Starting phenix.real_space_refine on Fri Sep 11 14:59:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wts_21898/09_2026/6wts_21898.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wts_21898/09_2026/6wts_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 { model { file = "/net/cci-nas-00/data/ceres_data/6wts_21898/09_2026/6wts_21898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wts_21898/09_2026/6wts_21898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wts_21898/09_2026/6wts_21898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wts_21898/09_2026/6wts_21898.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6wts_21898/09_2026/6wts_21898.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wts_21898/09_2026/6wts_21898.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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, 'ASP:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 3, 'GLU:plan': 3, 'PHE:plan': 1} 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: {'HIS:plan': 4, 'ASP:plan': 14, 'GLU:plan': 14, 'ARG:plan': 7, 'ASN:plan1': 3, 'GLN:plan1': 1, 'PHE:plan': 1} 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: {'ARG:plan': 2, 'GLU:plan': 6, 'ASP:plan': 11, 'ASN:plan1': 9, 'HIS:plan': 1, 'GLN:plan1': 3, 'PHE:plan': 2, 'TYR:plan': 1} 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 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 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 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 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 chiralities: 2 Time building chain proxies: 2.21, per 1000 atoms: 0.22 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: 0.98 Conformation dependent library (CDL) restraints added in 373.7 milliseconds 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: 0.36 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: 1.95 Time building geometry restraints manager: 1.29 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: 5490 16.30 - 32.61: 347 32.61 - 48.91: 79 48.91 - 65.21: 20 65.21 - 81.51: 3 Dihedral angle restraints: 5939 sinusoidal: 2176 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 5936 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 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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.430 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 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 : 11.688 81.514 3471 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.004 0.000 ARG A 514 TYR 0.010 0.001 TYR C1425 PHE 0.015 0.001 PHE C1585 TRP 0.005 0.001 TRP B 216 HIS 0.007 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (10084) covalent geometry : angle 0.50618 / 0.27 (13695) SS BOND : bond 0.00093 / 0.06 ( 14) SS BOND : angle 0.51937 / 0.35 ( 28) hydrogen bonds : bond 0.25126 / 16.15 ( 315) hydrogen bonds : angle 9.68529 / 6.52 ( 828) link_BETA1-4 : bond 0.00356 / 0.20 ( 3) link_BETA1-4 : angle 0.85980 / 0.63 ( 9) link_NAG-ASN : bond 0.00561 / 0.31 ( 7) link_NAG-ASN : angle 3.08861 / 1.72 ( 21) *********************** 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 : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 412 LEU cc_start: 0.7957 (mt) cc_final: 0.7710 (mt) outliers start: 4 outliers final: 0 residues processed: 405 average time/residue: 0.0986 time to fit residues: 56.3085 Evaluate side-chains 343 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 123 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 224 GLN A 346 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.163077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118729 restraints weight = 12671.767| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.23 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: 0.7795 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 10108 Z= 0.313 Angle : 0.753 15.564 13753 Z= 0.379 Chirality : 0.050 0.228 1575 Planarity : 0.005 0.054 1740 Dihedral : 4.737 58.140 1388 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.16 % Favored : 96.76 % Rotamer: Outliers : 4.58 % Allowed : 16.68 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.22), residues: 1265 helix: -0.56 (0.48), residues: 120 sheet: -0.58 (0.27), residues: 353 loop : -0.98 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 55 TYR 0.021 0.002 TYR C1425 PHE 0.022 0.003 PHE C1474 TRP 0.008 0.002 TRP B 535 HIS 0.004 0.001 HIS B 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.31 (10084) covalent geometry : angle 0.72680 / 0.37 (13695) SS BOND : bond 0.00456 / 0.28 ( 14) SS BOND : angle 1.54322 / 0.91 ( 28) hydrogen bonds : bond 0.04922 / 3.20 ( 315) hydrogen bonds : angle 7.18855 / 4.81 ( 828) link_BETA1-4 : bond 0.00306 / 0.19 ( 3) link_BETA1-4 : angle 1.31875 / 0.81 ( 9) link_NAG-ASN : bond 0.01525 / 0.89 ( 7) link_NAG-ASN : angle 4.78620 / 3.19 ( 21) *********************** 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 386 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 341 time to evaluate : 0.339 Fit side-chains REVERT: A 330 TYR cc_start: 0.9164 (m-80) cc_final: 0.8870 (m-80) REVERT: A 376 GLU cc_start: 0.8107 (mp0) cc_final: 0.7868 (mp0) REVERT: A 453 ARG cc_start: 0.8535 (mtt90) cc_final: 0.8278 (mtt90) REVERT: A 472 TYR cc_start: 0.8865 (t80) cc_final: 0.8479 (t80) REVERT: B 34 TYR cc_start: 0.8516 (t80) cc_final: 0.8130 (t80) REVERT: B 162 MET cc_start: 0.8643 (ttm) cc_final: 0.8266 (ttp) REVERT: B 170 LYS cc_start: 0.9040 (tttm) cc_final: 0.8835 (mmmt) REVERT: B 491 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8077 (mm-40) REVERT: C 1406 PHE cc_start: 0.8256 (p90) cc_final: 0.6022 (m-80) REVERT: C 1460 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8347 (tp) REVERT: C 1492 SER cc_start: 0.9070 (m) cc_final: 0.8791 (m) REVERT: C 1508 TYR cc_start: 0.8300 (m-80) cc_final: 0.7877 (m-80) outliers start: 45 outliers final: 32 residues processed: 356 average time/residue: 0.0925 time to fit residues: 47.0946 Evaluate side-chains 352 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 319 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 256 GLN Chi-restraints excluded: chain A residue 277 LEU 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 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 206 THR Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 289 SER 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 1528 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 chunk 107 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 HIS B 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.158821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115962 restraints weight = 12863.080| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.24 r_work: 0.3163 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2519 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= 0.129 Angle : 0.614 12.434 13753 Z= 0.310 Chirality : 0.047 0.393 1575 Planarity : 0.004 0.057 1740 Dihedral : 4.443 53.915 1388 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.92 % Rotamer: Outliers : 4.17 % Allowed : 18.82 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.23), residues: 1265 helix: -0.55 (0.46), residues: 133 sheet: -0.42 (0.26), residues: 366 loop : -0.73 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 55 TYR 0.018 0.001 TYR C1425 PHE 0.027 0.001 PHE C1474 TRP 0.005 0.001 TRP A 273 HIS 0.003 0.001 HIS B 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10084) covalent geometry : angle 0.59093 / 0.30 (13695) SS BOND : bond 0.00176 / 0.12 ( 14) SS BOND : angle 1.29680 / 0.78 ( 28) hydrogen bonds : bond 0.03988 / 2.57 ( 315) hydrogen bonds : angle 6.59463 / 4.43 ( 828) link_BETA1-4 : bond 0.00330 / 0.19 ( 3) link_BETA1-4 : angle 1.12755 / 0.73 ( 9) link_NAG-ASN : bond 0.00373 / 0.21 ( 7) link_NAG-ASN : angle 4.01757 / 2.17 ( 21) *********************** 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 388 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 347 time to evaluate : 0.405 Fit side-chains REVERT: A 64 MET cc_start: 0.8157 (mtt) cc_final: 0.7570 (mtt) REVERT: A 126 LYS cc_start: 0.8944 (ttpt) cc_final: 0.8744 (ttpt) REVERT: A 155 PHE cc_start: 0.8489 (t80) cc_final: 0.8282 (t80) REVERT: A 270 GLU cc_start: 0.8340 (tt0) cc_final: 0.7759 (tt0) REVERT: A 330 TYR cc_start: 0.9046 (m-80) cc_final: 0.8771 (m-80) REVERT: A 376 GLU cc_start: 0.8008 (mp0) cc_final: 0.7675 (mp0) REVERT: A 472 TYR cc_start: 0.8786 (t80) cc_final: 0.8541 (t80) REVERT: A 509 LYS cc_start: 0.8854 (tttt) cc_final: 0.8524 (tttm) REVERT: B 124 LEU cc_start: 0.8871 (tt) cc_final: 0.8627 (tt) REVERT: B 162 MET cc_start: 0.8637 (ttm) cc_final: 0.8150 (ttp) REVERT: B 170 LYS cc_start: 0.9000 (tttm) cc_final: 0.8716 (mmmt) REVERT: B 345 GLU cc_start: 0.6847 (pm20) cc_final: 0.6475 (pm20) REVERT: B 453 ARG cc_start: 0.7378 (mtp85) cc_final: 0.6964 (ptp-170) REVERT: C 1508 TYR cc_start: 0.8300 (m-80) cc_final: 0.7719 (m-80) outliers start: 41 outliers final: 26 residues processed: 357 average time/residue: 0.0896 time to fit residues: 46.3911 Evaluate side-chains 350 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 324 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 301 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 468 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 24 SER Chi-restraints excluded: chain B residue 230 ASP 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 338 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 1437 ILE Chi-restraints excluded: chain C residue 1460 ILE 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 3 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 91 optimal weight: 0.1980 chunk 37 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 overall best weight: 3.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 224 GLN A 346 GLN A 544 HIS B 37 GLN B 212 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.163526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119963 restraints weight = 12836.139| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.23 r_work: 0.3116 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10108 Z= 0.188 Angle : 0.604 8.042 13753 Z= 0.307 Chirality : 0.047 0.214 1575 Planarity : 0.004 0.056 1740 Dihedral : 4.518 54.701 1388 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.08 % Favored : 96.84 % Rotamer: Outliers : 5.09 % Allowed : 20.14 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.23), residues: 1265 helix: -0.07 (0.48), residues: 125 sheet: -0.41 (0.26), residues: 371 loop : -0.67 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 55 TYR 0.023 0.001 TYR B 34 PHE 0.025 0.002 PHE C1474 TRP 0.011 0.001 TRP B 216 HIS 0.007 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (10084) covalent geometry : angle 0.58883 / 0.30 (13695) SS BOND : bond 0.00238 / 0.15 ( 14) SS BOND : angle 1.03726 / 0.62 ( 28) hydrogen bonds : bond 0.03777 / 2.44 ( 315) hydrogen bonds : angle 6.43051 / 4.33 ( 828) link_BETA1-4 : bond 0.00240 / 0.15 ( 3) link_BETA1-4 : angle 1.17359 / 0.79 ( 9) link_NAG-ASN : bond 0.00470 / 0.27 ( 7) link_NAG-ASN : angle 3.23127 / 1.88 ( 21) *********************** 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 379 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 329 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.7987 (mtt) cc_final: 0.7601 (mtt) REVERT: A 270 GLU cc_start: 0.8201 (tt0) cc_final: 0.7614 (tt0) REVERT: A 325 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8467 (t) REVERT: A 330 TYR cc_start: 0.9138 (m-80) cc_final: 0.8866 (m-80) REVERT: A 376 GLU cc_start: 0.8137 (mp0) cc_final: 0.7772 (mp0) REVERT: B 145 ARG cc_start: 0.7632 (ttm110) cc_final: 0.7322 (ttm110) REVERT: B 162 MET cc_start: 0.8751 (ttm) cc_final: 0.8337 (ttp) REVERT: B 170 LYS cc_start: 0.9050 (tttm) cc_final: 0.8804 (mmmt) REVERT: C 1430 SER cc_start: 0.7214 (t) cc_final: 0.6521 (p) REVERT: C 1460 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8440 (tp) outliers start: 50 outliers final: 37 residues processed: 347 average time/residue: 0.0905 time to fit residues: 45.2924 Evaluate side-chains 351 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 312 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 256 GLN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 277 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 492 LEU Chi-restraints excluded: chain A residue 497 SER 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 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 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 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 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 105 optimal weight: 30.0000 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 126 optimal weight: 40.0000 chunk 85 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 346 GLN A 544 HIS B 37 GLN B 212 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.160991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117572 restraints weight = 12829.706| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.23 r_work: 0.3118 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10108 Z= 0.225 Angle : 0.629 9.033 13753 Z= 0.321 Chirality : 0.048 0.176 1575 Planarity : 0.004 0.059 1740 Dihedral : 4.646 55.223 1388 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.32 % Favored : 96.60 % Rotamer: Outliers : 6.21 % Allowed : 20.45 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.23), residues: 1265 helix: 0.12 (0.50), residues: 119 sheet: -0.41 (0.26), residues: 370 loop : -0.68 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 55 TYR 0.022 0.001 TYR B 34 PHE 0.016 0.002 PHE B 41 TRP 0.009 0.001 TRP B 216 HIS 0.010 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.22 (10084) covalent geometry : angle 0.61619 / 0.32 (13695) SS BOND : bond 0.00289 / 0.18 ( 14) SS BOND : angle 1.04000 / 0.65 ( 28) hydrogen bonds : bond 0.03838 / 2.50 ( 315) hydrogen bonds : angle 6.43701 / 4.34 ( 828) link_BETA1-4 : bond 0.00193 / 0.12 ( 3) link_BETA1-4 : angle 1.20040 / 0.85 ( 9) link_NAG-ASN : bond 0.00669 / 0.39 ( 7) link_NAG-ASN : angle 3.12117 / 1.90 ( 21) *********************** 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 368 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 307 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 92 SER cc_start: 0.8642 (t) cc_final: 0.8187 (p) REVERT: A 319 TYR cc_start: 0.8442 (m-80) cc_final: 0.8098 (m-80) REVERT: A 330 TYR cc_start: 0.9178 (m-80) cc_final: 0.8905 (m-80) REVERT: A 376 GLU cc_start: 0.8162 (mp0) cc_final: 0.7818 (mp0) REVERT: A 486 ARG cc_start: 0.8625 (mtp85) cc_final: 0.8202 (ttp-110) REVERT: A 525 CYS cc_start: 0.7454 (t) cc_final: 0.7155 (t) REVERT: A 526 ILE cc_start: 0.8352 (mm) cc_final: 0.8075 (mt) REVERT: B 145 ARG cc_start: 0.7650 (ttm110) cc_final: 0.7348 (ttm110) REVERT: B 170 LYS cc_start: 0.9075 (tttm) cc_final: 0.8810 (mmmt) REVERT: B 530 ASP cc_start: 0.8928 (t0) cc_final: 0.8725 (t0) REVERT: C 1430 SER cc_start: 0.7484 (t) cc_final: 0.6839 (p) REVERT: C 1459 TYR cc_start: 0.6948 (m-80) cc_final: 0.5781 (m-10) outliers start: 61 outliers final: 48 residues processed: 327 average time/residue: 0.0933 time to fit residues: 43.5743 Evaluate side-chains 342 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 294 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 206 THR Chi-restraints excluded: chain A residue 256 GLN 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 492 LEU Chi-restraints excluded: chain A residue 507 VAL 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 37 GLN Chi-restraints excluded: chain B residue 78 THR 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 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 1460 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 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 45 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 224 GLN A 346 GLN A 544 HIS B 491 GLN C1444 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.161808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118560 restraints weight = 12729.143| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.22 r_work: 0.3131 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10108 Z= 0.179 Angle : 0.635 12.392 13753 Z= 0.318 Chirality : 0.047 0.202 1575 Planarity : 0.004 0.060 1740 Dihedral : 4.704 54.712 1388 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.77 % Favored : 97.15 % Rotamer: Outliers : 6.00 % Allowed : 20.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.23), residues: 1265 helix: 0.14 (0.50), residues: 119 sheet: -0.37 (0.26), residues: 371 loop : -0.67 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 494 TYR 0.027 0.001 TYR B 330 PHE 0.019 0.002 PHE C1474 TRP 0.012 0.001 TRP B 216 HIS 0.003 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (10084) covalent geometry : angle 0.62129 / 0.32 (13695) SS BOND : bond 0.00308 / 0.17 ( 14) SS BOND : angle 0.94698 / 0.54 ( 28) hydrogen bonds : bond 0.03623 / 2.36 ( 315) hydrogen bonds : angle 6.37347 / 4.31 ( 828) link_BETA1-4 : bond 0.00239 / 0.14 ( 3) link_BETA1-4 : angle 1.15939 / 0.82 ( 9) link_NAG-ASN : bond 0.00259 / 0.14 ( 7) link_NAG-ASN : angle 3.19820 / 2.00 ( 21) *********************** 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 368 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 309 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 92 SER cc_start: 0.8598 (t) cc_final: 0.8186 (p) REVERT: A 319 TYR cc_start: 0.8382 (m-80) cc_final: 0.8041 (m-80) REVERT: A 330 TYR cc_start: 0.9148 (m-80) cc_final: 0.8906 (m-80) REVERT: A 376 GLU cc_start: 0.8176 (mp0) cc_final: 0.7873 (mp0) REVERT: A 476 LYS cc_start: 0.8932 (mttt) cc_final: 0.8604 (mttm) REVERT: A 486 ARG cc_start: 0.8670 (mtp85) cc_final: 0.8227 (ttp-110) REVERT: A 514 ARG cc_start: 0.7936 (ttm110) cc_final: 0.7683 (ttm-80) REVERT: A 525 CYS cc_start: 0.7423 (t) cc_final: 0.7113 (t) REVERT: A 526 ILE cc_start: 0.8328 (mm) cc_final: 0.8050 (mt) REVERT: B 145 ARG cc_start: 0.7661 (ttm110) cc_final: 0.6896 (ttm110) REVERT: B 170 LYS cc_start: 0.9066 (tttm) cc_final: 0.8796 (mmmt) REVERT: B 199 ARG cc_start: 0.8534 (ttt-90) cc_final: 0.7798 (ttt-90) REVERT: B 345 GLU cc_start: 0.7600 (pm20) cc_final: 0.7141 (pm20) REVERT: B 530 ASP cc_start: 0.8895 (t0) cc_final: 0.8596 (t0) REVERT: C 1430 SER cc_start: 0.7513 (t) cc_final: 0.6888 (p) REVERT: C 1459 TYR cc_start: 0.6864 (m-80) cc_final: 0.5605 (m-10) outliers start: 59 outliers final: 48 residues processed: 330 average time/residue: 0.0938 time to fit residues: 44.0871 Evaluate side-chains 352 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 304 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 99 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 256 GLN 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 354 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 470 SER 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 239 ILE Chi-restraints excluded: chain B residue 268 VAL 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 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 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 28 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 103 optimal weight: 0.0870 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 0.2980 chunk 94 optimal weight: 7.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 346 GLN A 544 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.165524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122694 restraints weight = 12668.754| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.22 r_work: 0.3190 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3372 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= 0.110 Angle : 0.607 11.127 13753 Z= 0.304 Chirality : 0.046 0.182 1575 Planarity : 0.004 0.060 1740 Dihedral : 4.495 52.011 1388 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.45 % Favored : 97.47 % Rotamer: Outliers : 3.97 % Allowed : 23.19 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.23), residues: 1265 helix: 0.17 (0.50), residues: 121 sheet: -0.25 (0.27), residues: 361 loop : -0.62 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 494 TYR 0.020 0.001 TYR B 330 PHE 0.021 0.001 PHE C1474 TRP 0.010 0.001 TRP B 216 HIS 0.002 0.000 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (10084) covalent geometry : angle 0.59366 / 0.30 (13695) SS BOND : bond 0.00255 / 0.13 ( 14) SS BOND : angle 0.72210 / 0.46 ( 28) hydrogen bonds : bond 0.03253 / 2.10 ( 315) hydrogen bonds : angle 6.14926 / 4.15 ( 828) link_BETA1-4 : bond 0.00334 / 0.19 ( 3) link_BETA1-4 : angle 1.07950 / 0.74 ( 9) link_NAG-ASN : bond 0.00200 / 0.12 ( 7) link_NAG-ASN : angle 3.25345 / 2.13 ( 21) *********************** 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 368 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 329 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8292 (ppp) cc_final: 0.7975 (ppp) REVERT: A 64 MET cc_start: 0.8949 (mpp) cc_final: 0.8741 (mpp) REVERT: A 158 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: A 270 GLU cc_start: 0.8030 (tt0) cc_final: 0.7520 (tt0) REVERT: A 376 GLU cc_start: 0.8150 (mp0) cc_final: 0.7818 (mp0) REVERT: A 486 ARG cc_start: 0.8642 (mtp85) cc_final: 0.8185 (ttp-110) REVERT: A 514 ARG cc_start: 0.7580 (ttm110) cc_final: 0.7343 (ttm-80) REVERT: B 145 ARG cc_start: 0.7416 (ttm110) cc_final: 0.7096 (ttm110) REVERT: B 170 LYS cc_start: 0.9056 (tttm) cc_final: 0.8756 (mmmt) REVERT: B 276 PHE cc_start: 0.8950 (t80) cc_final: 0.8496 (t80) REVERT: B 530 ASP cc_start: 0.8874 (t0) cc_final: 0.8510 (t0) REVERT: C 1430 SER cc_start: 0.7394 (t) cc_final: 0.6771 (p) REVERT: C 1459 TYR cc_start: 0.6461 (m-80) cc_final: 0.5200 (m-10) outliers start: 39 outliers final: 26 residues processed: 343 average time/residue: 0.0892 time to fit residues: 44.0934 Evaluate side-chains 337 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 310 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 103 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 285 VAL 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 C residue 1437 ILE Chi-restraints excluded: chain C residue 1516 ILE Chi-restraints excluded: chain C residue 1532 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 110 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 69 optimal weight: 5.9990 chunk 119 optimal weight: 40.0000 chunk 112 optimal weight: 0.0050 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 346 GLN A 544 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.164561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121651 restraints weight = 12697.381| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.22 r_work: 0.3170 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10108 Z= 0.135 Angle : 0.607 9.856 13753 Z= 0.304 Chirality : 0.047 0.193 1575 Planarity : 0.004 0.060 1740 Dihedral : 4.510 52.295 1388 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.92 % Rotamer: Outliers : 3.97 % Allowed : 22.48 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.23), residues: 1265 helix: 0.30 (0.51), residues: 120 sheet: -0.11 (0.27), residues: 374 loop : -0.65 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 55 TYR 0.013 0.001 TYR B 330 PHE 0.012 0.001 PHE B 406 TRP 0.008 0.001 TRP B 216 HIS 0.003 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (10084) covalent geometry : angle 0.59342 / 0.30 (13695) SS BOND : bond 0.00177 / 0.11 ( 14) SS BOND : angle 0.95326 / 0.54 ( 28) hydrogen bonds : bond 0.03379 / 2.23 ( 315) hydrogen bonds : angle 6.07444 / 4.10 ( 828) link_BETA1-4 : bond 0.00290 / 0.17 ( 3) link_BETA1-4 : angle 1.07523 / 0.74 ( 9) link_NAG-ASN : bond 0.00224 / 0.12 ( 7) link_NAG-ASN : angle 3.13436 / 2.11 ( 21) *********************** 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 350 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 311 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: A 376 GLU cc_start: 0.8146 (mp0) cc_final: 0.7833 (mp0) REVERT: A 377 ARG cc_start: 0.8136 (ptm-80) cc_final: 0.7766 (ptm-80) REVERT: A 486 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8181 (ttp-110) REVERT: A 525 CYS cc_start: 0.7387 (t) cc_final: 0.7074 (t) REVERT: B 145 ARG cc_start: 0.7403 (ttm110) cc_final: 0.7100 (ttm110) REVERT: B 170 LYS cc_start: 0.9053 (tttm) cc_final: 0.8754 (mmmt) REVERT: B 276 PHE cc_start: 0.8983 (t80) cc_final: 0.8606 (t80) REVERT: B 530 ASP cc_start: 0.8866 (t0) cc_final: 0.8479 (t0) REVERT: C 1430 SER cc_start: 0.7448 (t) cc_final: 0.6909 (p) outliers start: 39 outliers final: 31 residues processed: 324 average time/residue: 0.0911 time to fit residues: 42.5429 Evaluate side-chains 340 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 308 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 103 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 416 VAL 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 551 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 239 ILE 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 C residue 1492 SER Chi-restraints excluded: chain C residue 1516 ILE Chi-restraints excluded: chain C residue 1532 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 7.9990 chunk 38 optimal weight: 0.2980 chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 78 optimal weight: 0.2980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN A 544 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.165277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121876 restraints weight = 12582.877| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.25 r_work: 0.3182 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10108 Z= 0.125 Angle : 0.601 9.711 13753 Z= 0.302 Chirality : 0.046 0.178 1575 Planarity : 0.004 0.060 1740 Dihedral : 4.457 51.683 1388 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 4.17 % Allowed : 22.69 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.23), residues: 1265 helix: 0.31 (0.51), residues: 120 sheet: -0.07 (0.27), residues: 374 loop : -0.63 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 494 TYR 0.013 0.001 TYR B 330 PHE 0.021 0.001 PHE C1474 TRP 0.013 0.001 TRP B 216 HIS 0.002 0.000 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10084) covalent geometry : angle 0.59199 / 0.30 (13695) SS BOND : bond 0.00167 / 0.10 ( 14) SS BOND : angle 0.71948 / 0.43 ( 28) hydrogen bonds : bond 0.03268 / 2.14 ( 315) hydrogen bonds : angle 6.06615 / 4.09 ( 828) link_BETA1-4 : bond 0.00308 / 0.18 ( 3) link_BETA1-4 : angle 1.06980 / 0.76 ( 9) link_NAG-ASN : bond 0.00229 / 0.13 ( 7) link_NAG-ASN : angle 2.56347 / 1.65 ( 21) *********************** 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 361 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 320 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: A 342 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8157 (ptp90) REVERT: A 376 GLU cc_start: 0.8140 (mp0) cc_final: 0.7845 (mp0) REVERT: A 377 ARG cc_start: 0.8102 (ptm-80) cc_final: 0.7736 (ptm-80) REVERT: A 453 ARG cc_start: 0.8484 (mtt180) cc_final: 0.8172 (mtt90) REVERT: A 486 ARG cc_start: 0.8682 (mtp85) cc_final: 0.8273 (ttp-110) REVERT: A 525 CYS cc_start: 0.7367 (t) cc_final: 0.7051 (t) REVERT: B 145 ARG cc_start: 0.7520 (ttm110) cc_final: 0.6784 (ttm110) REVERT: B 162 MET cc_start: 0.8602 (ttm) cc_final: 0.8306 (ttp) REVERT: B 170 LYS cc_start: 0.9052 (tttm) cc_final: 0.8764 (mmmt) REVERT: B 276 PHE cc_start: 0.8964 (t80) cc_final: 0.8701 (t80) REVERT: B 494 ARG cc_start: 0.8403 (ttm110) cc_final: 0.8037 (mtp85) REVERT: B 530 ASP cc_start: 0.8843 (t0) cc_final: 0.8444 (t0) REVERT: C 1430 SER cc_start: 0.7564 (t) cc_final: 0.6931 (p) outliers start: 41 outliers final: 37 residues processed: 332 average time/residue: 0.0854 time to fit residues: 40.9090 Evaluate side-chains 343 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 305 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 103 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 354 THR 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 551 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 239 ILE 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 354 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain C residue 1460 ILE Chi-restraints excluded: chain C residue 1511 LYS Chi-restraints excluded: chain C residue 1516 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 93 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN A 544 HIS C1467 ASN C1496 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.159409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.115747 restraints weight = 12650.630| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.23 r_work: 0.3056 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 10108 Z= 0.301 Angle : 0.679 9.925 13753 Z= 0.347 Chirality : 0.050 0.186 1575 Planarity : 0.005 0.075 1740 Dihedral : 4.773 55.484 1388 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.18 % Rotamer: Outliers : 5.09 % Allowed : 21.97 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.24), residues: 1265 helix: 0.25 (0.51), residues: 120 sheet: -0.18 (0.27), residues: 377 loop : -0.71 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 494 TYR 0.020 0.002 TYR B 330 PHE 0.022 0.002 PHE B 251 TRP 0.015 0.002 TRP B 216 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.30 (10084) covalent geometry : angle 0.66988 / 0.34 (13695) SS BOND : bond 0.00374 / 0.22 ( 14) SS BOND : angle 1.18552 / 0.73 ( 28) hydrogen bonds : bond 0.03810 / 2.52 ( 315) hydrogen bonds : angle 6.32418 / 4.29 ( 828) link_BETA1-4 : bond 0.00217 / 0.14 ( 3) link_BETA1-4 : angle 1.21096 / 0.87 ( 9) link_NAG-ASN : bond 0.00342 / 0.19 ( 7) link_NAG-ASN : angle 2.60834 / 1.62 ( 21) ********************** 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 350 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 300 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8885 (m-30) cc_final: 0.8673 (m-30) REVERT: A 158 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: A 206 THR cc_start: 0.9287 (p) cc_final: 0.9043 (t) REVERT: A 376 GLU cc_start: 0.8226 (mp0) cc_final: 0.7911 (mp0) REVERT: A 391 PHE cc_start: 0.8381 (t80) cc_final: 0.8177 (t80) REVERT: A 486 ARG cc_start: 0.8704 (mtp85) cc_final: 0.8261 (ttp-110) REVERT: A 525 CYS cc_start: 0.7568 (t) cc_final: 0.7273 (t) REVERT: A 526 ILE cc_start: 0.8433 (mm) cc_final: 0.8198 (mt) REVERT: B 145 ARG cc_start: 0.7611 (ttm110) cc_final: 0.6948 (ttm110) REVERT: B 170 LYS cc_start: 0.9075 (tttm) cc_final: 0.8848 (mmmt) REVERT: B 345 GLU cc_start: 0.7690 (pm20) cc_final: 0.7268 (pm20) REVERT: B 530 ASP cc_start: 0.8898 (t0) cc_final: 0.8556 (t0) REVERT: C 1430 SER cc_start: 0.7804 (t) cc_final: 0.7306 (p) REVERT: C 1466 ASP cc_start: 0.7825 (t0) cc_final: 0.7624 (t0) REVERT: C 1526 LEU cc_start: 0.7226 (pp) cc_final: 0.6814 (pp) outliers start: 50 outliers final: 42 residues processed: 317 average time/residue: 0.0861 time to fit residues: 39.4598 Evaluate side-chains 331 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 288 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 103 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 354 THR 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 206 THR 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 334 ASP Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain C residue 1460 ILE Chi-restraints excluded: chain C residue 1467 ASN Chi-restraints excluded: chain C residue 1492 SER Chi-restraints excluded: chain C residue 1516 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 49 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 17 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 28 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN A 544 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.160214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116249 restraints weight = 12811.472| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.27 r_work: 0.3099 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.176 10108 Z= 0.291 Angle : 0.954 59.079 13753 Z= 0.543 Chirality : 0.056 0.951 1575 Planarity : 0.005 0.065 1740 Dihedral : 4.803 55.370 1388 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.66 % Favored : 95.18 % Rotamer: Outliers : 5.09 % Allowed : 21.77 % Favored : 73.14 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.24), residues: 1265 helix: 0.27 (0.52), residues: 120 sheet: -0.21 (0.27), residues: 377 loop : -0.71 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 494 TYR 0.020 0.002 TYR B 330 PHE 0.019 0.002 PHE C1474 TRP 0.013 0.001 TRP B 216 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.29 (10084) covalent geometry : angle 0.93928 / 0.54 (13695) SS BOND : bond 0.00275 / 0.16 ( 14) SS BOND : angle 1.17379 / 0.71 ( 28) hydrogen bonds : bond 0.03746 / 2.48 ( 315) hydrogen bonds : angle 6.32894 / 4.29 ( 828) link_BETA1-4 : bond 0.00216 / 0.13 ( 3) link_BETA1-4 : angle 1.19022 / 0.86 ( 9) link_NAG-ASN : bond 0.01257 / 0.74 ( 7) link_NAG-ASN : angle 4.30935 / 3.45 ( 21) =============================================================================== Job complete usr+sys time: 2410.55 seconds wall clock time: 42 minutes 3.75 seconds (2523.75 seconds total)