Starting phenix.real_space_refine on Tue Aug 26 05:51:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zgh_60079/08_2025/8zgh_60079.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zgh_60079/08_2025/8zgh_60079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zgh_60079/08_2025/8zgh_60079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zgh_60079/08_2025/8zgh_60079.map" model { file = "/net/cci-nas-00/data/ceres_data/8zgh_60079/08_2025/8zgh_60079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zgh_60079/08_2025/8zgh_60079.cif" } resolution = 3.93 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.051 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: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 Fe 2 7.16 5 P 4 5.49 5 S 100 5.16 5 C 21174 2.51 5 N 6295 2.21 5 O 6515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34092 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5756 Classifications: {'peptide': 706} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 662} Chain: "B" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5756 Classifications: {'peptide': 706} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 662} Chain: "C" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 3476 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 620} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 662} Unresolved chain link angles: 43 Unresolved non-hydrogen bonds: 2449 Unresolved non-hydrogen angles: 3176 Unresolved non-hydrogen dihedrals: 2099 Unresolved non-hydrogen chiralities: 183 Planarities with less than four sites: {'ASN:plan1': 26, 'GLU:plan': 49, 'TYR:plan': 32, 'ARG:plan': 50, 'PHE:plan': 36, 'TRP:plan': 17, 'ASP:plan': 47, 'GLN:plan1': 29, 'HIS:plan': 23} Unresolved non-hydrogen planarities: 1489 Chain: "D" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 3476 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 620} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 662} Unresolved chain link angles: 43 Unresolved non-hydrogen bonds: 2449 Unresolved non-hydrogen angles: 3176 Unresolved non-hydrogen dihedrals: 2099 Unresolved non-hydrogen chiralities: 183 Planarities with less than four sites: {'ASN:plan1': 26, 'GLU:plan': 49, 'TYR:plan': 32, 'ARG:plan': 50, 'PHE:plan': 36, 'TRP:plan': 17, 'ASP:plan': 47, 'GLN:plan1': 29, 'HIS:plan': 23} Unresolved non-hydrogen planarities: 1489 Chain: "U" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4801 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 549} Chain: "V" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4801 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 549} Chain: "W" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 2916 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 518} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 549} Unresolved chain link angles: 37 Unresolved non-hydrogen bonds: 2014 Unresolved non-hydrogen angles: 2583 Unresolved non-hydrogen dihedrals: 1729 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'TYR:plan': 24, 'PHE:plan': 23, 'GLU:plan': 44, 'ARG:plan': 49, 'TRP:plan': 13, 'GLN:plan1': 19, 'ASN:plan1': 18, 'HIS:plan': 19, 'ASP:plan': 38} Unresolved non-hydrogen planarities: 1183 Chain: "X" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 2916 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 518} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 549} Unresolved chain link angles: 37 Unresolved non-hydrogen bonds: 2014 Unresolved non-hydrogen angles: 2583 Unresolved non-hydrogen dihedrals: 1729 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'TYR:plan': 24, 'PHE:plan': 23, 'GLU:plan': 44, 'ARG:plan': 49, 'TRP:plan': 13, 'GLN:plan1': 19, 'ASN:plan1': 18, 'HIS:plan': 19, 'ASP:plan': 38} Unresolved non-hydrogen planarities: 1183 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {'AKG': 1, 'FE2': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {'AKG': 1, 'FE2': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' MN': 1, 'GDU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' MN': 1, 'GDU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.34, per 1000 atoms: 0.24 Number of scatterers: 34092 At special positions: 0 Unit cell: (178.2, 226.6, 238.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 Mn 2 24.99 S 100 16.00 P 4 15.00 O 6515 8.00 N 6295 7.00 C 21174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 385 " distance=2.03 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 385 " distance=2.04 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 698 " distance=2.03 Simple disulfide: pdb=" SG CYS U 228 " - pdb=" SG CYS U 283 " distance=2.05 Simple disulfide: pdb=" SG CYS V 228 " - pdb=" SG CYS V 283 " distance=2.05 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 801 " - " ASN A 548 " " NAG B 801 " - " ASN B 63 " " NAG B 802 " - " ASN B 548 " " NAG E 1 " - " ASN U 184 " " NAG F 1 " - " ASN V 184 " Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9760 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 58 sheets defined 32.8% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 49 through 62 removed outlier: 3.912A pdb=" N PHE A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 97 Processing helix chain 'A' and resid 98 through 101 Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 191 through 201 removed outlier: 4.026A pdb=" N ASP A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 225 through 229 removed outlier: 4.028A pdb=" N VAL A 229 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 310 through 320 removed outlier: 3.984A pdb=" N LEU A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU A 320 " --> pdb=" O GLN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 327 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 354 Proline residue: A 348 - end of helix Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.801A pdb=" N GLU A 364 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 Processing helix chain 'A' and resid 401 through 410 removed outlier: 4.130A pdb=" N ASN A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 removed outlier: 3.564A pdb=" N GLN A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 488 through 500 removed outlier: 3.544A pdb=" N ASP A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS A 500 " --> pdb=" O SER A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 544 Processing helix chain 'A' and resid 548 through 555 Processing helix chain 'A' and resid 573 through 588 Processing helix chain 'A' and resid 614 through 618 removed outlier: 3.558A pdb=" N GLY A 618 " --> pdb=" O MET A 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 618' Processing helix chain 'A' and resid 619 through 631 removed outlier: 3.518A pdb=" N VAL A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 639 Processing helix chain 'B' and resid 49 through 62 removed outlier: 3.600A pdb=" N LEU B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE B 62 " --> pdb=" O SER B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 98 removed outlier: 3.879A pdb=" N ARG B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 148 through 152 removed outlier: 4.479A pdb=" N GLU B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.854A pdb=" N ASP B 201 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 258 through 266 removed outlier: 3.549A pdb=" N LEU B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 318 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 339 through 354 removed outlier: 3.659A pdb=" N ILE B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) Proline residue: B 348 - end of helix Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.878A pdb=" N GLU B 364 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 382 removed outlier: 3.833A pdb=" N ASP B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 410 removed outlier: 4.056A pdb=" N ASN B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 449 removed outlier: 3.762A pdb=" N GLN B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.500A pdb=" N LEU B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 500 removed outlier: 4.038A pdb=" N LYS B 500 " --> pdb=" O SER B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 536 through 544 Processing helix chain 'B' and resid 548 through 555 Processing helix chain 'B' and resid 573 through 588 Processing helix chain 'B' and resid 614 through 618 Processing helix chain 'B' and resid 619 through 631 removed outlier: 3.551A pdb=" N VAL B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 49 through 62 removed outlier: 3.514A pdb=" N PHE C 62 " --> pdb=" O SER C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 97 removed outlier: 4.118A pdb=" N VAL C 90 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG C 91 " --> pdb=" O GLY C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 133 Processing helix chain 'C' and resid 148 through 152 removed outlier: 3.973A pdb=" N GLU C 152 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 190 through 201 removed outlier: 4.175A pdb=" N PHE C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP C 201 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 209 Processing helix chain 'C' and resid 258 through 266 Processing helix chain 'C' and resid 310 through 319 removed outlier: 3.745A pdb=" N LEU C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 339 through 354 Proline residue: C 348 - end of helix Processing helix chain 'C' and resid 361 through 365 removed outlier: 3.757A pdb=" N GLU C 364 " --> pdb=" O GLY C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 382 Processing helix chain 'C' and resid 401 through 410 removed outlier: 3.946A pdb=" N ASN C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 449 Processing helix chain 'C' and resid 469 through 475 Processing helix chain 'C' and resid 488 through 500 Processing helix chain 'C' and resid 527 through 534 removed outlier: 4.035A pdb=" N ILE C 533 " --> pdb=" O LEU C 530 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE C 534 " --> pdb=" O TRP C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 548 through 555 removed outlier: 3.505A pdb=" N GLY C 555 " --> pdb=" O ARG C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 588 Processing helix chain 'C' and resid 614 through 618 Processing helix chain 'C' and resid 619 through 630 Processing helix chain 'C' and resid 630 through 639 Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 49 through 62 Processing helix chain 'D' and resid 86 through 98 removed outlier: 3.839A pdb=" N VAL D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 133 Processing helix chain 'D' and resid 148 through 152 removed outlier: 3.638A pdb=" N GLU D 152 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 190 through 201 removed outlier: 4.115A pdb=" N PHE D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 209 Processing helix chain 'D' and resid 225 through 229 removed outlier: 3.983A pdb=" N VAL D 229 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 267 Processing helix chain 'D' and resid 310 through 319 removed outlier: 3.564A pdb=" N PHE D 314 " --> pdb=" O PHE D 310 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 339 through 354 Proline residue: D 348 - end of helix Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 367 through 382 Processing helix chain 'D' and resid 401 through 410 removed outlier: 3.780A pdb=" N ASN D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 448 Processing helix chain 'D' and resid 469 through 475 Processing helix chain 'D' and resid 488 through 500 Processing helix chain 'D' and resid 527 through 532 Processing helix chain 'D' and resid 536 through 545 Processing helix chain 'D' and resid 548 through 555 Processing helix chain 'D' and resid 573 through 588 removed outlier: 3.554A pdb=" N GLY D 588 " --> pdb=" O MET D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 618 Processing helix chain 'D' and resid 619 through 630 Processing helix chain 'D' and resid 630 through 639 removed outlier: 3.634A pdb=" N MET D 634 " --> pdb=" O TYR D 630 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 76 removed outlier: 3.662A pdb=" N ARG U 76 " --> pdb=" O GLY U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 107 removed outlier: 3.775A pdb=" N VAL U 100 " --> pdb=" O ASN U 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 139 through 144 Processing helix chain 'U' and resid 145 through 147 No H-bonds generated for 'chain 'U' and resid 145 through 147' Processing helix chain 'U' and resid 175 through 182 Processing helix chain 'U' and resid 217 through 222 Processing helix chain 'U' and resid 244 through 249 removed outlier: 3.776A pdb=" N ARG U 248 " --> pdb=" O ALA U 245 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN U 249 " --> pdb=" O ALA U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 273 Processing helix chain 'U' and resid 300 through 315 removed outlier: 3.594A pdb=" N GLU U 304 " --> pdb=" O THR U 300 " (cutoff:3.500A) Processing helix chain 'U' and resid 352 through 365 removed outlier: 3.622A pdb=" N GLU U 356 " --> pdb=" O GLN U 352 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG U 357 " --> pdb=" O ASP U 353 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET U 358 " --> pdb=" O ARG U 354 " (cutoff:3.500A) Processing helix chain 'U' and resid 381 through 388 Processing helix chain 'U' and resid 406 through 427 removed outlier: 3.794A pdb=" N LEU U 410 " --> pdb=" O THR U 406 " (cutoff:3.500A) Processing helix chain 'U' and resid 443 through 459 Processing helix chain 'U' and resid 503 through 511 Processing helix chain 'U' and resid 520 through 529 Proline residue: U 526 - end of helix removed outlier: 3.641A pdb=" N PHE U 529 " --> pdb=" O LEU U 525 " (cutoff:3.500A) Processing helix chain 'U' and resid 534 through 541 removed outlier: 3.729A pdb=" N LYS U 538 " --> pdb=" O VAL U 534 " (cutoff:3.500A) Processing helix chain 'U' and resid 569 through 573 removed outlier: 4.067A pdb=" N GLU U 572 " --> pdb=" O SER U 569 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 76 removed outlier: 3.986A pdb=" N ARG V 76 " --> pdb=" O GLY V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 109 Processing helix chain 'V' and resid 136 through 154 Processing helix chain 'V' and resid 175 through 182 Processing helix chain 'V' and resid 217 through 222 Processing helix chain 'V' and resid 244 through 249 removed outlier: 3.512A pdb=" N ARG V 248 " --> pdb=" O ALA V 245 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN V 249 " --> pdb=" O ALA V 246 " (cutoff:3.500A) Processing helix chain 'V' and resid 268 through 276 removed outlier: 3.727A pdb=" N SER V 272 " --> pdb=" O VAL V 268 " (cutoff:3.500A) Processing helix chain 'V' and resid 300 through 316 removed outlier: 3.545A pdb=" N GLU V 304 " --> pdb=" O THR V 300 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET V 316 " --> pdb=" O GLN V 312 " (cutoff:3.500A) Processing helix chain 'V' and resid 352 through 365 removed outlier: 3.724A pdb=" N GLU V 356 " --> pdb=" O GLN V 352 " (cutoff:3.500A) Processing helix chain 'V' and resid 381 through 386 Processing helix chain 'V' and resid 387 through 389 No H-bonds generated for 'chain 'V' and resid 387 through 389' Processing helix chain 'V' and resid 407 through 427 Processing helix chain 'V' and resid 443 through 459 Processing helix chain 'V' and resid 503 through 513 removed outlier: 4.028A pdb=" N GLU V 513 " --> pdb=" O LEU V 509 " (cutoff:3.500A) Processing helix chain 'V' and resid 520 through 529 Proline residue: V 526 - end of helix removed outlier: 3.873A pdb=" N PHE V 529 " --> pdb=" O LEU V 525 " (cutoff:3.500A) Processing helix chain 'V' and resid 534 through 541 removed outlier: 3.939A pdb=" N LYS V 538 " --> pdb=" O VAL V 534 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 65 No H-bonds generated for 'chain 'W' and resid 63 through 65' Processing helix chain 'W' and resid 66 through 75 removed outlier: 3.641A pdb=" N ALA W 73 " --> pdb=" O THR W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 96 through 108 removed outlier: 3.558A pdb=" N VAL W 100 " --> pdb=" O ASN W 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 136 through 154 Processing helix chain 'W' and resid 175 through 183 Processing helix chain 'W' and resid 216 through 222 Processing helix chain 'W' and resid 244 through 250 Processing helix chain 'W' and resid 264 through 276 removed outlier: 3.627A pdb=" N PHE W 269 " --> pdb=" O ASP W 265 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA W 270 " --> pdb=" O ILE W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 300 through 319 removed outlier: 3.677A pdb=" N GLU W 304 " --> pdb=" O THR W 300 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS W 318 " --> pdb=" O GLU W 314 " (cutoff:3.500A) Processing helix chain 'W' and resid 352 through 365 Processing helix chain 'W' and resid 381 through 386 removed outlier: 3.787A pdb=" N GLU W 386 " --> pdb=" O THR W 382 " (cutoff:3.500A) Processing helix chain 'W' and resid 406 through 427 Processing helix chain 'W' and resid 443 through 459 Processing helix chain 'W' and resid 503 through 513 Processing helix chain 'W' and resid 520 through 529 Proline residue: W 526 - end of helix Processing helix chain 'W' and resid 534 through 541 removed outlier: 4.018A pdb=" N LYS W 538 " --> pdb=" O VAL W 534 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 76 removed outlier: 3.756A pdb=" N GLY X 72 " --> pdb=" O PRO X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 109 removed outlier: 3.566A pdb=" N VAL X 100 " --> pdb=" O ASN X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 136 through 157 Processing helix chain 'X' and resid 175 through 180 Processing helix chain 'X' and resid 181 through 183 No H-bonds generated for 'chain 'X' and resid 181 through 183' Processing helix chain 'X' and resid 216 through 222 removed outlier: 3.694A pdb=" N LYS X 222 " --> pdb=" O ILE X 218 " (cutoff:3.500A) Processing helix chain 'X' and resid 244 through 250 removed outlier: 3.514A pdb=" N ASN X 249 " --> pdb=" O ALA X 246 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU X 250 " --> pdb=" O SER X 247 " (cutoff:3.500A) Processing helix chain 'X' and resid 267 through 275 removed outlier: 3.527A pdb=" N SER X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 300 through 319 removed outlier: 4.263A pdb=" N LYS X 318 " --> pdb=" O GLU X 314 " (cutoff:3.500A) Processing helix chain 'X' and resid 352 through 366 Processing helix chain 'X' and resid 381 through 386 Processing helix chain 'X' and resid 387 through 389 No H-bonds generated for 'chain 'X' and resid 387 through 389' Processing helix chain 'X' and resid 406 through 427 Processing helix chain 'X' and resid 443 through 459 Processing helix chain 'X' and resid 503 through 513 Processing helix chain 'X' and resid 520 through 529 Proline residue: X 526 - end of helix Processing helix chain 'X' and resid 534 through 541 removed outlier: 3.821A pdb=" N LYS X 538 " --> pdb=" O VAL X 534 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 69 removed outlier: 8.063A pdb=" N ARG A 67 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL A 41 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU A 69 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR A 43 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL A 44 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 171 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N SER A 166 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 10.639A pdb=" N GLU A 141 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY A 168 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 139 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.874A pdb=" N VAL A 252 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 230 through 231 Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 274 removed outlier: 3.927A pdb=" N THR A 274 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 300 removed outlier: 3.549A pdb=" N PHE A 389 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR A 465 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 302 through 304 removed outlier: 3.518A pdb=" N VAL A 304 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 358 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 332 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 360 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 334 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 396 through 397 removed outlier: 3.551A pdb=" N ARG A 514 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 455 through 458 removed outlier: 4.131A pdb=" N LEU A 504 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 567 through 570 removed outlier: 5.478A pdb=" N TRP A 707 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 678 " --> pdb=" O TRP A 707 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS A 711 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE A 673 " --> pdb=" O VAL A 736 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 736 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 735 " --> pdb=" O MET A 650 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N MET A 650 " --> pdb=" O PHE A 735 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 653 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB2, first strand: chain 'A' and resid 698 through 699 Processing sheet with id=AB3, first strand: chain 'B' and resid 66 through 67 removed outlier: 8.041A pdb=" N ARG B 67 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL B 41 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY B 168 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU B 136 " --> pdb=" O ASN B 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.615A pdb=" N VAL B 252 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.551A pdb=" N ARG B 239 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 359 through 360 removed outlier: 3.780A pdb=" N VAL B 360 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN B 334 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ALA B 301 " --> pdb=" O LEU B 391 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 395 through 396 Processing sheet with id=AB8, first strand: chain 'B' and resid 431 through 432 Processing sheet with id=AB9, first strand: chain 'B' and resid 455 through 458 removed outlier: 3.901A pdb=" N LEU B 506 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU B 504 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 567 through 570 removed outlier: 5.218A pdb=" N TRP B 707 " --> pdb=" O ALA B 678 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B 678 " --> pdb=" O TRP B 707 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS B 711 " --> pdb=" O THR B 674 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE B 673 " --> pdb=" O VAL B 736 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 736 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N MET B 650 " --> pdb=" O PHE B 735 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 686 through 687 Processing sheet with id=AC3, first strand: chain 'B' and resid 698 through 699 Processing sheet with id=AC4, first strand: chain 'C' and resid 66 through 69 removed outlier: 8.330A pdb=" N ARG C 67 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL C 41 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU C 69 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR C 43 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU C 40 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL C 111 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE C 42 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N GLY C 167 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 11.712A pdb=" N LEU C 137 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU C 136 " --> pdb=" O ASN C 211 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 116 through 118 removed outlier: 6.103A pdb=" N GLN C 220 " --> pdb=" O HIS C 253 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 230 through 233 Processing sheet with id=AC7, first strand: chain 'C' and resid 356 through 360 removed outlier: 4.037A pdb=" N ALA C 356 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL C 298 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE C 331 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU C 300 " --> pdb=" O PHE C 331 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N HIS C 333 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL C 302 " --> pdb=" O HIS C 333 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE C 389 " --> pdb=" O PHE C 299 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL C 413 " --> pdb=" O HIS C 505 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N SER C 507 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA C 415 " --> pdb=" O SER C 507 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C 504 " --> pdb=" O VAL C 458 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 418 through 419 removed outlier: 3.936A pdb=" N SER C 419 " --> pdb=" O GLY C 513 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 431 through 432 Processing sheet with id=AD1, first strand: chain 'C' and resid 568 through 570 removed outlier: 6.132A pdb=" N TRP C 707 " --> pdb=" O ALA C 678 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 678 " --> pdb=" O TRP C 707 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE C 673 " --> pdb=" O VAL C 736 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 736 " --> pdb=" O PHE C 673 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU C 675 " --> pdb=" O SER C 734 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 734 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET C 650 " --> pdb=" O PHE C 735 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 686 through 688 Processing sheet with id=AD3, first strand: chain 'C' and resid 691 through 693 Processing sheet with id=AD4, first strand: chain 'D' and resid 66 through 69 removed outlier: 8.057A pdb=" N ARG D 67 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL D 41 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU D 69 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR D 43 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU D 40 " --> pdb=" O MET D 109 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL D 111 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE D 42 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP D 112 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N GLY D 167 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER D 139 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N GLY D 167 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N LEU D 137 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU D 136 " --> pdb=" O ASN D 211 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 116 through 118 removed outlier: 3.608A pdb=" N VAL D 252 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS D 253 " --> pdb=" O GLN D 220 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 232 through 233 removed outlier: 3.612A pdb=" N LYS D 232 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG D 239 " --> pdb=" O LYS D 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 359 through 360 removed outlier: 3.538A pdb=" N VAL D 360 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN D 334 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL D 298 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N PHE D 331 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU D 300 " --> pdb=" O PHE D 331 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N HIS D 333 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL D 302 " --> pdb=" O HIS D 333 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE D 299 " --> pdb=" O PHE D 389 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU D 391 " --> pdb=" O PHE D 299 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA D 301 " --> pdb=" O LEU D 391 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 396 through 397 Processing sheet with id=AD9, first strand: chain 'D' and resid 431 through 432 removed outlier: 3.688A pdb=" N ALA D 431 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 456 through 457 Processing sheet with id=AE2, first strand: chain 'D' and resid 567 through 570 removed outlier: 3.551A pdb=" N PHE D 569 " --> pdb=" O ALA D 708 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP D 707 " --> pdb=" O ALA D 678 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA D 678 " --> pdb=" O TRP D 707 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET D 650 " --> pdb=" O PHE D 735 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 686 through 687 Processing sheet with id=AE4, first strand: chain 'D' and resid 698 through 699 removed outlier: 3.563A pdb=" N CYS D 698 " --> pdb=" O PHE D 693 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'U' and resid 59 through 60 removed outlier: 3.666A pdb=" N ALA U 60 " --> pdb=" O ALA U 89 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP U 91 " --> pdb=" O ALA U 60 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N THR U 84 " --> pdb=" O SER U 114 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLU U 116 " --> pdb=" O THR U 84 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU U 86 " --> pdb=" O GLU U 116 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ARG U 118 " --> pdb=" O LEU U 86 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL U 88 " --> pdb=" O ARG U 118 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N ALA U 120 " --> pdb=" O VAL U 88 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N THR U 90 " --> pdb=" O ALA U 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'U' and resid 59 through 60 removed outlier: 3.666A pdb=" N ALA U 60 " --> pdb=" O ALA U 89 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP U 91 " --> pdb=" O ALA U 60 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU U 55 " --> pdb=" O LEU U 163 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE U 238 " --> pdb=" O PHE U 164 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL U 188 " --> pdb=" O LEU U 239 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL U 187 " --> pdb=" O TYR U 281 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N CYS U 283 " --> pdb=" O VAL U 187 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA U 189 " --> pdb=" O CYS U 283 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL U 282 " --> pdb=" O PHE U 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE U 229 " --> pdb=" O VAL U 282 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'U' and resid 170 through 171 Processing sheet with id=AE8, first strand: chain 'U' and resid 371 through 373 removed outlier: 3.821A pdb=" N VAL U 372 " --> pdb=" O MET U 345 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN U 347 " --> pdb=" O VAL U 372 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU U 342 " --> pdb=" O LYS U 430 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR U 499 " --> pdb=" O VAL U 433 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA U 498 " --> pdb=" O VAL U 467 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL U 467 " --> pdb=" O ALA U 498 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'U' and resid 439 through 440 Processing sheet with id=AF1, first strand: chain 'U' and resid 488 through 489 Processing sheet with id=AF2, first strand: chain 'V' and resid 162 through 163 removed outlier: 3.636A pdb=" N ILE V 162 " --> pdb=" O ILE V 240 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL V 188 " --> pdb=" O LEU V 239 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'V' and resid 170 through 171 Processing sheet with id=AF4, first strand: chain 'V' and resid 370 through 371 removed outlier: 5.919A pdb=" N VAL V 343 " --> pdb=" O ARG V 370 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU V 342 " --> pdb=" O LYS V 430 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR V 499 " --> pdb=" O VAL V 433 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N TYR V 494 " --> pdb=" O ARG V 471 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG V 471 " --> pdb=" O TYR V 494 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR V 496 " --> pdb=" O ARG V 469 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ARG V 469 " --> pdb=" O THR V 496 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA V 498 " --> pdb=" O VAL V 467 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE V 465 " --> pdb=" O VAL V 500 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 487 through 489 Processing sheet with id=AF6, first strand: chain 'W' and resid 114 through 115 removed outlier: 5.940A pdb=" N LEU W 55 " --> pdb=" O LEU W 163 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE W 164 " --> pdb=" O PHE W 238 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL W 187 " --> pdb=" O TYR W 281 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N CYS W 283 " --> pdb=" O VAL W 187 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA W 189 " --> pdb=" O CYS W 283 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 59 through 60 removed outlier: 5.932A pdb=" N ALA W 60 " --> pdb=" O ASP W 91 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR W 90 " --> pdb=" O ALA W 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'W' and resid 170 through 171 Processing sheet with id=AF9, first strand: chain 'W' and resid 201 through 202 removed outlier: 3.886A pdb=" N MET W 233 " --> pdb=" O TRP W 202 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 370 through 371 removed outlier: 6.186A pdb=" N VAL W 343 " --> pdb=" O ARG W 370 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU W 342 " --> pdb=" O LYS W 430 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR W 496 " --> pdb=" O ARG W 469 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ARG W 469 " --> pdb=" O THR W 496 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA W 498 " --> pdb=" O VAL W 467 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL W 467 " --> pdb=" O ALA W 498 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 438 through 440 Processing sheet with id=AG3, first strand: chain 'X' and resid 189 through 190 removed outlier: 6.266A pdb=" N ALA X 189 " --> pdb=" O CYS X 283 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 370 through 373 removed outlier: 5.450A pdb=" N VAL X 343 " --> pdb=" O ARG X 370 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL X 372 " --> pdb=" O VAL X 343 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N MET X 345 " --> pdb=" O VAL X 372 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU X 342 " --> pdb=" O LYS X 430 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE X 434 " --> pdb=" O PHE X 344 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE X 346 " --> pdb=" O PHE X 434 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE X 501 " --> pdb=" O SER X 431 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL X 433 " --> pdb=" O TYR X 499 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR X 499 " --> pdb=" O VAL X 433 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR X 496 " --> pdb=" O GLY X 468 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY X 468 " --> pdb=" O THR X 496 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ALA X 498 " --> pdb=" O TYR X 466 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR X 466 " --> pdb=" O ALA X 498 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL X 500 " --> pdb=" O LEU X 464 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU X 464 " --> pdb=" O VAL X 500 " (cutoff:3.500A) 1210 hydrogen bonds defined for protein. 3429 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: 7.94 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11036 1.33 - 1.46: 8814 1.46 - 1.59: 14656 1.59 - 1.72: 4 1.72 - 1.85: 168 Bond restraints: 34678 Sorted by residual: bond pdb=" C1 AKG A 802 " pdb=" C2 AKG A 802 " ideal model delta sigma weight residual 1.559 1.484 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C1 AKG B 803 " pdb=" C2 AKG B 803 " ideal model delta sigma weight residual 1.559 1.492 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" O3A GDU U 701 " pdb=" PA GDU U 701 " ideal model delta sigma weight residual 1.647 1.589 0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" O3A GDU V 701 " pdb=" PA GDU V 701 " ideal model delta sigma weight residual 1.647 1.589 0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" C TRP A 273 " pdb=" N THR A 274 " ideal model delta sigma weight residual 1.331 1.277 0.054 2.07e-02 2.33e+03 6.80e+00 ... (remaining 34673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 47370 3.85 - 7.71: 155 7.71 - 11.56: 19 11.56 - 15.42: 0 15.42 - 19.27: 1 Bond angle restraints: 47545 Sorted by residual: angle pdb=" CA LEU V 359 " pdb=" CB LEU V 359 " pdb=" CG LEU V 359 " ideal model delta sigma weight residual 116.30 135.57 -19.27 3.50e+00 8.16e-02 3.03e+01 angle pdb=" C SER W 236 " pdb=" CA SER W 236 " pdb=" CB SER W 236 " ideal model delta sigma weight residual 117.23 110.16 7.07 1.36e+00 5.41e-01 2.70e+01 angle pdb=" N VAL U 467 " pdb=" CA VAL U 467 " pdb=" C VAL U 467 " ideal model delta sigma weight residual 113.20 108.45 4.75 9.60e-01 1.09e+00 2.45e+01 angle pdb=" C SER V 236 " pdb=" CA SER V 236 " pdb=" CB SER V 236 " ideal model delta sigma weight residual 117.23 110.68 6.55 1.36e+00 5.41e-01 2.32e+01 angle pdb=" N GLU X 621 " pdb=" CA GLU X 621 " pdb=" C GLU X 621 " ideal model delta sigma weight residual 114.75 109.06 5.69 1.26e+00 6.30e-01 2.04e+01 ... (remaining 47540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.89: 19481 25.89 - 51.78: 1093 51.78 - 77.67: 118 77.67 - 103.56: 20 103.56 - 129.45: 9 Dihedral angle restraints: 20721 sinusoidal: 5685 harmonic: 15036 Sorted by residual: dihedral pdb=" CB CYS A 563 " pdb=" SG CYS A 563 " pdb=" SG CYS A 698 " pdb=" CB CYS A 698 " ideal model delta sinusoidal sigma weight residual 93.00 170.71 -77.71 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 385 " pdb=" CB CYS A 385 " ideal model delta sinusoidal sigma weight residual 93.00 152.92 -59.92 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B 279 " pdb=" SG CYS B 279 " pdb=" SG CYS B 282 " pdb=" CB CYS B 282 " ideal model delta sinusoidal sigma weight residual -86.00 -35.51 -50.49 1 1.00e+01 1.00e-02 3.49e+01 ... (remaining 20718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 4153 0.046 - 0.093: 1045 0.093 - 0.139: 369 0.139 - 0.185: 14 0.185 - 0.231: 4 Chirality restraints: 5585 Sorted by residual: chirality pdb=" C1D GDU V 701 " pdb=" C2D GDU V 701 " pdb=" N1 GDU V 701 " pdb=" O4D GDU V 701 " both_signs ideal model delta sigma weight residual False 2.21 2.44 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C1 NAG B 802 " pdb=" ND2 ASN B 548 " pdb=" C2 NAG B 802 " pdb=" O5 NAG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C1D GDU U 701 " pdb=" C2D GDU U 701 " pdb=" N1 GDU U 701 " pdb=" O4D GDU U 701 " both_signs ideal model delta sigma weight residual False 2.21 2.40 -0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 5582 not shown) Planarity restraints: 6456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 92 " 0.025 2.00e-02 2.50e+03 1.65e-02 6.85e+00 pdb=" CG TRP B 92 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 92 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 92 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 92 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 92 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 92 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 92 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 92 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 382 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO A 383 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 383 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 383 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 458 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A 459 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 459 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 459 " 0.032 5.00e-02 4.00e+02 ... (remaining 6453 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 171 2.49 - 3.09: 24035 3.09 - 3.70: 49202 3.70 - 4.30: 61659 4.30 - 4.90: 103404 Nonbonded interactions: 238471 Sorted by model distance: nonbonded pdb=" O3A GDU U 701 " pdb="MN MN U 702 " model vdw 1.890 2.320 nonbonded pdb=" OG1 THR V 406 " pdb=" OG SER V 574 " model vdw 2.118 3.040 nonbonded pdb=" OH TYR U 259 " pdb=" O SER U 262 " model vdw 2.132 3.040 nonbonded pdb=" O1A GDU U 701 " pdb="MN MN U 702 " model vdw 2.149 2.320 nonbonded pdb=" O ARG V 483 " pdb=" NE ARG V 483 " model vdw 2.171 3.120 ... (remaining 238466 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 33 through 50 and (name N or name CA or name C or name O \ or name CB )) or resid 51 or (resid 52 through 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 or (resid 71 and (name N or name CA or na \ me C or name O or name CB )) or resid 72 or (resid 73 through 76 and (name N or \ name CA or name C or name O or name CB )) or resid 77 through 78 or (resid 79 th \ rough 84 and (name N or name CA or name C or name O or name CB )) or resid 85 th \ rough 87 or (resid 88 through 119 and (name N or name CA or name C or name O or \ name CB )) or resid 120 or (resid 121 through 132 and (name N or name CA or name \ C or name O or name CB )) or resid 133 or (resid 134 through 148 and (name N or \ name CA or name C or name O or name CB )) or resid 149 or (resid 150 through 15 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 158 or (resi \ d 159 and (name N or name CA or name C or name O or name CB )) or resid 160 or ( \ resid 161 through 166 and (name N or name CA or name C or name O or name CB )) o \ r resid 167 through 168 or (resid 169 through 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 or (resid 172 through 202 and (name N or \ name CA or name C or name O or name CB )) or resid 203 or (resid 204 through 22 \ 3 and (name N or name CA or name C or name O or name CB )) or (resid 224 through \ 253 and (name N or name CA or name C or name O or name CB )) or resid 254 or (r \ esid 255 and (name N or name CA or name C or name O or name CB )) or resid 256 o \ r (resid 257 through 265 and (name N or name CA or name C or name O or name CB ) \ ) or resid 266 or (resid 267 through 271 and (name N or name CA or name C or nam \ e O or name CB )) or resid 272 or (resid 273 through 276 and (name N or name CA \ or name C or name O or name CB )) or resid 277 through 278 or (resid 279 and (na \ me N or name CA or name C or name O or name CB )) or resid 280 or (resid 281 thr \ ough 290 and (name N or name CA or name C or name O or name CB )) or resid 291 t \ hrough 292 or (resid 293 through 360 and (name N or name CA or name C or name O \ or name CB )) or resid 361 or (resid 362 through 368 and (name N or name CA or n \ ame C or name O or name CB )) or resid 369 or (resid 370 through 421 and (name N \ or name CA or name C or name O or name CB )) or resid 422 or (resid 423 through \ 429 and (name N or name CA or name C or name O or name CB )) or (resid 430 thro \ ugh 453 and (name N or name CA or name C or name O or name CB )) or resid 454 or \ (resid 455 through 468 and (name N or name CA or name C or name O or name CB )) \ or resid 469 or (resid 470 through 483 and (name N or name CA or name C or name \ O or name CB )) or resid 484 or (resid 485 through 500 and (name N or name CA o \ r name C or name O or name CB )) or resid 501 or (resid 502 through 512 and (nam \ e N or name CA or name C or name O or name CB )) or resid 513 or (resid 514 thro \ ugh 554 and (name N or name CA or name C or name O or name CB )) or resid 555 or \ (resid 556 and (name N or name CA or name C or name O or name CB )) or resid 55 \ 7 or (resid 558 through 587 and (name N or name CA or name C or name O or name C \ B )) or resid 588 or (resid 589 through 591 and (name N or name CA or name C or \ name O or name CB )) or resid 592 through 593 or (resid 594 through 601 and (nam \ e N or name CA or name C or name O or name CB )) or resid 602 through 603 or (re \ sid 604 through 617 and (name N or name CA or name C or name O or name CB )) or \ resid 618 or (resid 619 through 631 and (name N or name CA or name C or name O o \ r name CB )) or resid 632 or (resid 633 through 640 and (name N or name CA or na \ me C or name O or name CB )) or resid 641 or (resid 642 through 682 and (name N \ or name CA or name C or name O or name CB )) or resid 683 or (resid 684 through \ 687 and (name N or name CA or name C or name O or name CB )) or resid 688 throug \ h 690 or (resid 691 through 705 and (name N or name CA or name C or name O or na \ me CB )) or resid 706 or (resid 707 through 712 and (name N or name CA or name C \ or name O or name CB )) or resid 713 or (resid 714 through 720 and (name N or n \ ame CA or name C or name O or name CB )) or resid 721 or (resid 722 through 726 \ and (name N or name CA or name C or name O or name CB )) or resid 727 or (resid \ 728 through 738 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 33 through 50 and (name N or name CA or name C or name O \ or name CB )) or resid 51 or (resid 52 through 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 or (resid 71 and (name N or name CA or na \ me C or name O or name CB )) or resid 72 or (resid 73 through 76 and (name N or \ name CA or name C or name O or name CB )) or resid 77 through 78 or (resid 79 th \ rough 84 and (name N or name CA or name C or name O or name CB )) or resid 85 th \ rough 87 or (resid 88 through 119 and (name N or name CA or name C or name O or \ name CB )) or resid 120 or (resid 121 through 132 and (name N or name CA or name \ C or name O or name CB )) or resid 133 or (resid 134 through 148 and (name N or \ name CA or name C or name O or name CB )) or resid 149 or (resid 150 through 15 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 158 or (resi \ d 159 and (name N or name CA or name C or name O or name CB )) or resid 160 or ( \ resid 161 through 166 and (name N or name CA or name C or name O or name CB )) o \ r resid 167 through 168 or (resid 169 through 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 or (resid 172 through 202 and (name N or \ name CA or name C or name O or name CB )) or resid 203 or (resid 204 through 22 \ 3 and (name N or name CA or name C or name O or name CB )) or (resid 224 through \ 253 and (name N or name CA or name C or name O or name CB )) or resid 254 or (r \ esid 255 and (name N or name CA or name C or name O or name CB )) or resid 256 o \ r (resid 257 through 265 and (name N or name CA or name C or name O or name CB ) \ ) or resid 266 or (resid 267 through 271 and (name N or name CA or name C or nam \ e O or name CB )) or resid 272 or (resid 273 through 276 and (name N or name CA \ or name C or name O or name CB )) or resid 277 through 278 or (resid 279 and (na \ me N or name CA or name C or name O or name CB )) or resid 280 or (resid 281 thr \ ough 290 and (name N or name CA or name C or name O or name CB )) or resid 291 t \ hrough 292 or (resid 293 through 360 and (name N or name CA or name C or name O \ or name CB )) or resid 361 or (resid 362 through 368 and (name N or name CA or n \ ame C or name O or name CB )) or resid 369 or (resid 370 through 421 and (name N \ or name CA or name C or name O or name CB )) or resid 422 or (resid 423 through \ 429 and (name N or name CA or name C or name O or name CB )) or (resid 430 thro \ ugh 453 and (name N or name CA or name C or name O or name CB )) or resid 454 or \ (resid 455 through 468 and (name N or name CA or name C or name O or name CB )) \ or resid 469 or (resid 470 through 483 and (name N or name CA or name C or name \ O or name CB )) or resid 484 or (resid 485 through 500 and (name N or name CA o \ r name C or name O or name CB )) or resid 501 or (resid 502 through 512 and (nam \ e N or name CA or name C or name O or name CB )) or resid 513 or (resid 514 thro \ ugh 554 and (name N or name CA or name C or name O or name CB )) or resid 555 or \ (resid 556 and (name N or name CA or name C or name O or name CB )) or resid 55 \ 7 or (resid 558 through 587 and (name N or name CA or name C or name O or name C \ B )) or resid 588 or (resid 589 through 591 and (name N or name CA or name C or \ name O or name CB )) or resid 592 through 593 or (resid 594 through 601 and (nam \ e N or name CA or name C or name O or name CB )) or resid 602 through 603 or (re \ sid 604 through 617 and (name N or name CA or name C or name O or name CB )) or \ resid 618 or (resid 619 through 631 and (name N or name CA or name C or name O o \ r name CB )) or resid 632 or (resid 633 through 640 and (name N or name CA or na \ me C or name O or name CB )) or resid 641 or (resid 642 through 682 and (name N \ or name CA or name C or name O or name CB )) or resid 683 or (resid 684 through \ 687 and (name N or name CA or name C or name O or name CB )) or resid 688 throug \ h 690 or (resid 691 through 705 and (name N or name CA or name C or name O or na \ me CB )) or resid 706 or (resid 707 through 712 and (name N or name CA or name C \ or name O or name CB )) or resid 713 or (resid 714 through 720 and (name N or n \ ame CA or name C or name O or name CB )) or resid 721 or (resid 722 through 726 \ and (name N or name CA or name C or name O or name CB )) or resid 727 or (resid \ 728 through 738 and (name N or name CA or name C or name O or name CB )))) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'U' and ((resid 36 through 71 and (name N or name CA or name C or name O \ or name CB )) or (resid 72 through 130 and (name N or name CA or name C or name \ O or name CB )) or resid 131 or (resid 132 through 203 and (name N or name CA or \ name C or name O or name CB )) or resid 204 or (resid 205 through 208 and (name \ N or name CA or name C or name O or name CB )) or resid 209 or (resid 210 throu \ gh 226 and (name N or name CA or name C or name O or name CB )) or resid 227 or \ (resid 228 through 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 or (resid 290 through 338 and (name N or name CA or name C or name \ O or name CB )) or resid 339 or (resid 340 through 376 and (name N or name CA or \ name C or name O or name CB )) or resid 377 or (resid 378 through 388 and (name \ N or name CA or name C or name O or name CB )) or resid 389 or (resid 390 throu \ gh 394 and (name N or name CA or name C or name O or name CB )) or resid 395 or \ (resid 396 through 401 and (name N or name CA or name C or name O or name CB )) \ or resid 402 or (resid 403 through 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 or (resid 409 through 410 and (name N or name CA or \ name C or name O or name CB )) or resid 411 or (resid 412 through 426 and (name \ N or name CA or name C or name O or name CB )) or resid 427 or (resid 428 throu \ gh 458 and (name N or name CA or name C or name O or name CB )) or resid 459 or \ (resid 460 through 467 and (name N or name CA or name C or name O or name CB )) \ or resid 468 or (resid 469 through 504 and (name N or name CA or name C or name \ O or name CB )) or (resid 505 through 562 and (name N or name CA or name C or na \ me O or name CB )) or resid 563 or (resid 564 through 565 and (name N or name CA \ or name C or name O or name CB )) or resid 566 or (resid 567 through 622 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'V' and ((resid 36 through 71 and (name N or name CA or name C or name O \ or name CB )) or (resid 72 through 130 and (name N or name CA or name C or name \ O or name CB )) or resid 131 or (resid 132 through 203 and (name N or name CA or \ name C or name O or name CB )) or resid 204 or (resid 205 through 208 and (name \ N or name CA or name C or name O or name CB )) or resid 209 or (resid 210 throu \ gh 226 and (name N or name CA or name C or name O or name CB )) or resid 227 or \ (resid 228 through 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 or (resid 290 through 338 and (name N or name CA or name C or name \ O or name CB )) or resid 339 or (resid 340 through 376 and (name N or name CA or \ name C or name O or name CB )) or resid 377 or (resid 378 through 388 and (name \ N or name CA or name C or name O or name CB )) or resid 389 or (resid 390 throu \ gh 394 and (name N or name CA or name C or name O or name CB )) or resid 395 or \ (resid 396 through 401 and (name N or name CA or name C or name O or name CB )) \ or resid 402 or (resid 403 through 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 or (resid 409 through 410 and (name N or name CA or \ name C or name O or name CB )) or resid 411 or (resid 412 through 426 and (name \ N or name CA or name C or name O or name CB )) or resid 427 or (resid 428 throu \ gh 458 and (name N or name CA or name C or name O or name CB )) or resid 459 or \ (resid 460 through 467 and (name N or name CA or name C or name O or name CB )) \ or resid 468 or (resid 469 through 504 and (name N or name CA or name C or name \ O or name CB )) or (resid 505 through 562 and (name N or name CA or name C or na \ me O or name CB )) or resid 563 or (resid 564 through 565 and (name N or name CA \ or name C or name O or name CB )) or resid 566 or (resid 567 through 622 and (n \ ame N or name CA or name C or name O or name CB )))) selection = chain 'W' selection = chain 'X' } 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 group one per residue 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: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 31.650 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.060 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34693 Z= 0.185 Angle : 0.673 19.270 47582 Z= 0.357 Chirality : 0.045 0.231 5585 Planarity : 0.004 0.060 6451 Dihedral : 16.287 129.448 10937 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % Rotamer: Outliers : 0.35 % Allowed : 30.58 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -1.10 (0.12), residues: 5156 helix: 1.51 (0.15), residues: 1440 sheet: -1.69 (0.20), residues: 752 loop : -1.67 (0.11), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.023 0.001 TYR V 253 PHE 0.029 0.002 PHE U 413 TRP 0.041 0.001 TRP B 92 HIS 0.008 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00409 (34678) covalent geometry : angle 0.67051 (47545) SS BOND : bond 0.00946 ( 8) SS BOND : angle 2.04873 ( 16) hydrogen bonds : bond 0.19638 ( 1210) hydrogen bonds : angle 6.78348 ( 3429) link_BETA1-4 : bond 0.00263 ( 2) link_BETA1-4 : angle 2.04503 ( 6) link_NAG-ASN : bond 0.00260 ( 5) link_NAG-ASN : angle 2.36199 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 279 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASN cc_start: 0.8585 (t0) cc_final: 0.8364 (t0) REVERT: V 233 MET cc_start: 0.9186 (tpp) cc_final: 0.8867 (tpt) REVERT: V 392 MET cc_start: 0.6705 (ppp) cc_final: 0.6434 (ppp) outliers start: 8 outliers final: 4 residues processed: 286 average time/residue: 0.1700 time to fit residues: 84.6099 Evaluate side-chains 264 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 260 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain U residue 345 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 5.9990 chunk 497 optimal weight: 50.0000 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 40.0000 chunk 366 optimal weight: 0.5980 chunk 223 optimal weight: 50.0000 chunk 142 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS A 427 ASN A 711 HIS B 253 HIS ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 HIS U 416 HIS U 418 ASN ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.192922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.165556 restraints weight = 61987.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.161403 restraints weight = 92150.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.159363 restraints weight = 75908.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.159015 restraints weight = 75839.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.157578 restraints weight = 61117.999| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 34693 Z= 0.334 Angle : 0.731 12.753 47582 Z= 0.381 Chirality : 0.049 0.229 5585 Planarity : 0.006 0.080 6451 Dihedral : 7.400 123.652 5746 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.29 % Favored : 90.65 % Rotamer: Outliers : 5.62 % Allowed : 28.16 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -1.20 (0.12), residues: 5156 helix: 1.43 (0.14), residues: 1476 sheet: -1.69 (0.20), residues: 736 loop : -1.81 (0.11), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 235 TYR 0.040 0.002 TYR B 465 PHE 0.031 0.002 PHE B 389 TRP 0.026 0.002 TRP B 92 HIS 0.008 0.002 HIS B 510 Details of bonding type rmsd covalent geometry : bond 0.00797 (34678) covalent geometry : angle 0.72826 (47545) SS BOND : bond 0.00905 ( 8) SS BOND : angle 2.16784 ( 16) hydrogen bonds : bond 0.04662 ( 1210) hydrogen bonds : angle 5.38496 ( 3429) link_BETA1-4 : bond 0.00760 ( 2) link_BETA1-4 : angle 2.28977 ( 6) link_NAG-ASN : bond 0.00441 ( 5) link_NAG-ASN : angle 2.34386 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 277 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASN cc_start: 0.8522 (t0) cc_final: 0.8313 (t0) REVERT: A 417 MET cc_start: 0.8680 (tpp) cc_final: 0.8408 (tpp) REVERT: A 427 ASN cc_start: 0.9429 (OUTLIER) cc_final: 0.9107 (p0) REVERT: A 584 MET cc_start: 0.7354 (tpp) cc_final: 0.7132 (tpp) REVERT: B 92 TRP cc_start: 0.8979 (OUTLIER) cc_final: 0.8439 (m-90) REVERT: B 380 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6939 (ttm170) REVERT: U 313 LEU cc_start: 0.9352 (tp) cc_final: 0.9004 (tt) REVERT: U 479 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8265 (pttm) REVERT: V 53 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7079 (mpt180) REVERT: V 392 MET cc_start: 0.6906 (ppp) cc_final: 0.6405 (ppp) outliers start: 128 outliers final: 78 residues processed: 386 average time/residue: 0.1816 time to fit residues: 120.4908 Evaluate side-chains 349 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 266 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 92 TRP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 569 PHE Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 720 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 233 MET Chi-restraints excluded: chain U residue 238 PHE Chi-restraints excluded: chain U residue 239 LEU Chi-restraints excluded: chain U residue 262 SER Chi-restraints excluded: chain U residue 298 HIS Chi-restraints excluded: chain U residue 479 LYS Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 144 MET Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 176 THR Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 203 CYS Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 273 CYS Chi-restraints excluded: chain V residue 282 VAL Chi-restraints excluded: chain V residue 283 CYS Chi-restraints excluded: chain V residue 298 HIS Chi-restraints excluded: chain V residue 300 THR Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 621 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 290 optimal weight: 1.9990 chunk 415 optimal weight: 20.0000 chunk 240 optimal weight: 50.0000 chunk 413 optimal weight: 0.8980 chunk 407 optimal weight: 10.0000 chunk 52 optimal weight: 0.0030 chunk 35 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 302 optimal weight: 0.4980 chunk 327 optimal weight: 0.3980 chunk 299 optimal weight: 3.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS B 532 GLN B 536 ASN ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 HIS U 416 HIS V 92 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.197487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.167152 restraints weight = 61968.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.163848 restraints weight = 97102.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.159636 restraints weight = 74637.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.159615 restraints weight = 69065.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.158515 restraints weight = 54050.826| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34693 Z= 0.113 Angle : 0.551 16.218 47582 Z= 0.285 Chirality : 0.044 0.167 5585 Planarity : 0.004 0.055 6451 Dihedral : 6.285 110.039 5741 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 3.69 % Allowed : 29.09 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.91 (0.12), residues: 5156 helix: 1.66 (0.14), residues: 1492 sheet: -1.61 (0.21), residues: 724 loop : -1.62 (0.11), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 235 TYR 0.017 0.001 TYR V 253 PHE 0.018 0.001 PHE B 428 TRP 0.024 0.001 TRP B 92 HIS 0.006 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00257 (34678) covalent geometry : angle 0.54887 (47545) SS BOND : bond 0.00713 ( 8) SS BOND : angle 1.60537 ( 16) hydrogen bonds : bond 0.03343 ( 1210) hydrogen bonds : angle 4.69778 ( 3429) link_BETA1-4 : bond 0.00538 ( 2) link_BETA1-4 : angle 1.50215 ( 6) link_NAG-ASN : bond 0.00292 ( 5) link_NAG-ASN : angle 1.96548 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 276 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 MET cc_start: 0.8632 (tpp) cc_final: 0.8318 (tpp) REVERT: A 427 ASN cc_start: 0.9394 (OUTLIER) cc_final: 0.9136 (p0) REVERT: B 92 TRP cc_start: 0.8880 (OUTLIER) cc_final: 0.8288 (m-90) REVERT: B 193 LEU cc_start: 0.8020 (pt) cc_final: 0.7332 (tp) REVERT: B 380 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7365 (ttp-170) REVERT: U 145 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8311 (ttmm) REVERT: V 41 GLU cc_start: 0.7694 (pp20) cc_final: 0.7424 (pp20) REVERT: V 157 MET cc_start: 0.8378 (ttm) cc_final: 0.8168 (ttm) REVERT: V 392 MET cc_start: 0.6999 (ppp) cc_final: 0.6709 (ppp) outliers start: 84 outliers final: 40 residues processed: 340 average time/residue: 0.1822 time to fit residues: 106.6118 Evaluate side-chains 303 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 259 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 92 TRP Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 720 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 145 LYS Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain U residue 206 THR Chi-restraints excluded: chain U residue 233 MET Chi-restraints excluded: chain U residue 268 VAL Chi-restraints excluded: chain U residue 298 HIS Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain V residue 144 MET Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 273 CYS Chi-restraints excluded: chain V residue 282 VAL Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 575 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 106 optimal weight: 3.9990 chunk 344 optimal weight: 2.9990 chunk 206 optimal weight: 50.0000 chunk 389 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 150 optimal weight: 50.0000 chunk 333 optimal weight: 30.0000 chunk 412 optimal weight: 50.0000 chunk 490 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 368 optimal weight: 0.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS U 416 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.194049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.166419 restraints weight = 61780.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.161329 restraints weight = 90975.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.159526 restraints weight = 73674.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.159017 restraints weight = 71419.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.157634 restraints weight = 58758.388| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 34693 Z= 0.240 Angle : 0.627 14.367 47582 Z= 0.323 Chirality : 0.046 0.236 5585 Planarity : 0.005 0.072 6451 Dihedral : 6.309 103.540 5741 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.34 % Favored : 91.60 % Rotamer: Outliers : 5.62 % Allowed : 28.38 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.96 (0.12), residues: 5156 helix: 1.70 (0.14), residues: 1476 sheet: -1.67 (0.20), residues: 780 loop : -1.66 (0.11), residues: 2900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 235 TYR 0.032 0.002 TYR B 465 PHE 0.024 0.002 PHE B 428 TRP 0.024 0.002 TRP B 92 HIS 0.006 0.001 HIS U 142 Details of bonding type rmsd covalent geometry : bond 0.00573 (34678) covalent geometry : angle 0.62439 (47545) SS BOND : bond 0.00809 ( 8) SS BOND : angle 2.35742 ( 16) hydrogen bonds : bond 0.03647 ( 1210) hydrogen bonds : angle 4.67581 ( 3429) link_BETA1-4 : bond 0.00584 ( 2) link_BETA1-4 : angle 1.91648 ( 6) link_NAG-ASN : bond 0.00341 ( 5) link_NAG-ASN : angle 2.08462 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 261 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASN cc_start: 0.9427 (OUTLIER) cc_final: 0.9191 (p0) REVERT: A 584 MET cc_start: 0.7478 (tpp) cc_final: 0.7226 (tpp) REVERT: B 92 TRP cc_start: 0.8888 (OUTLIER) cc_final: 0.8354 (m-90) REVERT: B 193 LEU cc_start: 0.8131 (pt) cc_final: 0.7436 (tp) REVERT: B 380 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6809 (ttm170) REVERT: B 400 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9025 (mm) REVERT: B 568 TRP cc_start: 0.8568 (OUTLIER) cc_final: 0.6868 (t60) REVERT: U 145 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8286 (ttmm) REVERT: U 313 LEU cc_start: 0.9234 (tp) cc_final: 0.8900 (tt) REVERT: V 41 GLU cc_start: 0.7773 (pp20) cc_final: 0.7562 (pp20) REVERT: V 53 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6844 (mpt180) REVERT: V 139 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6673 (ttt180) REVERT: V 392 MET cc_start: 0.6953 (ppp) cc_final: 0.6304 (ppp) REVERT: V 517 LYS cc_start: 0.6254 (OUTLIER) cc_final: 0.4783 (mtmm) outliers start: 128 outliers final: 87 residues processed: 370 average time/residue: 0.1771 time to fit residues: 112.6380 Evaluate side-chains 355 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 259 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 92 TRP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 720 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain U residue 62 ASN Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 145 LYS Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 233 MET Chi-restraints excluded: chain U residue 238 PHE Chi-restraints excluded: chain U residue 239 LEU Chi-restraints excluded: chain U residue 262 SER Chi-restraints excluded: chain U residue 268 VAL Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 298 HIS Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 116 GLU Chi-restraints excluded: chain V residue 139 ARG Chi-restraints excluded: chain V residue 144 MET Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 176 THR Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 203 CYS Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 267 ILE Chi-restraints excluded: chain V residue 272 SER Chi-restraints excluded: chain V residue 273 CYS Chi-restraints excluded: chain V residue 282 VAL Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 517 LYS Chi-restraints excluded: chain V residue 573 THR Chi-restraints excluded: chain V residue 575 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 349 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 224 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 172 optimal weight: 50.0000 chunk 118 optimal weight: 0.8980 chunk 507 optimal weight: 3.9990 chunk 379 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN A 410 ASN A 427 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS U 416 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.197002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.168523 restraints weight = 61908.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.164181 restraints weight = 88642.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.160062 restraints weight = 70815.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.159886 restraints weight = 67708.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.158684 restraints weight = 55550.563| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34693 Z= 0.124 Angle : 0.547 15.357 47582 Z= 0.278 Chirality : 0.044 0.197 5585 Planarity : 0.004 0.055 6451 Dihedral : 5.834 93.276 5741 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 4.75 % Allowed : 29.09 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.88 (0.12), residues: 5156 helix: 1.66 (0.14), residues: 1524 sheet: -1.55 (0.20), residues: 780 loop : -1.62 (0.11), residues: 2852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 235 TYR 0.016 0.001 TYR V 253 PHE 0.019 0.001 PHE B 428 TRP 0.023 0.001 TRP B 92 HIS 0.005 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00293 (34678) covalent geometry : angle 0.54475 (47545) SS BOND : bond 0.00803 ( 8) SS BOND : angle 1.79945 ( 16) hydrogen bonds : bond 0.02963 ( 1210) hydrogen bonds : angle 4.37842 ( 3429) link_BETA1-4 : bond 0.00566 ( 2) link_BETA1-4 : angle 1.52432 ( 6) link_NAG-ASN : bond 0.00263 ( 5) link_NAG-ASN : angle 1.89633 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 270 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASN cc_start: 0.9361 (OUTLIER) cc_final: 0.9125 (p0) REVERT: A 614 MET cc_start: 0.8804 (mmm) cc_final: 0.8052 (mmm) REVERT: B 92 TRP cc_start: 0.8856 (OUTLIER) cc_final: 0.8286 (m-90) REVERT: B 193 LEU cc_start: 0.8028 (pt) cc_final: 0.7339 (tp) REVERT: B 380 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6625 (ttm170) REVERT: B 556 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: B 568 TRP cc_start: 0.8429 (OUTLIER) cc_final: 0.7106 (t60) REVERT: U 144 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8093 (mpp) REVERT: U 145 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8410 (ttmm) REVERT: U 313 LEU cc_start: 0.9250 (tp) cc_final: 0.8885 (tt) REVERT: V 41 GLU cc_start: 0.7685 (pp20) cc_final: 0.7405 (pp20) REVERT: V 53 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.7145 (mpt180) REVERT: V 116 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: V 139 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6704 (ttt180) REVERT: V 191 MET cc_start: 0.8202 (ttp) cc_final: 0.7959 (ttt) REVERT: V 392 MET cc_start: 0.6886 (ppp) cc_final: 0.6182 (ppp) REVERT: V 483 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7245 (tpm170) REVERT: V 528 MET cc_start: 0.8287 (mmp) cc_final: 0.7938 (mmp) outliers start: 108 outliers final: 67 residues processed: 356 average time/residue: 0.1712 time to fit residues: 104.2428 Evaluate side-chains 338 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 260 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 92 TRP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 720 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 144 MET Chi-restraints excluded: chain U residue 145 LYS Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain U residue 206 THR Chi-restraints excluded: chain U residue 233 MET Chi-restraints excluded: chain U residue 239 LEU Chi-restraints excluded: chain U residue 262 SER Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 298 HIS Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 431 SER Chi-restraints excluded: chain U residue 550 SER Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 116 GLU Chi-restraints excluded: chain V residue 139 ARG Chi-restraints excluded: chain V residue 144 MET Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 203 CYS Chi-restraints excluded: chain V residue 267 ILE Chi-restraints excluded: chain V residue 273 CYS Chi-restraints excluded: chain V residue 282 VAL Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 483 ARG Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 560 HIS Chi-restraints excluded: chain V residue 573 THR Chi-restraints excluded: chain V residue 575 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 376 optimal weight: 9.9990 chunk 27 optimal weight: 0.1980 chunk 357 optimal weight: 0.9990 chunk 442 optimal weight: 50.0000 chunk 274 optimal weight: 10.0000 chunk 401 optimal weight: 20.0000 chunk 275 optimal weight: 8.9990 chunk 203 optimal weight: 50.0000 chunk 67 optimal weight: 2.9990 chunk 399 optimal weight: 7.9990 chunk 167 optimal weight: 50.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS U 416 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.192156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.165237 restraints weight = 61972.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.160733 restraints weight = 92970.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.156419 restraints weight = 73028.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.156159 restraints weight = 70733.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.154627 restraints weight = 58986.740| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.116 34693 Z= 0.391 Angle : 0.772 16.041 47582 Z= 0.395 Chirality : 0.051 0.281 5585 Planarity : 0.006 0.106 6451 Dihedral : 6.550 104.479 5741 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.87 % Favored : 90.03 % Rotamer: Outliers : 6.85 % Allowed : 27.37 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -1.11 (0.12), residues: 5156 helix: 1.64 (0.14), residues: 1452 sheet: -1.78 (0.20), residues: 772 loop : -1.75 (0.11), residues: 2932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 372 TYR 0.047 0.003 TYR B 465 PHE 0.034 0.003 PHE B 389 TRP 0.023 0.002 TRP B 92 HIS 0.009 0.002 HIS B 510 Details of bonding type rmsd covalent geometry : bond 0.00937 (34678) covalent geometry : angle 0.76949 (47545) SS BOND : bond 0.00877 ( 8) SS BOND : angle 2.67333 ( 16) hydrogen bonds : bond 0.04207 ( 1210) hydrogen bonds : angle 4.84446 ( 3429) link_BETA1-4 : bond 0.00761 ( 2) link_BETA1-4 : angle 2.52748 ( 6) link_NAG-ASN : bond 0.00467 ( 5) link_NAG-ASN : angle 2.26165 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 267 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASN cc_start: 0.9444 (OUTLIER) cc_final: 0.9148 (p0) REVERT: A 465 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8554 (p90) REVERT: A 614 MET cc_start: 0.8999 (mmm) cc_final: 0.8263 (mmm) REVERT: B 92 TRP cc_start: 0.8914 (OUTLIER) cc_final: 0.8387 (m-90) REVERT: B 193 LEU cc_start: 0.8179 (pt) cc_final: 0.7331 (tp) REVERT: B 380 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7052 (ttm170) REVERT: B 400 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9118 (mm) REVERT: B 514 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8432 (ptt-90) REVERT: B 568 TRP cc_start: 0.8641 (OUTLIER) cc_final: 0.6883 (t60) REVERT: U 144 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8013 (mpp) REVERT: U 145 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8582 (ttmm) REVERT: U 596 GLU cc_start: 0.6141 (OUTLIER) cc_final: 0.5459 (tm-30) REVERT: V 41 GLU cc_start: 0.7912 (pp20) cc_final: 0.7650 (pp20) REVERT: V 53 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6826 (mpt180) REVERT: V 94 MET cc_start: 0.7816 (mmp) cc_final: 0.7552 (mmp) REVERT: V 139 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6993 (ttt90) REVERT: V 213 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8167 (ttm170) REVERT: V 368 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: V 392 MET cc_start: 0.6890 (ppp) cc_final: 0.6226 (ppp) REVERT: V 483 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7305 (tpm170) outliers start: 156 outliers final: 119 residues processed: 402 average time/residue: 0.1688 time to fit residues: 116.8919 Evaluate side-chains 393 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 259 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 92 TRP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 569 PHE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 720 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 62 ASN Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 144 MET Chi-restraints excluded: chain U residue 145 LYS Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 233 MET Chi-restraints excluded: chain U residue 237 THR Chi-restraints excluded: chain U residue 238 PHE Chi-restraints excluded: chain U residue 239 LEU Chi-restraints excluded: chain U residue 268 VAL Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 298 HIS Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 431 SER Chi-restraints excluded: chain U residue 442 ILE Chi-restraints excluded: chain U residue 550 SER Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain U residue 596 GLU Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 116 GLU Chi-restraints excluded: chain V residue 139 ARG Chi-restraints excluded: chain V residue 144 MET Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 171 ILE Chi-restraints excluded: chain V residue 176 THR Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 203 CYS Chi-restraints excluded: chain V residue 213 ARG Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 267 ILE Chi-restraints excluded: chain V residue 272 SER Chi-restraints excluded: chain V residue 273 CYS Chi-restraints excluded: chain V residue 282 VAL Chi-restraints excluded: chain V residue 298 HIS Chi-restraints excluded: chain V residue 300 THR Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 359 LEU Chi-restraints excluded: chain V residue 368 GLU Chi-restraints excluded: chain V residue 424 VAL Chi-restraints excluded: chain V residue 442 ILE Chi-restraints excluded: chain V residue 463 ASP Chi-restraints excluded: chain V residue 483 ARG Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 501 ILE Chi-restraints excluded: chain V residue 560 HIS Chi-restraints excluded: chain V residue 573 THR Chi-restraints excluded: chain V residue 575 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 507 optimal weight: 7.9990 chunk 390 optimal weight: 0.8980 chunk 266 optimal weight: 0.6980 chunk 224 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 373 optimal weight: 20.0000 chunk 196 optimal weight: 40.0000 chunk 67 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS U 416 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.194763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.166250 restraints weight = 62098.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.161760 restraints weight = 95023.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.159512 restraints weight = 72585.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.159523 restraints weight = 57108.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.159513 restraints weight = 46108.474| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 34693 Z= 0.193 Angle : 0.623 15.480 47582 Z= 0.317 Chirality : 0.045 0.225 5585 Planarity : 0.004 0.070 6451 Dihedral : 6.137 97.513 5741 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.12 % Favored : 92.79 % Rotamer: Outliers : 5.93 % Allowed : 29.00 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.97 (0.12), residues: 5156 helix: 1.70 (0.14), residues: 1476 sheet: -1.71 (0.20), residues: 716 loop : -1.67 (0.11), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 235 TYR 0.021 0.001 TYR B 465 PHE 0.024 0.002 PHE B 428 TRP 0.026 0.001 TRP V 462 HIS 0.005 0.001 HIS U 547 Details of bonding type rmsd covalent geometry : bond 0.00462 (34678) covalent geometry : angle 0.62074 (47545) SS BOND : bond 0.01013 ( 8) SS BOND : angle 2.21182 ( 16) hydrogen bonds : bond 0.03333 ( 1210) hydrogen bonds : angle 4.53806 ( 3429) link_BETA1-4 : bond 0.00457 ( 2) link_BETA1-4 : angle 1.92397 ( 6) link_NAG-ASN : bond 0.00300 ( 5) link_NAG-ASN : angle 2.04179 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 263 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASN cc_start: 0.9353 (OUTLIER) cc_final: 0.9099 (p0) REVERT: A 465 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.8475 (p90) REVERT: A 614 MET cc_start: 0.8884 (mmm) cc_final: 0.8318 (mmm) REVERT: A 651 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8642 (p0) REVERT: B 92 TRP cc_start: 0.8862 (OUTLIER) cc_final: 0.8342 (m-90) REVERT: B 193 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7251 (tp) REVERT: B 380 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6721 (ttm170) REVERT: B 400 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.8949 (mm) REVERT: B 568 TRP cc_start: 0.8478 (OUTLIER) cc_final: 0.7205 (t60) REVERT: U 53 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7324 (mtm-85) REVERT: U 144 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7843 (mpp) REVERT: U 145 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8330 (ttmm) REVERT: U 264 ASP cc_start: 0.6681 (m-30) cc_final: 0.6053 (m-30) REVERT: U 313 LEU cc_start: 0.9252 (tp) cc_final: 0.8935 (tt) REVERT: U 596 GLU cc_start: 0.5944 (OUTLIER) cc_final: 0.5393 (tm-30) REVERT: V 41 GLU cc_start: 0.7773 (pp20) cc_final: 0.7488 (pp20) REVERT: V 53 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6635 (mpt180) REVERT: V 94 MET cc_start: 0.7706 (mmp) cc_final: 0.7379 (mmt) REVERT: V 139 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6851 (ttt90) REVERT: V 146 LEU cc_start: 0.9109 (tp) cc_final: 0.8862 (tp) REVERT: V 360 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7351 (mtp85) REVERT: V 392 MET cc_start: 0.6856 (ppp) cc_final: 0.6220 (ppp) REVERT: V 483 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7268 (tpm170) REVERT: V 517 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.4283 (mtmm) outliers start: 135 outliers final: 96 residues processed: 379 average time/residue: 0.1810 time to fit residues: 118.0737 Evaluate side-chains 374 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 261 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 92 TRP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 720 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 144 MET Chi-restraints excluded: chain U residue 145 LYS Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 166 ASP Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 233 MET Chi-restraints excluded: chain U residue 239 LEU Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 298 HIS Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 422 GLU Chi-restraints excluded: chain U residue 431 SER Chi-restraints excluded: chain U residue 550 SER Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain U residue 596 GLU Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 116 GLU Chi-restraints excluded: chain V residue 139 ARG Chi-restraints excluded: chain V residue 144 MET Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 203 CYS Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 267 ILE Chi-restraints excluded: chain V residue 272 SER Chi-restraints excluded: chain V residue 273 CYS Chi-restraints excluded: chain V residue 282 VAL Chi-restraints excluded: chain V residue 300 THR Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 360 ARG Chi-restraints excluded: chain V residue 463 ASP Chi-restraints excluded: chain V residue 483 ARG Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 501 ILE Chi-restraints excluded: chain V residue 517 LYS Chi-restraints excluded: chain V residue 560 HIS Chi-restraints excluded: chain V residue 573 THR Chi-restraints excluded: chain V residue 575 VAL Chi-restraints excluded: chain V residue 621 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 333 optimal weight: 20.0000 chunk 484 optimal weight: 30.0000 chunk 40 optimal weight: 4.9990 chunk 338 optimal weight: 0.0030 chunk 281 optimal weight: 0.8980 chunk 356 optimal weight: 0.6980 chunk 174 optimal weight: 20.0000 chunk 346 optimal weight: 0.3980 chunk 402 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 493 optimal weight: 30.0000 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS U 416 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.197433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.168531 restraints weight = 61820.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.163615 restraints weight = 90434.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.159773 restraints weight = 79655.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.159898 restraints weight = 71322.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.158443 restraints weight = 62665.756| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34693 Z= 0.106 Angle : 0.565 17.267 47582 Z= 0.284 Chirality : 0.044 0.248 5585 Planarity : 0.004 0.055 6451 Dihedral : 5.551 87.628 5741 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.84 % Favored : 94.08 % Rotamer: Outliers : 4.66 % Allowed : 30.27 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.78 (0.12), residues: 5156 helix: 1.78 (0.14), residues: 1500 sheet: -1.52 (0.20), residues: 736 loop : -1.55 (0.11), residues: 2920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 235 TYR 0.017 0.001 TYR V 417 PHE 0.021 0.001 PHE U 413 TRP 0.027 0.001 TRP V 462 HIS 0.006 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00252 (34678) covalent geometry : angle 0.56301 (47545) SS BOND : bond 0.00856 ( 8) SS BOND : angle 1.81944 ( 16) hydrogen bonds : bond 0.02737 ( 1210) hydrogen bonds : angle 4.25899 ( 3429) link_BETA1-4 : bond 0.00519 ( 2) link_BETA1-4 : angle 1.48060 ( 6) link_NAG-ASN : bond 0.00280 ( 5) link_NAG-ASN : angle 1.83763 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 278 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASN cc_start: 0.9266 (OUTLIER) cc_final: 0.9046 (p0) REVERT: A 614 MET cc_start: 0.8957 (mmm) cc_final: 0.8295 (mmm) REVERT: B 92 TRP cc_start: 0.8821 (OUTLIER) cc_final: 0.8237 (m-90) REVERT: B 193 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7229 (tp) REVERT: B 380 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7069 (ttp-170) REVERT: B 568 TRP cc_start: 0.8372 (OUTLIER) cc_final: 0.7355 (t60) REVERT: U 144 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7825 (mpp) REVERT: U 145 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8352 (ttmm) REVERT: U 264 ASP cc_start: 0.6590 (m-30) cc_final: 0.6147 (m-30) REVERT: U 596 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5647 (tm-30) REVERT: V 41 GLU cc_start: 0.7722 (pp20) cc_final: 0.7400 (pp20) REVERT: V 94 MET cc_start: 0.7673 (mmp) cc_final: 0.7402 (mmt) REVERT: V 139 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6827 (ttt90) REVERT: V 360 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7299 (mtp85) REVERT: V 392 MET cc_start: 0.6960 (ppp) cc_final: 0.6316 (ppp) REVERT: V 483 ARG cc_start: 0.7543 (tpm170) cc_final: 0.7309 (tpm170) outliers start: 106 outliers final: 75 residues processed: 362 average time/residue: 0.1855 time to fit residues: 115.1152 Evaluate side-chains 355 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 270 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 92 TRP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 720 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 144 MET Chi-restraints excluded: chain U residue 145 LYS Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 163 LEU Chi-restraints excluded: chain U residue 166 ASP Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 206 THR Chi-restraints excluded: chain U residue 233 MET Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 298 HIS Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 431 SER Chi-restraints excluded: chain U residue 550 SER Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain U residue 596 GLU Chi-restraints excluded: chain V residue 116 GLU Chi-restraints excluded: chain V residue 139 ARG Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 273 CYS Chi-restraints excluded: chain V residue 282 VAL Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 347 ASN Chi-restraints excluded: chain V residue 360 ARG Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 560 HIS Chi-restraints excluded: chain V residue 573 THR Chi-restraints excluded: chain V residue 575 VAL Chi-restraints excluded: chain V residue 621 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 128 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 350 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 447 optimal weight: 20.0000 chunk 193 optimal weight: 50.0000 chunk 307 optimal weight: 2.9990 chunk 376 optimal weight: 1.9990 chunk 264 optimal weight: 0.0870 chunk 488 optimal weight: 8.9990 chunk 359 optimal weight: 0.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS U 416 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.197478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.169555 restraints weight = 61970.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.164368 restraints weight = 86005.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.159686 restraints weight = 71407.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.159387 restraints weight = 70801.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.158133 restraints weight = 56990.295| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34693 Z= 0.114 Angle : 0.571 16.703 47582 Z= 0.286 Chirality : 0.044 0.327 5585 Planarity : 0.004 0.106 6451 Dihedral : 5.229 88.184 5741 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 4.22 % Allowed : 30.40 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.70 (0.12), residues: 5156 helix: 1.85 (0.14), residues: 1492 sheet: -1.45 (0.21), residues: 716 loop : -1.50 (0.11), residues: 2948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 235 TYR 0.014 0.001 TYR V 253 PHE 0.024 0.001 PHE U 413 TRP 0.028 0.001 TRP V 462 HIS 0.010 0.001 HIS V 256 Details of bonding type rmsd covalent geometry : bond 0.00273 (34678) covalent geometry : angle 0.56937 (47545) SS BOND : bond 0.00794 ( 8) SS BOND : angle 1.70318 ( 16) hydrogen bonds : bond 0.02720 ( 1210) hydrogen bonds : angle 4.20709 ( 3429) link_BETA1-4 : bond 0.00578 ( 2) link_BETA1-4 : angle 1.53800 ( 6) link_NAG-ASN : bond 0.00246 ( 5) link_NAG-ASN : angle 1.74072 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 277 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASN cc_start: 0.9321 (OUTLIER) cc_final: 0.9112 (p0) REVERT: A 614 MET cc_start: 0.9006 (mmm) cc_final: 0.8286 (mmm) REVERT: B 193 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7232 (tp) REVERT: B 380 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7126 (ttp-170) REVERT: B 568 TRP cc_start: 0.8378 (OUTLIER) cc_final: 0.7288 (t60) REVERT: U 75 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7037 (tm-30) REVERT: U 144 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.7974 (mpp) REVERT: U 145 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8292 (ttmm) REVERT: U 264 ASP cc_start: 0.6603 (m-30) cc_final: 0.6168 (m-30) REVERT: U 372 VAL cc_start: 0.7405 (OUTLIER) cc_final: 0.7115 (t) REVERT: U 596 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5612 (tm-30) REVERT: V 41 GLU cc_start: 0.7778 (pp20) cc_final: 0.7415 (pp20) REVERT: V 94 MET cc_start: 0.7640 (mmp) cc_final: 0.7369 (mmt) REVERT: V 116 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: V 139 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6793 (ttt90) REVERT: V 191 MET cc_start: 0.8296 (ttp) cc_final: 0.7970 (ttt) REVERT: V 360 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7318 (mtp85) REVERT: V 392 MET cc_start: 0.6984 (ppp) cc_final: 0.6330 (ppp) outliers start: 96 outliers final: 78 residues processed: 354 average time/residue: 0.1764 time to fit residues: 107.4153 Evaluate side-chains 359 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 270 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 92 TRP Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 144 MET Chi-restraints excluded: chain U residue 145 LYS Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 163 LEU Chi-restraints excluded: chain U residue 166 ASP Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 233 MET Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 298 HIS Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 431 SER Chi-restraints excluded: chain U residue 550 SER Chi-restraints excluded: chain U residue 596 GLU Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 105 LEU Chi-restraints excluded: chain V residue 116 GLU Chi-restraints excluded: chain V residue 139 ARG Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 273 CYS Chi-restraints excluded: chain V residue 282 VAL Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 347 ASN Chi-restraints excluded: chain V residue 360 ARG Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 501 ILE Chi-restraints excluded: chain V residue 560 HIS Chi-restraints excluded: chain V residue 573 THR Chi-restraints excluded: chain V residue 575 VAL Chi-restraints excluded: chain V residue 621 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 479 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 435 optimal weight: 50.0000 chunk 509 optimal weight: 0.1980 chunk 442 optimal weight: 8.9990 chunk 186 optimal weight: 50.0000 chunk 392 optimal weight: 0.0970 chunk 242 optimal weight: 6.9990 chunk 237 optimal weight: 40.0000 chunk 35 optimal weight: 0.9990 chunk 420 optimal weight: 20.0000 overall best weight: 3.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 427 ASN ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN B 253 HIS U 416 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.192775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.165811 restraints weight = 62324.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.160420 restraints weight = 93341.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.158696 restraints weight = 80686.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.158344 restraints weight = 76852.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.156796 restraints weight = 69031.192| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 34693 Z= 0.326 Angle : 0.735 16.380 47582 Z= 0.373 Chirality : 0.049 0.287 5585 Planarity : 0.006 0.139 6451 Dihedral : 5.868 88.973 5741 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.12 % Favored : 90.81 % Rotamer: Outliers : 4.66 % Allowed : 30.05 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.91 (0.12), residues: 5156 helix: 1.67 (0.14), residues: 1480 sheet: -1.61 (0.22), residues: 672 loop : -1.61 (0.11), residues: 3004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 147 TYR 0.041 0.002 TYR B 465 PHE 0.031 0.002 PHE B 428 TRP 0.031 0.002 TRP B 92 HIS 0.009 0.002 HIS V 256 Details of bonding type rmsd covalent geometry : bond 0.00783 (34678) covalent geometry : angle 0.73299 (47545) SS BOND : bond 0.00901 ( 8) SS BOND : angle 2.35680 ( 16) hydrogen bonds : bond 0.03828 ( 1210) hydrogen bonds : angle 4.58982 ( 3429) link_BETA1-4 : bond 0.00619 ( 2) link_BETA1-4 : angle 2.34757 ( 6) link_NAG-ASN : bond 0.00396 ( 5) link_NAG-ASN : angle 2.06480 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 261 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8977 (p0) REVERT: A 614 MET cc_start: 0.9009 (mmm) cc_final: 0.8305 (mmm) REVERT: B 193 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7253 (tp) REVERT: B 380 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7000 (ttm170) REVERT: B 514 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8598 (ptt-90) REVERT: B 568 TRP cc_start: 0.8566 (OUTLIER) cc_final: 0.7045 (t60) REVERT: B 614 MET cc_start: 0.8559 (mmm) cc_final: 0.8319 (mmt) REVERT: U 144 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7862 (mpp) REVERT: U 145 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8456 (ttmm) REVERT: U 264 ASP cc_start: 0.6702 (m-30) cc_final: 0.6437 (m-30) REVERT: U 596 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5672 (tm-30) REVERT: V 41 GLU cc_start: 0.7941 (pp20) cc_final: 0.7637 (pp20) REVERT: V 94 MET cc_start: 0.7581 (mmp) cc_final: 0.7295 (mmt) REVERT: V 139 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7000 (ttt90) REVERT: V 360 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7457 (mtp85) REVERT: V 392 MET cc_start: 0.7078 (ppp) cc_final: 0.6333 (ppp) outliers start: 106 outliers final: 87 residues processed: 351 average time/residue: 0.1757 time to fit residues: 105.2459 Evaluate side-chains 358 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 261 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 92 TRP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 144 MET Chi-restraints excluded: chain U residue 145 LYS Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 166 ASP Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 233 MET Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 298 HIS Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 431 SER Chi-restraints excluded: chain U residue 550 SER Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain U residue 596 GLU Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 105 LEU Chi-restraints excluded: chain V residue 116 GLU Chi-restraints excluded: chain V residue 139 ARG Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 272 SER Chi-restraints excluded: chain V residue 273 CYS Chi-restraints excluded: chain V residue 282 VAL Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 347 ASN Chi-restraints excluded: chain V residue 360 ARG Chi-restraints excluded: chain V residue 463 ASP Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 501 ILE Chi-restraints excluded: chain V residue 560 HIS Chi-restraints excluded: chain V residue 573 THR Chi-restraints excluded: chain V residue 575 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 290 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 442 optimal weight: 50.0000 chunk 425 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 486 optimal weight: 10.0000 chunk 328 optimal weight: 8.9990 chunk 198 optimal weight: 40.0000 chunk 66 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 overall best weight: 2.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS U 416 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.194581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.166586 restraints weight = 61783.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.162033 restraints weight = 92733.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.158607 restraints weight = 77057.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.158224 restraints weight = 73472.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.156931 restraints weight = 58486.528| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 34693 Z= 0.227 Angle : 0.656 16.639 47582 Z= 0.331 Chirality : 0.046 0.327 5585 Planarity : 0.005 0.077 6451 Dihedral : 5.694 89.126 5741 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.62 % Favored : 92.30 % Rotamer: Outliers : 4.39 % Allowed : 30.49 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.87 (0.12), residues: 5156 helix: 1.74 (0.14), residues: 1480 sheet: -1.65 (0.21), residues: 676 loop : -1.59 (0.11), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 235 TYR 0.028 0.002 TYR B 465 PHE 0.023 0.002 PHE B 428 TRP 0.032 0.001 TRP B 92 HIS 0.009 0.001 HIS V 256 Details of bonding type rmsd covalent geometry : bond 0.00546 (34678) covalent geometry : angle 0.65344 (47545) SS BOND : bond 0.00990 ( 8) SS BOND : angle 2.16438 ( 16) hydrogen bonds : bond 0.03377 ( 1210) hydrogen bonds : angle 4.44720 ( 3429) link_BETA1-4 : bond 0.00389 ( 2) link_BETA1-4 : angle 2.07261 ( 6) link_NAG-ASN : bond 0.00312 ( 5) link_NAG-ASN : angle 1.95953 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5110.55 seconds wall clock time: 88 minutes 37.07 seconds (5317.07 seconds total)