Starting phenix.real_space_refine on Mon Jul 28 03:24:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wts_21898/07_2025/6wts_21898.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wts_21898/07_2025/6wts_21898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wts_21898/07_2025/6wts_21898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wts_21898/07_2025/6wts_21898.map" model { file = "/net/cci-nas-00/data/ceres_data/6wts_21898/07_2025/6wts_21898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wts_21898/07_2025/6wts_21898.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6317 2.51 5 N 1645 2.21 5 O 1835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9863 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4170 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 508} Chain breaks: 2 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 70 Chain: "B" Number of atoms: 3964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3964 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 26, 'TRANS': 505} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 14, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 172 Chain: "C" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1589 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 9, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 130 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: 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: "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: "A" 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: "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 Time building chain proxies: 5.94, per 1000 atoms: 0.60 Number of scatterers: 9863 At special positions: 0 Unit cell: (99.91, 108.15, 132.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1835 8.00 N 1645 7.00 C 6317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 117 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 144 " distance=2.03 Simple disulfide: pdb=" SG CYS A 258 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 542 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 605 " - " ASN A 33 " " NAG A 606 " - " ASN A 65 " " NAG B1303 " - " ASN B 434 " " NAG B1304 " - " ASN B 65 " " NAG D 1 " - " ASN A 434 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN B 282 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2426 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 27 sheets defined 13.9% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 100 through 109 removed outlier: 4.057A pdb=" N THR A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.664A pdb=" N PHE A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 385 through 395 Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.869A pdb=" N ARG A 408 " --> pdb=" O ILE A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 514 through 519 removed outlier: 4.234A pdb=" N TYR A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 519 " --> pdb=" O CYS A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 514 through 519' Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'B' and resid 100 through 111 removed outlier: 3.611A pdb=" N GLY B 111 " --> pdb=" O CYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 removed outlier: 4.116A pdb=" N PHE B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.656A pdb=" N VAL B 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 395 Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.912A pdb=" N ARG B 408 " --> pdb=" O ILE B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 514 through 519 removed outlier: 3.786A pdb=" N TYR B 518 " --> pdb=" O ARG B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 529 removed outlier: 3.704A pdb=" N ARG B 529 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 1434 through 1438 removed outlier: 3.657A pdb=" N GLU C1438 " --> pdb=" O LYS C1435 " (cutoff:3.500A) Processing helix chain 'C' and resid 1439 through 1450 Processing helix chain 'C' and resid 1499 through 1502 removed outlier: 3.598A pdb=" N SER C1502 " --> pdb=" O MET C1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1499 through 1502' Processing helix chain 'C' and resid 1560 through 1565 Processing helix chain 'C' and resid 1565 through 1570 Processing helix chain 'C' and resid 1583 through 1589 Processing helix chain 'C' and resid 1590 through 1594 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.514A pdb=" N GLU A 468 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS A 422 " --> pdb=" O GLY A 441 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 64 removed outlier: 3.730A pdb=" N MET A 60 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 62 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 93 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 126 Processing sheet with id=AA4, first strand: chain 'A' and resid 174 through 178 removed outlier: 3.561A pdb=" N LEU A 207 " --> pdb=" O ARG A 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 228 removed outlier: 5.306A pdb=" N PHE A 222 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG A 237 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N VAL A 402 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG A 280 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.519A pdb=" N VAL A 285 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE A 291 " --> pdb=" O VAL A 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 295 through 299 removed outlier: 6.683A pdb=" N THR A 314 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL A 299 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 312 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 295 through 299 removed outlier: 6.683A pdb=" N THR A 314 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL A 299 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 312 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 344 through 345 Processing sheet with id=AB1, first strand: chain 'A' and resid 489 through 493 removed outlier: 3.601A pdb=" N GLY A 489 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 541 through 542 removed outlier: 3.536A pdb=" N ALA A 541 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 536 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 29 through 30 removed outlier: 6.971A pdb=" N SER B 30 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N PHE B 465 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU B 451 " --> pdb=" O PHE B 465 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N HIS B 435 " --> pdb=" O ALA B 428 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA B 428 " --> pdb=" O HIS B 435 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS B 422 " --> pdb=" O GLY B 441 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.717A pdb=" N GLY B 489 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 60 through 64 Processing sheet with id=AB6, first strand: chain 'B' and resid 121 through 128 removed outlier: 3.777A pdb=" N LYS B 127 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 174 through 177 removed outlier: 3.784A pdb=" N LEU B 207 " --> pdb=" O ARG B 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 221 through 228 removed outlier: 5.235A pdb=" N PHE B 222 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG B 237 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 277 " --> pdb=" O GLN B 256 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N VAL B 402 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ARG B 280 " --> pdb=" O VAL B 402 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 284 through 285 removed outlier: 3.557A pdb=" N VAL B 285 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE B 291 " --> pdb=" O VAL B 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 295 through 299 removed outlier: 6.619A pdb=" N THR B 314 " --> pdb=" O GLN B 297 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL B 299 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 312 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 295 through 299 removed outlier: 6.619A pdb=" N THR B 314 " --> pdb=" O GLN B 297 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL B 299 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 312 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 344 through 346 Processing sheet with id=AC4, first strand: chain 'B' and resid 533 through 535 Processing sheet with id=AC5, first strand: chain 'C' and resid 1401 through 1402 removed outlier: 3.628A pdb=" N ILE C1402 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C1418 " --> pdb=" O ILE C1402 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C1406 " --> pdb=" O ILE C1414 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1401 through 1402 removed outlier: 3.628A pdb=" N ILE C1402 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C1418 " --> pdb=" O ILE C1402 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1459 through 1466 removed outlier: 3.983A pdb=" N ASP C1466 " --> pdb=" O THR C1469 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU C1487 " --> pdb=" O LYS C1470 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER C1492 " --> pdb=" O SER C1509 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N SER C1509 " --> pdb=" O SER C1492 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE C1494 " --> pdb=" O ILE C1507 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE C1507 " --> pdb=" O ILE C1494 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASN C1496 " --> pdb=" O LEU C1505 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C1505 " --> pdb=" O ASN C1496 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN C1503 " --> pdb=" O TYR C1498 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1514 through 1518 removed outlier: 5.845A pdb=" N ASP C1515 " --> pdb=" O ASN C1530 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASN C1530 " --> pdb=" O ASP C1515 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C1527 " --> pdb=" O PHE C1542 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C1538 " --> pdb=" O TYR C1531 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR C1543 " --> pdb=" O LEU C1552 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU C1552 " --> pdb=" O THR C1543 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU C1545 " --> pdb=" O ILE C1550 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE C1550 " --> pdb=" O GLU C1545 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE C1550 " --> pdb=" O ILE C1606 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1613 through 1614 removed outlier: 6.807A pdb=" N GLU C1623 " --> pdb=" O TYR C1635 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN C1633 " --> pdb=" O ILE C1625 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.94 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1586 1.31 - 1.44: 2790 1.44 - 1.56: 5613 1.56 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 10084 Sorted by residual: bond pdb=" C LYS A 110 " pdb=" O LYS A 110 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" CA LYS A 110 " pdb=" CB LYS A 110 " ideal model delta sigma weight residual 1.529 1.494 0.035 1.63e-02 3.76e+03 4.62e+00 bond pdb=" CA LYS A 110 " pdb=" C LYS A 110 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.37e-02 5.33e+03 4.55e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.46e+00 bond pdb=" C LYS A 110 " pdb=" N GLY A 111 " ideal model delta sigma weight residual 1.331 1.300 0.030 1.46e-02 4.69e+03 4.32e+00 ... (remaining 10079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 13518 1.83 - 3.66: 161 3.66 - 5.49: 10 5.49 - 7.33: 5 7.33 - 9.16: 1 Bond angle restraints: 13695 Sorted by residual: angle pdb=" C HIS A 212 " pdb=" CA HIS A 212 " pdb=" CB HIS A 212 " ideal model delta sigma weight residual 111.89 108.17 3.72 1.42e+00 4.96e-01 6.87e+00 angle pdb=" CA LEU C1540 " pdb=" CB LEU C1540 " pdb=" CG LEU C1540 " ideal model delta sigma weight residual 116.30 125.46 -9.16 3.50e+00 8.16e-02 6.85e+00 angle pdb=" C PRO A 362 " pdb=" N LYS A 363 " pdb=" CA LYS A 363 " ideal model delta sigma weight residual 121.80 115.59 6.21 2.44e+00 1.68e-01 6.49e+00 angle pdb=" C SER C1424 " pdb=" N TYR C1425 " pdb=" CA TYR C1425 " ideal model delta sigma weight residual 120.82 124.11 -3.29 1.47e+00 4.63e-01 5.01e+00 angle pdb=" C LYS C1511 " pdb=" CA LYS C1511 " pdb=" CB LYS C1511 " ideal model delta sigma weight residual 109.65 105.88 3.77 1.74e+00 3.30e-01 4.69e+00 ... (remaining 13690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 5674 16.30 - 32.61: 359 32.61 - 48.91: 87 48.91 - 65.21: 26 65.21 - 81.51: 3 Dihedral angle restraints: 6149 sinusoidal: 2386 harmonic: 3763 Sorted by residual: dihedral pdb=" CA LYS A 363 " pdb=" C LYS A 363 " pdb=" N PRO A 364 " pdb=" CA PRO A 364 " ideal model delta harmonic sigma weight residual 180.00 118.59 61.41 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA PHE B 293 " pdb=" C PHE B 293 " pdb=" N ASN B 294 " pdb=" CA ASN B 294 " ideal model delta harmonic sigma weight residual -180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.53e+00 dihedral pdb=" CA LYS A 248 " pdb=" CB LYS A 248 " pdb=" CG LYS A 248 " pdb=" CD LYS A 248 " ideal model delta sinusoidal sigma weight residual -180.00 -123.22 -56.78 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 6146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1399 0.074 - 0.148: 173 0.148 - 0.223: 2 0.223 - 0.297: 0 0.297 - 0.371: 1 Chirality restraints: 1575 Sorted by residual: chirality pdb=" CA LYS A 110 " pdb=" N LYS A 110 " pdb=" C LYS A 110 " pdb=" CB LYS A 110 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA HIS A 212 " pdb=" N HIS A 212 " pdb=" C HIS A 212 " pdb=" CB HIS A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" C1 NAG A 606 " pdb=" ND2 ASN A 65 " pdb=" C2 NAG A 606 " pdb=" O5 NAG A 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 1572 not shown) Planarity restraints: 1747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 363 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO A 364 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 110 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C LYS A 110 " -0.027 2.00e-02 2.50e+03 pdb=" O LYS A 110 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY A 111 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C1499 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO C1500 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C1500 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C1500 " -0.020 5.00e-02 4.00e+02 ... (remaining 1744 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2483 2.80 - 3.32: 8581 3.32 - 3.85: 15442 3.85 - 4.37: 17617 4.37 - 4.90: 31607 Nonbonded interactions: 75730 Sorted by model distance: nonbonded pdb=" OG1 THR C1547 " pdb=" OD1 ASN C1548 " model vdw 2.272 3.040 nonbonded pdb=" O GLY C1431 " pdb=" OH TYR C1462 " model vdw 2.307 3.040 nonbonded pdb=" O SER B 348 " pdb=" OG SER B 351 " model vdw 2.327 3.040 nonbonded pdb=" OH TYR C1508 " pdb=" O THR C1547 " model vdw 2.340 3.040 nonbonded pdb=" OD2 ASP A 426 " pdb=" OH TYR A 532 " model vdw 2.359 3.040 ... (remaining 75725 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 'A' and (resid 19 through 44 or resid 55 through 73 or (resid 74 and (nam \ e N or name CA or name C or name O or name CB )) or resid 75 through 81 or (resi \ d 82 through 88 and (name N or name CA or name C or name O or name CB )) or resi \ d 89 through 93 or (resid 94 and (name N or name CA or name C or name O or name \ CB )) or resid 95 through 102 or (resid 103 and (name N or name CA or name C or \ name O or name CB )) or resid 104 or (resid 105 and (name N or name CA or name C \ or name O or name CB )) or resid 106 through 107 or (resid 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 through 111 or (resid 112 \ through 114 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 5 or (resid 116 and (name N or name CA or name C or name O or name CB )) or resi \ d 117 through 129 or (resid 130 through 131 and (name N or name CA or name C or \ name O or name CB )) or resid 132 through 147 or (resid 148 and (name N or name \ CA or name C or name O or name CB )) or resid 149 through 150 or (resid 151 and \ (name N or name CA or name C or name O or name CB )) or resid 152 or (resid 153 \ and (name N or name CA or name C or name O or name CB )) or resid 154 through 16 \ 7 or (resid 168 through 169 and (name N or name CA or name C or name O or name C \ B )) or resid 170 through 190 or (resid 191 through 192 and (name N or name CA o \ r name C or name O or name CB )) or resid 193 through 200 or (resid 201 and (nam \ e N or name CA or name C or name O or name CB )) or resid 202 through 213 or (re \ sid 214 through 215 and (name N or name CA or name C or name O or name CB )) or \ resid 216 through 243 or (resid 244 through 245 and (name N or name CA or name C \ or name O or name CB )) or (resid 248 and (name N or name CA or name C or name \ O or name CB )) or resid 249 through 265 or (resid 266 through 267 and (name N o \ r name CA or name C or name O or name CB )) or resid 268 through 269 or (resid 2 \ 70 through 271 and (name N or name CA or name C or name O or name CB )) or resid \ 272 through 308 or (resid 309 and (name N or name CA or name C or name O or nam \ e CB )) or resid 310 through 349 or (resid 350 and (name N or name CA or name C \ or name O or name CB )) or resid 351 through 357 or (resid 358 through 359 and ( \ name N or name CA or name C or name O or name CB )) or resid 360 through 362 or \ (resid 363 and (name N or name CA or name C or name O or name CB )) or resid 364 \ through 375 or (resid 376 through 377 and (name N or name CA or name C or name \ O or name CB )) or resid 378 through 399 or (resid 400 through 401 and (name N o \ r name CA or name C or name O or name CB )) or resid 402 through 443 or (resid 4 \ 44 and (name N or name CA or name C or name O or name CB )) or resid 445 through \ 461 or (resid 462 and (name N or name CA or name C or name O or name CB )) or r \ esid 463 through 466 or (resid 467 and (name N or name CA or name C or name O or \ name CB )) or resid 468 through 479 or (resid 480 and (name N or name CA or nam \ e C or name O or name CB )) or resid 481 through 504 or (resid 505 and (name N o \ r name CA or name C or name O or name CB )) or resid 506 through 513 or (resid 5 \ 14 and (name N or name CA or name C or name O or name CB )) or resid 515 or (res \ id 516 and (name N or name CA or name C or name O or name CB )) or resid 517 thr \ ough 519 or (resid 520 and (name N or name CA or name C or name O or name CB )) \ or resid 521 through 536 or (resid 537 through 538 and (name N or name CA or nam \ e C or name O or name CB )) or resid 539 through 543 or (resid 544 through 551 a \ nd (name N or name CA or name C or name O or name CB )) or resid 552 through 553 \ or (resid 554 and (name N or name CA or name C or name O or name CB )) or resid \ 555 through 564 or (resid 565 and (name N or name CA or name C or name O or nam \ e CB )) or resid 566 or resid 605 through 606)) selection = (chain 'B' and (resid 19 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 319 or (resid 320 and (name N or n \ ame CA or name C or name O or name CB )) or resid 321 through 492 or (resid 493 \ and (name N or name CA or name C or name O or name CB )) or resid 494 through 54 \ 8 or (resid 549 through 551 and (name N or name CA or name C or name O or name C \ B )) or resid 552 through 566 or resid 1303 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.200 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 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 : 0.003 0.046 10108 Z= 0.139 Angle : 0.520 10.275 13753 Z= 0.275 Chirality : 0.045 0.371 1575 Planarity : 0.004 0.064 1740 Dihedral : 11.845 81.514 3681 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.05 % Rotamer: Outliers : 0.41 % Allowed : 7.43 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.22), residues: 1265 helix: -1.47 (0.42), residues: 131 sheet: -0.60 (0.26), residues: 342 loop : -1.27 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 216 HIS 0.007 0.001 HIS A 212 PHE 0.015 0.001 PHE C1585 TYR 0.010 0.001 TYR C1425 ARG 0.004 0.000 ARG A 514 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 7) link_NAG-ASN : angle 3.08861 ( 21) link_BETA1-4 : bond 0.00356 ( 3) link_BETA1-4 : angle 0.85980 ( 9) hydrogen bonds : bond 0.25126 ( 315) hydrogen bonds : angle 9.68529 ( 828) SS BOND : bond 0.00093 ( 14) SS BOND : angle 0.51937 ( 28) covalent geometry : bond 0.00267 (10084) covalent geometry : angle 0.50618 (13695) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 403 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 412 LEU cc_start: 0.7957 (mt) cc_final: 0.7711 (mt) outliers start: 4 outliers final: 0 residues processed: 405 average time/residue: 0.2279 time to fit residues: 128.9926 Evaluate side-chains 344 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 32 optimal weight: 30.0000 chunk 64 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 30.0000 chunk 74 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 224 GLN A 435 HIS A 544 HIS B 37 GLN B 224 GLN B 390 ASN B 435 HIS C1444 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.158042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114764 restraints weight = 12772.234| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.22 r_work: 0.3148 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10108 Z= 0.238 Angle : 0.720 16.756 13753 Z= 0.361 Chirality : 0.049 0.218 1575 Planarity : 0.004 0.054 1740 Dihedral : 5.801 56.725 1598 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.85 % Favored : 97.08 % Rotamer: Outliers : 4.07 % Allowed : 16.89 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.22), residues: 1265 helix: -0.64 (0.46), residues: 127 sheet: -0.51 (0.26), residues: 363 loop : -0.92 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 97 HIS 0.004 0.001 HIS B 290 PHE 0.023 0.002 PHE C1474 TYR 0.022 0.002 TYR C1425 ARG 0.006 0.001 ARG A 55 Details of bonding type rmsd link_NAG-ASN : bond 0.01915 ( 7) link_NAG-ASN : angle 4.51968 ( 21) link_BETA1-4 : bond 0.00363 ( 3) link_BETA1-4 : angle 1.13939 ( 9) hydrogen bonds : bond 0.04766 ( 315) hydrogen bonds : angle 7.10030 ( 828) SS BOND : bond 0.00339 ( 14) SS BOND : angle 1.60387 ( 28) covalent geometry : bond 0.00556 (10084) covalent geometry : angle 0.69547 (13695) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 347 time to evaluate : 1.159 Fit side-chains REVERT: A 325 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8334 (t) REVERT: A 330 TYR cc_start: 0.9085 (m-80) cc_final: 0.8806 (m-80) REVERT: A 376 GLU cc_start: 0.8054 (mp0) cc_final: 0.7780 (mp0) REVERT: B 34 TYR cc_start: 0.8304 (t80) cc_final: 0.7935 (t80) REVERT: B 62 MET cc_start: 0.7015 (ptm) cc_final: 0.6737 (ptm) REVERT: B 162 MET cc_start: 0.8604 (ttm) cc_final: 0.8164 (ttp) REVERT: B 170 LYS cc_start: 0.9016 (tttm) cc_final: 0.8748 (mmmt) REVERT: B 345 GLU cc_start: 0.8143 (pt0) cc_final: 0.7799 (pm20) REVERT: C 1434 ILE cc_start: 0.8768 (mm) cc_final: 0.8448 (mm) REVERT: C 1460 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8269 (tp) REVERT: C 1492 SER cc_start: 0.9102 (m) cc_final: 0.8812 (m) REVERT: C 1508 TYR cc_start: 0.8124 (m-80) cc_final: 0.7574 (m-80) outliers start: 40 outliers final: 24 residues processed: 360 average time/residue: 0.2071 time to fit residues: 105.0622 Evaluate side-chains 356 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 330 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1427 ILE Chi-restraints excluded: chain C residue 1437 ILE Chi-restraints excluded: chain C residue 1460 ILE Chi-restraints excluded: chain C residue 1485 THR Chi-restraints excluded: chain C residue 1589 ILE Chi-restraints excluded: chain C residue 1613 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 37 optimal weight: 9.9990 chunk 60 optimal weight: 30.0000 chunk 97 optimal weight: 0.0030 chunk 111 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 544 HIS B 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.159427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115973 restraints weight = 13000.485| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.30 r_work: 0.3173 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10108 Z= 0.132 Angle : 0.615 12.819 13753 Z= 0.310 Chirality : 0.047 0.372 1575 Planarity : 0.004 0.057 1740 Dihedral : 5.616 58.464 1598 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 4.48 % Allowed : 18.62 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.96 (0.23), residues: 1265 helix: -0.46 (0.47), residues: 127 sheet: -0.39 (0.26), residues: 363 loop : -0.76 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 273 HIS 0.003 0.001 HIS B 395 PHE 0.029 0.001 PHE C1474 TYR 0.017 0.001 TYR C1425 ARG 0.006 0.001 ARG A 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 7) link_NAG-ASN : angle 4.24530 ( 21) link_BETA1-4 : bond 0.00376 ( 3) link_BETA1-4 : angle 1.17586 ( 9) hydrogen bonds : bond 0.04016 ( 315) hydrogen bonds : angle 6.60685 ( 828) SS BOND : bond 0.00205 ( 14) SS BOND : angle 1.33678 ( 28) covalent geometry : bond 0.00308 (10084) covalent geometry : angle 0.58928 (13695) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 342 time to evaluate : 1.697 Fit side-chains REVERT: A 64 MET cc_start: 0.8148 (mtt) cc_final: 0.7575 (mtt) REVERT: A 126 LYS cc_start: 0.8973 (ttpt) cc_final: 0.8748 (ttpt) REVERT: A 270 GLU cc_start: 0.8330 (tt0) cc_final: 0.7799 (tt0) REVERT: A 325 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8345 (t) REVERT: A 330 TYR cc_start: 0.9106 (m-80) cc_final: 0.8847 (m-80) REVERT: A 376 GLU cc_start: 0.8003 (mp0) cc_final: 0.7676 (mp0) REVERT: A 509 LYS cc_start: 0.8879 (tttt) cc_final: 0.8550 (tttm) REVERT: B 124 LEU cc_start: 0.8697 (tt) cc_final: 0.8461 (tt) REVERT: B 162 MET cc_start: 0.8604 (ttm) cc_final: 0.8171 (ttp) REVERT: B 170 LYS cc_start: 0.8991 (tttm) cc_final: 0.8735 (mmmt) REVERT: B 280 ARG cc_start: 0.8651 (ttt180) cc_final: 0.8329 (ttt90) REVERT: B 345 GLU cc_start: 0.8209 (pt0) cc_final: 0.7899 (pm20) REVERT: B 453 ARG cc_start: 0.7487 (mtp85) cc_final: 0.6954 (ptp90) outliers start: 44 outliers final: 30 residues processed: 356 average time/residue: 0.2245 time to fit residues: 114.2852 Evaluate side-chains 360 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 329 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1437 ILE Chi-restraints excluded: chain C residue 1460 ILE Chi-restraints excluded: chain C residue 1485 THR Chi-restraints excluded: chain C residue 1532 PHE Chi-restraints excluded: chain C residue 1543 THR Chi-restraints excluded: chain C residue 1589 ILE Chi-restraints excluded: chain C residue 1613 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 8 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 35 optimal weight: 0.0070 chunk 4 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 119 optimal weight: 40.0000 chunk 13 optimal weight: 0.1980 chunk 109 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 overall best weight: 4.6404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 224 GLN A 544 HIS B 37 GLN C1496 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.161839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118434 restraints weight = 12648.051| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.19 r_work: 0.3064 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 10108 Z= 0.237 Angle : 0.635 8.481 13753 Z= 0.325 Chirality : 0.048 0.188 1575 Planarity : 0.004 0.057 1740 Dihedral : 5.619 59.792 1598 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.52 % Rotamer: Outliers : 5.70 % Allowed : 19.02 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.90 (0.23), residues: 1265 helix: 0.07 (0.51), residues: 113 sheet: -0.50 (0.26), residues: 361 loop : -0.72 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 216 HIS 0.007 0.001 HIS B 212 PHE 0.024 0.002 PHE C1474 TYR 0.026 0.002 TYR B 34 ARG 0.005 0.001 ARG B 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 7) link_NAG-ASN : angle 3.29048 ( 21) link_BETA1-4 : bond 0.00264 ( 3) link_BETA1-4 : angle 1.26475 ( 9) hydrogen bonds : bond 0.04016 ( 315) hydrogen bonds : angle 6.49117 ( 828) SS BOND : bond 0.00322 ( 14) SS BOND : angle 1.09942 ( 28) covalent geometry : bond 0.00554 (10084) covalent geometry : angle 0.62081 (13695) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 330 time to evaluate : 1.163 Fit side-chains REVERT: A 64 MET cc_start: 0.7962 (mtt) cc_final: 0.7609 (mtt) REVERT: A 270 GLU cc_start: 0.8262 (tt0) cc_final: 0.7704 (tt0) REVERT: A 330 TYR cc_start: 0.9150 (m-80) cc_final: 0.8875 (m-80) REVERT: A 376 GLU cc_start: 0.8131 (mp0) cc_final: 0.7783 (mp0) REVERT: A 466 LEU cc_start: 0.9177 (mt) cc_final: 0.8974 (mt) REVERT: A 467 GLU cc_start: 0.7622 (mp0) cc_final: 0.7021 (mp0) REVERT: A 472 TYR cc_start: 0.8876 (t80) cc_final: 0.8615 (t80) REVERT: A 486 ARG cc_start: 0.8592 (mtp85) cc_final: 0.8193 (ttp-110) REVERT: A 526 ILE cc_start: 0.8326 (mm) cc_final: 0.8023 (mt) REVERT: B 124 LEU cc_start: 0.8854 (tt) cc_final: 0.8595 (tt) REVERT: B 145 ARG cc_start: 0.7623 (ttm110) cc_final: 0.7331 (ttm110) REVERT: B 170 LYS cc_start: 0.9038 (tttm) cc_final: 0.8811 (mmmt) REVERT: C 1430 SER cc_start: 0.7311 (t) cc_final: 0.6605 (p) REVERT: C 1460 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8416 (tp) outliers start: 56 outliers final: 44 residues processed: 351 average time/residue: 0.2490 time to fit residues: 123.8618 Evaluate side-chains 349 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 304 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1427 ILE Chi-restraints excluded: chain C residue 1437 ILE Chi-restraints excluded: chain C residue 1460 ILE Chi-restraints excluded: chain C residue 1485 THR Chi-restraints excluded: chain C residue 1528 ILE Chi-restraints excluded: chain C residue 1532 PHE Chi-restraints excluded: chain C residue 1541 SER Chi-restraints excluded: chain C residue 1543 THR Chi-restraints excluded: chain C residue 1544 ILE Chi-restraints excluded: chain C residue 1589 ILE Chi-restraints excluded: chain C residue 1613 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 112 optimal weight: 0.0070 chunk 101 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 33 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 overall best weight: 2.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 544 HIS B 37 GLN B 212 HIS C1503 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.163707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.120541 restraints weight = 12572.814| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.20 r_work: 0.3124 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10108 Z= 0.140 Angle : 0.600 8.739 13753 Z= 0.306 Chirality : 0.046 0.234 1575 Planarity : 0.004 0.059 1740 Dihedral : 5.443 59.812 1598 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 5.39 % Allowed : 19.94 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.78 (0.23), residues: 1265 helix: -0.00 (0.49), residues: 119 sheet: -0.40 (0.27), residues: 364 loop : -0.62 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 216 HIS 0.011 0.001 HIS B 212 PHE 0.021 0.001 PHE C1474 TYR 0.020 0.001 TYR B 34 ARG 0.005 0.001 ARG B 494 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 7) link_NAG-ASN : angle 3.19082 ( 21) link_BETA1-4 : bond 0.00373 ( 3) link_BETA1-4 : angle 1.22926 ( 9) hydrogen bonds : bond 0.03561 ( 315) hydrogen bonds : angle 6.29384 ( 828) SS BOND : bond 0.00177 ( 14) SS BOND : angle 1.03144 ( 28) covalent geometry : bond 0.00325 (10084) covalent geometry : angle 0.58578 (13695) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 324 time to evaluate : 1.461 Fit side-chains REVERT: A 270 GLU cc_start: 0.8244 (tt0) cc_final: 0.7614 (tt0) REVERT: A 325 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8471 (t) REVERT: A 330 TYR cc_start: 0.9117 (m-80) cc_final: 0.8812 (m-80) REVERT: A 376 GLU cc_start: 0.8112 (mp0) cc_final: 0.7740 (mp0) REVERT: A 486 ARG cc_start: 0.8562 (mtp85) cc_final: 0.8136 (ttp-110) REVERT: B 145 ARG cc_start: 0.7574 (ttm110) cc_final: 0.7229 (ttm110) REVERT: B 170 LYS cc_start: 0.9045 (tttm) cc_final: 0.8776 (mmmt) REVERT: C 1430 SER cc_start: 0.7274 (t) cc_final: 0.6589 (p) REVERT: C 1459 TYR cc_start: 0.6767 (m-80) cc_final: 0.5753 (m-10) REVERT: C 1460 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8393 (tp) outliers start: 53 outliers final: 40 residues processed: 340 average time/residue: 0.2110 time to fit residues: 101.9493 Evaluate side-chains 347 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 305 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1437 ILE Chi-restraints excluded: chain C residue 1447 ILE Chi-restraints excluded: chain C residue 1460 ILE Chi-restraints excluded: chain C residue 1485 THR Chi-restraints excluded: chain C residue 1528 ILE Chi-restraints excluded: chain C residue 1532 PHE Chi-restraints excluded: chain C residue 1541 SER Chi-restraints excluded: chain C residue 1543 THR Chi-restraints excluded: chain C residue 1544 ILE Chi-restraints excluded: chain C residue 1589 ILE Chi-restraints excluded: chain C residue 1613 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 53 optimal weight: 0.0870 chunk 52 optimal weight: 10.0000 chunk 101 optimal weight: 40.0000 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 119 optimal weight: 30.0000 chunk 65 optimal weight: 20.0000 chunk 58 optimal weight: 0.0060 chunk 107 optimal weight: 7.9990 overall best weight: 1.1376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 75 HIS A 224 GLN A 544 HIS B 491 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.165991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123062 restraints weight = 12549.223| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.21 r_work: 0.3154 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10108 Z= 0.113 Angle : 0.603 15.303 13753 Z= 0.302 Chirality : 0.046 0.192 1575 Planarity : 0.004 0.079 1740 Dihedral : 5.348 58.635 1598 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.13 % Favored : 97.79 % Rotamer: Outliers : 3.76 % Allowed : 21.87 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.68 (0.23), residues: 1265 helix: 0.11 (0.50), residues: 119 sheet: -0.29 (0.27), residues: 373 loop : -0.58 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 216 HIS 0.003 0.001 HIS B 212 PHE 0.019 0.001 PHE B 41 TYR 0.020 0.001 TYR B 34 ARG 0.006 0.000 ARG B 494 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 7) link_NAG-ASN : angle 3.13393 ( 21) link_BETA1-4 : bond 0.00404 ( 3) link_BETA1-4 : angle 1.16580 ( 9) hydrogen bonds : bond 0.03331 ( 315) hydrogen bonds : angle 6.12008 ( 828) SS BOND : bond 0.00428 ( 14) SS BOND : angle 0.63301 ( 28) covalent geometry : bond 0.00260 (10084) covalent geometry : angle 0.59053 (13695) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 325 time to evaluate : 1.471 Fit side-chains REVERT: A 77 TYR cc_start: 0.9062 (m-80) cc_final: 0.8859 (m-80) REVERT: A 270 GLU cc_start: 0.8254 (tt0) cc_final: 0.7624 (tt0) REVERT: A 330 TYR cc_start: 0.9125 (m-80) cc_final: 0.8828 (m-80) REVERT: A 360 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7022 (ttp-170) REVERT: A 376 GLU cc_start: 0.8117 (mp0) cc_final: 0.7745 (mp0) REVERT: A 486 ARG cc_start: 0.8624 (mtp85) cc_final: 0.8150 (ttp-110) REVERT: B 145 ARG cc_start: 0.7429 (ttm110) cc_final: 0.7159 (ttm110) REVERT: B 170 LYS cc_start: 0.9046 (tttm) cc_final: 0.8758 (mmmt) REVERT: B 290 HIS cc_start: 0.8427 (m-70) cc_final: 0.8150 (m-70) REVERT: B 345 GLU cc_start: 0.6914 (pm20) cc_final: 0.6625 (pm20) REVERT: C 1430 SER cc_start: 0.7233 (t) cc_final: 0.6528 (p) REVERT: C 1459 TYR cc_start: 0.6733 (m-80) cc_final: 0.5564 (m-10) outliers start: 37 outliers final: 29 residues processed: 339 average time/residue: 0.2724 time to fit residues: 132.1873 Evaluate side-chains 350 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 320 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 1437 ILE Chi-restraints excluded: chain C residue 1532 PHE Chi-restraints excluded: chain C residue 1541 SER Chi-restraints excluded: chain C residue 1543 THR Chi-restraints excluded: chain C residue 1544 ILE Chi-restraints excluded: chain C residue 1553 ASN Chi-restraints excluded: chain C residue 1589 ILE Chi-restraints excluded: chain C residue 1613 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 18 optimal weight: 5.9990 chunk 121 optimal weight: 40.0000 chunk 92 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 544 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1444 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.162132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118893 restraints weight = 12854.021| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.24 r_work: 0.3101 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10108 Z= 0.211 Angle : 0.636 11.888 13753 Z= 0.321 Chirality : 0.047 0.172 1575 Planarity : 0.005 0.082 1740 Dihedral : 5.438 59.157 1598 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.16 % Favored : 96.76 % Rotamer: Outliers : 5.29 % Allowed : 21.46 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.72 (0.23), residues: 1265 helix: 0.13 (0.50), residues: 119 sheet: -0.36 (0.27), residues: 374 loop : -0.59 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 216 HIS 0.004 0.001 HIS B 118 PHE 0.017 0.002 PHE C1474 TYR 0.014 0.001 TYR B 34 ARG 0.007 0.001 ARG B 494 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 7) link_NAG-ASN : angle 3.45956 ( 21) link_BETA1-4 : bond 0.00274 ( 3) link_BETA1-4 : angle 1.19699 ( 9) hydrogen bonds : bond 0.03564 ( 315) hydrogen bonds : angle 6.18285 ( 828) SS BOND : bond 0.00360 ( 14) SS BOND : angle 0.85393 ( 28) covalent geometry : bond 0.00499 (10084) covalent geometry : angle 0.62074 (13695) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 317 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 376 GLU cc_start: 0.8183 (mp0) cc_final: 0.7866 (mp0) REVERT: A 486 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8260 (ttp-110) REVERT: A 514 ARG cc_start: 0.8128 (ttm110) cc_final: 0.7430 (ttm-80) REVERT: A 525 CYS cc_start: 0.7474 (t) cc_final: 0.7196 (t) REVERT: B 145 ARG cc_start: 0.7569 (ttm110) cc_final: 0.6876 (ttm110) REVERT: B 162 MET cc_start: 0.8729 (ttm) cc_final: 0.8459 (ttp) REVERT: B 170 LYS cc_start: 0.9061 (tttm) cc_final: 0.8801 (mmmt) REVERT: B 345 GLU cc_start: 0.7090 (pm20) cc_final: 0.6765 (pm20) REVERT: C 1430 SER cc_start: 0.7473 (t) cc_final: 0.6788 (p) REVERT: C 1459 TYR cc_start: 0.6584 (m-80) cc_final: 0.5394 (m-10) outliers start: 52 outliers final: 45 residues processed: 333 average time/residue: 0.2141 time to fit residues: 101.2173 Evaluate side-chains 356 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 311 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain C residue 1437 ILE Chi-restraints excluded: chain C residue 1485 THR Chi-restraints excluded: chain C residue 1492 SER Chi-restraints excluded: chain C residue 1494 ILE Chi-restraints excluded: chain C residue 1528 ILE Chi-restraints excluded: chain C residue 1532 PHE Chi-restraints excluded: chain C residue 1540 LEU Chi-restraints excluded: chain C residue 1541 SER Chi-restraints excluded: chain C residue 1543 THR Chi-restraints excluded: chain C residue 1544 ILE Chi-restraints excluded: chain C residue 1553 ASN Chi-restraints excluded: chain C residue 1589 ILE Chi-restraints excluded: chain C residue 1613 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.161051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117851 restraints weight = 12707.542| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.21 r_work: 0.3121 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10108 Z= 0.219 Angle : 0.676 13.627 13753 Z= 0.335 Chirality : 0.051 0.603 1575 Planarity : 0.005 0.080 1740 Dihedral : 5.249 53.917 1598 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.64 % Favored : 96.28 % Rotamer: Outliers : 4.98 % Allowed : 22.58 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.73 (0.23), residues: 1265 helix: 0.02 (0.51), residues: 120 sheet: -0.32 (0.27), residues: 368 loop : -0.61 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 216 HIS 0.002 0.001 HIS B 212 PHE 0.022 0.002 PHE C1474 TYR 0.018 0.001 TYR B 330 ARG 0.006 0.001 ARG A 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00686 ( 7) link_NAG-ASN : angle 4.65218 ( 21) link_BETA1-4 : bond 0.00282 ( 3) link_BETA1-4 : angle 1.18416 ( 9) hydrogen bonds : bond 0.03615 ( 315) hydrogen bonds : angle 6.25672 ( 828) SS BOND : bond 0.00256 ( 14) SS BOND : angle 1.46589 ( 28) covalent geometry : bond 0.00519 (10084) covalent geometry : angle 0.64877 (13695) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 312 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: A 376 GLU cc_start: 0.8237 (mp0) cc_final: 0.7931 (mp0) REVERT: A 377 ARG cc_start: 0.8131 (ptm-80) cc_final: 0.7753 (ptm-80) REVERT: A 486 ARG cc_start: 0.8669 (mtp85) cc_final: 0.8243 (ttp-110) REVERT: A 525 CYS cc_start: 0.7489 (t) cc_final: 0.7202 (t) REVERT: A 526 ILE cc_start: 0.8355 (mm) cc_final: 0.8096 (mt) REVERT: B 145 ARG cc_start: 0.7633 (ttm110) cc_final: 0.6904 (ttm110) REVERT: B 162 MET cc_start: 0.8730 (ttm) cc_final: 0.8446 (ttp) REVERT: B 170 LYS cc_start: 0.9068 (tttm) cc_final: 0.8794 (mmmt) REVERT: B 345 GLU cc_start: 0.7163 (pm20) cc_final: 0.6831 (pm20) REVERT: B 491 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8003 (mm-40) REVERT: C 1430 SER cc_start: 0.7612 (t) cc_final: 0.6968 (p) REVERT: C 1526 LEU cc_start: 0.7297 (pp) cc_final: 0.6947 (pp) outliers start: 49 outliers final: 43 residues processed: 325 average time/residue: 0.2082 time to fit residues: 95.4048 Evaluate side-chains 353 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 309 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain C residue 1437 ILE Chi-restraints excluded: chain C residue 1447 ILE Chi-restraints excluded: chain C residue 1485 THR Chi-restraints excluded: chain C residue 1494 ILE Chi-restraints excluded: chain C residue 1511 LYS Chi-restraints excluded: chain C residue 1528 ILE Chi-restraints excluded: chain C residue 1532 PHE Chi-restraints excluded: chain C residue 1540 LEU Chi-restraints excluded: chain C residue 1541 SER Chi-restraints excluded: chain C residue 1543 THR Chi-restraints excluded: chain C residue 1544 ILE Chi-restraints excluded: chain C residue 1553 ASN Chi-restraints excluded: chain C residue 1589 ILE Chi-restraints excluded: chain C residue 1613 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 17 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 544 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.161267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117364 restraints weight = 12693.015| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.25 r_work: 0.3088 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10108 Z= 0.204 Angle : 0.661 14.714 13753 Z= 0.329 Chirality : 0.050 0.511 1575 Planarity : 0.005 0.095 1740 Dihedral : 5.155 54.213 1598 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 5.60 % Allowed : 21.87 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.76 (0.24), residues: 1265 helix: 0.04 (0.50), residues: 122 sheet: -0.34 (0.27), residues: 369 loop : -0.63 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 216 HIS 0.002 0.001 HIS B 290 PHE 0.023 0.002 PHE C1474 TYR 0.016 0.001 TYR B 330 ARG 0.009 0.001 ARG B 494 Details of bonding type rmsd link_NAG-ASN : bond 0.00653 ( 7) link_NAG-ASN : angle 4.64156 ( 21) link_BETA1-4 : bond 0.00280 ( 3) link_BETA1-4 : angle 1.17202 ( 9) hydrogen bonds : bond 0.03581 ( 315) hydrogen bonds : angle 6.26641 ( 828) SS BOND : bond 0.00237 ( 14) SS BOND : angle 0.91738 ( 28) covalent geometry : bond 0.00485 (10084) covalent geometry : angle 0.63445 (13695) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 315 time to evaluate : 1.043 Fit side-chains REVERT: A 92 SER cc_start: 0.8612 (t) cc_final: 0.8219 (p) REVERT: A 158 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: A 376 GLU cc_start: 0.8264 (mp0) cc_final: 0.7931 (mp0) REVERT: A 486 ARG cc_start: 0.8656 (mtp85) cc_final: 0.8218 (ttp-110) REVERT: A 525 CYS cc_start: 0.7488 (t) cc_final: 0.7198 (t) REVERT: A 526 ILE cc_start: 0.8330 (mm) cc_final: 0.8073 (mt) REVERT: B 145 ARG cc_start: 0.7624 (ttm110) cc_final: 0.6883 (ttm110) REVERT: B 170 LYS cc_start: 0.9064 (tttm) cc_final: 0.8793 (mmmt) REVERT: B 345 GLU cc_start: 0.7344 (pm20) cc_final: 0.7070 (pm20) REVERT: C 1430 SER cc_start: 0.7759 (t) cc_final: 0.7145 (p) REVERT: C 1526 LEU cc_start: 0.7195 (pp) cc_final: 0.6793 (pp) outliers start: 55 outliers final: 50 residues processed: 329 average time/residue: 0.2038 time to fit residues: 94.9835 Evaluate side-chains 363 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 312 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1437 ILE Chi-restraints excluded: chain C residue 1447 ILE Chi-restraints excluded: chain C residue 1485 THR Chi-restraints excluded: chain C residue 1492 SER Chi-restraints excluded: chain C residue 1494 ILE Chi-restraints excluded: chain C residue 1511 LYS Chi-restraints excluded: chain C residue 1516 ILE Chi-restraints excluded: chain C residue 1518 ILE Chi-restraints excluded: chain C residue 1528 ILE Chi-restraints excluded: chain C residue 1532 PHE Chi-restraints excluded: chain C residue 1540 LEU Chi-restraints excluded: chain C residue 1541 SER Chi-restraints excluded: chain C residue 1543 THR Chi-restraints excluded: chain C residue 1544 ILE Chi-restraints excluded: chain C residue 1553 ASN Chi-restraints excluded: chain C residue 1589 ILE Chi-restraints excluded: chain C residue 1613 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 78 optimal weight: 0.4980 chunk 69 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 19 optimal weight: 0.0970 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.164139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120426 restraints weight = 12636.967| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.27 r_work: 0.3124 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10108 Z= 0.127 Angle : 0.646 14.232 13753 Z= 0.318 Chirality : 0.048 0.408 1575 Planarity : 0.004 0.080 1740 Dihedral : 5.165 51.707 1598 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 4.27 % Allowed : 23.09 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.69 (0.24), residues: 1265 helix: 0.04 (0.50), residues: 122 sheet: -0.13 (0.27), residues: 371 loop : -0.67 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.003 0.001 HIS B 118 PHE 0.023 0.001 PHE A 391 TYR 0.014 0.001 TYR B 330 ARG 0.007 0.000 ARG B 494 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 7) link_NAG-ASN : angle 5.07372 ( 21) link_BETA1-4 : bond 0.00394 ( 3) link_BETA1-4 : angle 1.13265 ( 9) hydrogen bonds : bond 0.03274 ( 315) hydrogen bonds : angle 6.09651 ( 828) SS BOND : bond 0.00199 ( 14) SS BOND : angle 0.84311 ( 28) covalent geometry : bond 0.00299 (10084) covalent geometry : angle 0.61396 (13695) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 316 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: A 376 GLU cc_start: 0.8204 (mp0) cc_final: 0.7856 (mp0) REVERT: A 453 ARG cc_start: 0.8468 (mtt180) cc_final: 0.8164 (mtt90) REVERT: A 486 ARG cc_start: 0.8690 (mtp85) cc_final: 0.8200 (ttp-110) REVERT: A 525 CYS cc_start: 0.7475 (t) cc_final: 0.7181 (t) REVERT: B 145 ARG cc_start: 0.7468 (ttm110) cc_final: 0.7180 (ttm110) REVERT: B 162 MET cc_start: 0.8686 (ttm) cc_final: 0.8389 (ttp) REVERT: B 170 LYS cc_start: 0.9048 (tttm) cc_final: 0.8761 (mmmt) REVERT: B 345 GLU cc_start: 0.7369 (pm20) cc_final: 0.7020 (pm20) REVERT: C 1430 SER cc_start: 0.7580 (t) cc_final: 0.7045 (p) REVERT: C 1526 LEU cc_start: 0.7071 (pp) cc_final: 0.6654 (pp) outliers start: 42 outliers final: 36 residues processed: 327 average time/residue: 0.2059 time to fit residues: 95.6612 Evaluate side-chains 345 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 308 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain C residue 1511 LYS Chi-restraints excluded: chain C residue 1516 ILE Chi-restraints excluded: chain C residue 1532 PHE Chi-restraints excluded: chain C residue 1540 LEU Chi-restraints excluded: chain C residue 1541 SER Chi-restraints excluded: chain C residue 1543 THR Chi-restraints excluded: chain C residue 1544 ILE Chi-restraints excluded: chain C residue 1553 ASN Chi-restraints excluded: chain C residue 1589 ILE Chi-restraints excluded: chain C residue 1613 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 86 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 19 optimal weight: 0.0070 chunk 48 optimal weight: 10.0000 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.165882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.123141 restraints weight = 12578.748| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.22 r_work: 0.3156 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10108 Z= 0.115 Angle : 0.634 13.954 13753 Z= 0.314 Chirality : 0.048 0.359 1575 Planarity : 0.004 0.069 1740 Dihedral : 5.065 50.939 1598 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 3.66 % Allowed : 23.60 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % 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: -0.64 (0.24), residues: 1265 helix: 0.15 (0.51), residues: 120 sheet: -0.13 (0.27), residues: 387 loop : -0.64 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 216 HIS 0.002 0.000 HIS A 75 PHE 0.022 0.001 PHE C1474 TYR 0.014 0.001 TYR B 330 ARG 0.010 0.001 ARG B 494 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 7) link_NAG-ASN : angle 4.43919 ( 21) link_BETA1-4 : bond 0.00403 ( 3) link_BETA1-4 : angle 1.07904 ( 9) hydrogen bonds : bond 0.03193 ( 315) hydrogen bonds : angle 6.03949 ( 828) SS BOND : bond 0.00200 ( 14) SS BOND : angle 0.57374 ( 28) covalent geometry : bond 0.00267 (10084) covalent geometry : angle 0.60947 (13695) =============================================================================== Job complete usr+sys time: 5395.86 seconds wall clock time: 96 minutes 16.50 seconds (5776.50 seconds total)