0.8120 (m-30)
REVERT: A  485 LEU cc_start: 0.8212 (mp) cc_final: 0.7875 (tt)
REVERT: A  648 MET cc_start: 0.9210 (mmp) cc_final: 0.8790 (mmp)
REVERT: A 1335 ASP cc_start: 0.8342 (t70) cc_final: 0.7905 (t0)
REVERT: A 1374 TRP cc_start: 0.9293 (OUTLIER) cc_final: 0.9008 (p-90)
REVERT: C  675 ASN cc_start: 0.6421 (t0) cc_final: 0.6203 (t0)
REVERT: C  770 ASN cc_start: 0.8039 (m110) cc_final: 0.7727 (m110)
REVERT: C  799 GLU cc_start: 0.7831 (mp0) cc_final: 0.7601 (mp0)
REVERT: C  848 MET cc_start: 0.3683 (OUTLIER) cc_final: 0.3183 (ptt)
  outliers start: 56
  outliers final: 47
  residues processed: 254
  average time/residue: 0.2453
  time to fit residues: 95.9140
Evaluate side-chains
  262 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 212
  time to evaluate  : 1.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  633 ASP
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  679 SER
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  706 LEU
Chi-restraints excluded: chain A residue 1211 ILE
Chi-restraints excluded: chain A residue 1230 VAL
Chi-restraints excluded: chain A residue 1253 THR
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1294 ILE
Chi-restraints excluded: chain A residue 1374 TRP
Chi-restraints excluded: chain A residue 1421 LEU
Chi-restraints excluded: chain A residue 1505 THR
Chi-restraints excluded: chain A residue 1584 ILE
Chi-restraints excluded: chain A residue 1586 LEU
Chi-restraints excluded: chain A residue 1626 MET
Chi-restraints excluded: chain A residue 1648 SER
Chi-restraints excluded: chain A residue 1670 LEU
Chi-restraints excluded: chain A residue 1675 GLU
Chi-restraints excluded: chain A residue 1697 ASP
Chi-restraints excluded: chain A residue 1701 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  357 ILE
Chi-restraints excluded: chain C residue  506 LEU
Chi-restraints excluded: chain C residue  515 ILE
Chi-restraints excluded: chain C residue  585 GLU
Chi-restraints excluded: chain C residue  587 THR
Chi-restraints excluded: chain C residue  667 CYS
Chi-restraints excluded: chain C residue  691 THR
Chi-restraints excluded: chain C residue  740 ILE
Chi-restraints excluded: chain C residue  741 THR
Chi-restraints excluded: chain C residue  795 SER
Chi-restraints excluded: chain C residue  848 MET
Chi-restraints excluded: chain C residue  979 THR
Chi-restraints excluded: chain C residue 1032 ILE
Chi-restraints excluded: chain C residue 1037 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 121 optimal weight:    3.9990
   chunk 175 optimal weight:    6.9990
   chunk 154 optimal weight:    3.9990
   chunk 64 optimal weight:    0.5980
   chunk 142 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 156 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 191 optimal weight:    0.6980
   chunk 77 optimal weight:    4.9990
   overall best weight:    2.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.157183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.119910 restraints weight = 20027.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.38
r_work: 0.3043 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  15810  Z= 0.188
  Angle     :  0.623   9.745  21472  Z= 0.308
  Chirality :  0.045   0.276   2475
  Planarity :  0.004   0.039   2702
  Dihedral  :  9.480 114.924   2393
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.45 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.73 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.19), residues: 1909
  helix:  1.49 (0.17), residues: 964
  sheet: -0.46 (0.34), residues: 205
  loop : -1.42 (0.22), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1374 
 HIS   0.003   0.001   HIS A 497 
 PHE   0.025   0.002   PHE C 686 
 TYR   0.014   0.001   TYR C 629 
 ARG   0.006   0.000   ARG A1258 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00511 (    7)
  link_NAG-ASN         : angle       2.80399 (   21)
  link_BETA1-4         : bond        0.00812 (    7)
  link_BETA1-4         : angle       2.96562 (   21)
  hydrogen bonds       : bond        0.04118 (  793)
  hydrogen bonds       : angle       4.09422 ( 2304)
  SS BOND              : bond        0.00284 (   10)
  SS BOND              : angle       1.37130 (   20)
  covalent geometry    : bond        0.00453 (15786)
  covalent geometry    : angle       0.60911 (21410)

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

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

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 214
  time to evaluate  : 1.672 
Fit side-chains
REVERT: A  190 ARG cc_start: 0.7073 (ptt90) cc_final: 0.6237 (ptm160)
REVERT: A  278 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6546 (pp20)
REVERT: A  287 ASP cc_start: 0.8554 (t0) cc_final: 0.8041 (t0)
REVERT: A  523 MET cc_start: 0.4829 (ttm) cc_final: 0.4235 (ttt)
REVERT: A  706 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7066 (mp)
REVERT: A 1335 ASP cc_start: 0.8371 (t70) cc_final: 0.8041 (t0)
REVERT: A 1374 TRP cc_start: 0.9319 (OUTLIER) cc_final: 0.9099 (p-90)
REVERT: C  770 ASN cc_start: 0.8153 (m110) cc_final: 0.7805 (m110)
REVERT: C  799 GLU cc_start: 0.7851 (mp0) cc_final: 0.7619 (mp0)
REVERT: C  848 MET cc_start: 0.3658 (OUTLIER) cc_final: 0.3120 (ptt)
  outliers start: 57
  outliers final: 50
  residues processed: 256
  average time/residue: 0.2592
  time to fit residues: 101.5020
Evaluate side-chains
  263 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 209
  time to evaluate  : 1.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain A residue  480 TRP
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  633 ASP
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  679 SER
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  706 LEU
Chi-restraints excluded: chain A residue 1211 ILE
Chi-restraints excluded: chain A residue 1253 THR
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1294 ILE
Chi-restraints excluded: chain A residue 1374 TRP
Chi-restraints excluded: chain A residue 1421 LEU
Chi-restraints excluded: chain A residue 1505 THR
Chi-restraints excluded: chain A residue 1584 ILE
Chi-restraints excluded: chain A residue 1586 LEU
Chi-restraints excluded: chain A residue 1626 MET
Chi-restraints excluded: chain A residue 1648 SER
Chi-restraints excluded: chain A residue 1670 LEU
Chi-restraints excluded: chain A residue 1675 GLU
Chi-restraints excluded: chain A residue 1697 ASP
Chi-restraints excluded: chain A residue 1701 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  199 GLU
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  357 ILE
Chi-restraints excluded: chain C residue  506 LEU
Chi-restraints excluded: chain C residue  515 ILE
Chi-restraints excluded: chain C residue  585 GLU
Chi-restraints excluded: chain C residue  587 THR
Chi-restraints excluded: chain C residue  667 CYS
Chi-restraints excluded: chain C residue  691 THR
Chi-restraints excluded: chain C residue  740 ILE
Chi-restraints excluded: chain C residue  741 THR
Chi-restraints excluded: chain C residue  795 SER
Chi-restraints excluded: chain C residue  848 MET
Chi-restraints excluded: chain C residue  979 THR
Chi-restraints excluded: chain C residue 1032 ILE
Chi-restraints excluded: chain C residue 1037 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 126 optimal weight:    2.9990
   chunk 141 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 157 optimal weight:    9.9990
   chunk 101 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 180 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 189 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.157819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.120829 restraints weight = 20167.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.42
r_work: 0.3094 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15810  Z= 0.163
  Angle     :  0.605   9.653  21472  Z= 0.298
  Chirality :  0.044   0.270   2475
  Planarity :  0.003   0.041   2702
  Dihedral  :  9.398 115.228   2393
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.40 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 20.04 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.19), residues: 1909
  helix:  1.48 (0.17), residues: 964
  sheet: -0.56 (0.36), residues: 191
  loop : -1.43 (0.22), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 185 
 HIS   0.003   0.001   HIS A 497 
 PHE   0.023   0.001   PHE C 686 
 TYR   0.014   0.001   TYR C 629 
 ARG   0.009   0.000   ARG A1187 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00529 (    7)
  link_NAG-ASN         : angle       2.76756 (   21)
  link_BETA1-4         : bond        0.00793 (    7)
  link_BETA1-4         : angle       2.95012 (   21)
  hydrogen bonds       : bond        0.03914 (  793)
  hydrogen bonds       : angle       4.06226 ( 2304)
  SS BOND              : bond        0.00206 (   10)
  SS BOND              : angle       1.23020 (   20)
  covalent geometry    : bond        0.00388 (15786)
  covalent geometry    : angle       0.59095 (21410)

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

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

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3818 Ramachandran restraints generated.
    1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 210
  time to evaluate  : 1.679 
Fit side-chains
REVERT: A  190 ARG cc_start: 0.7081 (ptt90) cc_final: 0.6278 (ptm160)
REVERT: A  278 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6554 (pp20)
REVERT: A  287 ASP cc_start: 0.8512 (t0) cc_final: 0.8020 (t0)
REVERT: A  523 MET cc_start: 0.4740 (OUTLIER) cc_final: 0.4464 (ttt)
REVERT: A  706 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7098 (mp)
REVERT: A 1335 ASP cc_start: 0.8361 (t70) cc_final: 0.7926 (t0)
REVERT: A 1374 TRP cc_start: 0.9312 (OUTLIER) cc_final: 0.9041 (p-90)
REVERT: C  284 SER cc_start: 0.9013 (t) cc_final: 0.8765 (m)
REVERT: C  799 GLU cc_start: 0.7884 (mp0) cc_final: 0.7676 (mp0)
REVERT: C  848 MET cc_start: 0.3656 (OUTLIER) cc_final: 0.3098 (ptt)
  outliers start: 54
  outliers final: 47
  residues processed: 251
  average time/residue: 0.2581
  time to fit residues: 98.3387
Evaluate side-chains
  260 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 208
  time to evaluate  : 1.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  523 MET
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  633 ASP
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  679 SER
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  706 LEU
Chi-restraints excluded: chain A residue 1211 ILE
Chi-restraints excluded: chain A residue 1253 THR
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1294 ILE
Chi-restraints excluded: chain A residue 1374 TRP
Chi-restraints excluded: chain A residue 1421 LEU
Chi-restraints excluded: chain A residue 1505 THR
Chi-restraints excluded: chain A residue 1584 ILE
Chi-restraints excluded: chain A residue 1586 LEU
Chi-restraints excluded: chain A residue 1626 MET
Chi-restraints excluded: chain A residue 1648 SER
Chi-restraints excluded: chain A residue 1670 LEU
Chi-restraints excluded: chain A residue 1697 ASP
Chi-restraints excluded: chain A residue 1701 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  199 GLU
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  357 ILE
Chi-restraints excluded: chain C residue  506 LEU
Chi-restraints excluded: chain C residue  515 ILE
Chi-restraints excluded: chain C residue  585 GLU
Chi-restraints excluded: chain C residue  587 THR
Chi-restraints excluded: chain C residue  667 CYS
Chi-restraints excluded: chain C residue  691 THR
Chi-restraints excluded: chain C residue  740 ILE
Chi-restraints excluded: chain C residue  741 THR
Chi-restraints excluded: chain C residue  795 SER
Chi-restraints excluded: chain C residue  848 MET
Chi-restraints excluded: chain C residue  979 THR
Chi-restraints excluded: chain C residue 1032 ILE
Chi-restraints excluded: chain C residue 1037 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 127 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9990
   chunk 172 optimal weight:    9.9990
   chunk 146 optimal weight:    0.7980
   chunk 85 optimal weight:    8.9990
   chunk 103 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 128 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 705 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.160050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.122601 restraints weight = 19947.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.41
r_work: 0.3090 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15810  Z= 0.118
  Angle     :  0.577  11.202  21472  Z= 0.284
  Chirality :  0.042   0.261   2475
  Planarity :  0.003   0.042   2702
  Dihedral  :  9.217 115.234   2393
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.55 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 20.04 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.20), residues: 1909
  helix:  1.60 (0.17), residues: 962
  sheet: -0.40 (0.35), residues: 203
  loop : -1.36 (0.23), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 185 
 HIS   0.002   0.001   HIS A 497 
 PHE   0.022   0.001   PHE C 686 
 TYR   0.011   0.001   TYR C 629 
 ARG   0.007   0.000   ARG A1187 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00566 (    7)
  link_NAG-ASN         : angle       2.55963 (   21)
  link_BETA1-4         : bond        0.00795 (    7)
  link_BETA1-4         : angle       2.81880 (   21)
  hydrogen bonds       : bond        0.03538 (  793)
  hydrogen bonds       : angle       3.96356 ( 2304)
  SS BOND              : bond        0.00177 (   10)
  SS BOND              : angle       1.07100 (   20)
  covalent geometry    : bond        0.00265 (15786)
  covalent geometry    : angle       0.56411 (21410)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8941.27 seconds
wall clock time: 155 minutes 8.43 seconds (9308.43 seconds total)