Starting phenix.real_space_refine on Wed Jun 25 00:13:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7u_38111/06_2025/8x7u_38111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7u_38111/06_2025/8x7u_38111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x7u_38111/06_2025/8x7u_38111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7u_38111/06_2025/8x7u_38111.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7u_38111/06_2025/8x7u_38111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7u_38111/06_2025/8x7u_38111.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 3 5.21 5 S 83 5.16 5 C 18300 2.51 5 N 5164 2.21 5 O 5270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28832 Number of models: 1 Model: "" Number of chains: 11 Chain: "D" Number of atoms: 4922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 4922 Classifications: {'peptide': 654} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 30, 'TRANS': 623} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 170 Chain: "C" Number of atoms: 4893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 4893 Classifications: {'peptide': 654} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 30, 'TRANS': 623} Chain breaks: 2 Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 24, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 209 Chain: "B" Number of atoms: 4817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 4817 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 29, 'TRANS': 612} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 19, 'ASN:plan1': 3, 'ARG:plan': 7, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 168 Chain: "E" Number of atoms: 4881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 4881 Classifications: {'peptide': 654} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 30, 'TRANS': 623} Chain breaks: 2 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 10, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 191 Chain: "A" Number of atoms: 4343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4343 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 28, 'TRANS': 554} Chain breaks: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 14, 'PHE:plan': 1, 'GLU:plan': 24, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 214 Chain: "F" Number of atoms: 4830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 4830 Classifications: {'peptide': 653} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 30, 'TRANS': 622} Chain breaks: 2 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 247 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 19.10, per 1000 atoms: 0.66 Number of scatterers: 28832 At special positions: 0 Unit cell: (139.8, 138.868, 179.876, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 83 16.00 P 12 15.00 Mg 3 11.99 O 5270 8.00 N 5164 7.00 C 18300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 7.31 Conformation dependent library (CDL) restraints added in 3.9 seconds 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7286 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 44 sheets defined 42.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.567A pdb=" N VAL D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 53 Processing helix chain 'D' and resid 53 through 63 removed outlier: 3.599A pdb=" N ALA D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 81 removed outlier: 3.953A pdb=" N ALA D 69 " --> pdb=" O GLU D 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.573A pdb=" N ILE D 113 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 278 through 287 Processing helix chain 'D' and resid 294 through 306 Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.648A pdb=" N VAL D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D 343 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 385 Processing helix chain 'D' and resid 401 through 404 removed outlier: 3.662A pdb=" N SER D 404 " --> pdb=" O ARG D 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 401 through 404' Processing helix chain 'D' and resid 405 through 412 removed outlier: 3.735A pdb=" N GLU D 411 " --> pdb=" O HIS D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 422 removed outlier: 3.749A pdb=" N GLY D 421 " --> pdb=" O SER D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 461 removed outlier: 3.634A pdb=" N LEU D 460 " --> pdb=" O PRO D 456 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER D 461 " --> pdb=" O PRO D 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 456 through 461' Processing helix chain 'D' and resid 474 through 491 Processing helix chain 'D' and resid 501 through 516 Processing helix chain 'D' and resid 521 through 536 Processing helix chain 'D' and resid 553 through 571 removed outlier: 3.720A pdb=" N ARG D 571 " --> pdb=" O HIS D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 596 Processing helix chain 'D' and resid 614 through 620 Processing helix chain 'D' and resid 640 through 651 Processing helix chain 'D' and resid 654 through 669 Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.555A pdb=" N ALA C 8 " --> pdb=" O GLU C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.986A pdb=" N LEU C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.505A pdb=" N PHE C 52 " --> pdb=" O HIS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 63 removed outlier: 3.648A pdb=" N LEU C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 78 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.583A pdb=" N ILE C 113 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 removed outlier: 3.590A pdb=" N GLU C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.624A pdb=" N GLN C 268 " --> pdb=" O PRO C 264 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 269 " --> pdb=" O GLU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 287 Processing helix chain 'C' and resid 294 through 306 Processing helix chain 'C' and resid 334 through 346 removed outlier: 3.894A pdb=" N VAL C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN C 344 " --> pdb=" O ARG C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 Processing helix chain 'C' and resid 405 through 412 removed outlier: 4.035A pdb=" N GLU C 411 " --> pdb=" O HIS C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 453 removed outlier: 3.717A pdb=" N GLN C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 461 removed outlier: 3.512A pdb=" N LEU C 460 " --> pdb=" O PRO C 456 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C 461 " --> pdb=" O PRO C 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 456 through 461' Processing helix chain 'C' and resid 474 through 491 Processing helix chain 'C' and resid 492 through 497 removed outlier: 3.856A pdb=" N VAL C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 516 removed outlier: 3.922A pdb=" N LYS C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 538 Processing helix chain 'C' and resid 553 through 571 removed outlier: 3.520A pdb=" N LEU C 557 " --> pdb=" O THR C 553 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG C 571 " --> pdb=" O HIS C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 596 Processing helix chain 'C' and resid 603 through 608 removed outlier: 4.116A pdb=" N ILE C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 622 Processing helix chain 'C' and resid 640 through 645 removed outlier: 3.708A pdb=" N ILE C 644 " --> pdb=" O GLU C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 650 removed outlier: 3.541A pdb=" N ALA C 650 " --> pdb=" O ALA C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 668 removed outlier: 3.672A pdb=" N SER C 667 " --> pdb=" O ASN C 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 28 through 36 removed outlier: 3.640A pdb=" N ASP B 32 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.546A pdb=" N LEU B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 81 removed outlier: 3.904A pdb=" N ALA B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.722A pdb=" N HIS B 112 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 113 " --> pdb=" O SER B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 113' Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.658A pdb=" N GLY B 198 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.671A pdb=" N GLN B 268 " --> pdb=" O PRO B 264 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 294 through 306 Processing helix chain 'B' and resid 334 through 346 removed outlier: 3.800A pdb=" N LEU B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.544A pdb=" N ALA B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 410 removed outlier: 3.691A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N HIS B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 removed outlier: 3.686A pdb=" N GLN B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 462 Processing helix chain 'B' and resid 474 through 491 Processing helix chain 'B' and resid 501 through 513 removed outlier: 3.532A pdb=" N LYS B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 536 removed outlier: 3.579A pdb=" N ARG B 536 " --> pdb=" O TYR B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 571 Processing helix chain 'B' and resid 577 through 595 removed outlier: 3.527A pdb=" N THR B 594 " --> pdb=" O ALA B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 622 removed outlier: 3.611A pdb=" N ILE B 620 " --> pdb=" O LYS B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 650 removed outlier: 3.695A pdb=" N ILE B 644 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU B 645 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 648 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.692A pdb=" N LEU B 662 " --> pdb=" O ILE B 658 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 668 " --> pdb=" O GLU B 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 14 Processing helix chain 'E' and resid 28 through 36 removed outlier: 3.864A pdb=" N ASP E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 53 removed outlier: 3.535A pdb=" N SER E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE E 52 " --> pdb=" O HIS E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 63 removed outlier: 3.611A pdb=" N LEU E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 81 removed outlier: 3.595A pdb=" N ALA E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU E 81 " --> pdb=" O ILE E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 Processing helix chain 'E' and resid 263 through 276 Processing helix chain 'E' and resid 278 through 287 Processing helix chain 'E' and resid 294 through 306 Processing helix chain 'E' and resid 334 through 346 removed outlier: 3.659A pdb=" N ALA E 343 " --> pdb=" O LEU E 339 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN E 344 " --> pdb=" O ARG E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 385 Processing helix chain 'E' and resid 394 through 398 removed outlier: 3.785A pdb=" N MET E 398 " --> pdb=" O PHE E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 405 removed outlier: 4.426A pdb=" N ALA E 405 " --> pdb=" O ARG E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 412 removed outlier: 3.697A pdb=" N LEU E 410 " --> pdb=" O ILE E 406 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU E 411 " --> pdb=" O HIS E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 461 removed outlier: 3.577A pdb=" N LEU E 460 " --> pdb=" O PRO E 456 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER E 461 " --> pdb=" O PRO E 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 456 through 461' Processing helix chain 'E' and resid 474 through 491 removed outlier: 3.640A pdb=" N SER E 480 " --> pdb=" O LYS E 476 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E 483 " --> pdb=" O ALA E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 497 removed outlier: 4.025A pdb=" N VAL E 496 " --> pdb=" O GLU E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 513 removed outlier: 3.813A pdb=" N LYS E 507 " --> pdb=" O ASP E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 537 Processing helix chain 'E' and resid 539 through 543 removed outlier: 3.741A pdb=" N ASP E 543 " --> pdb=" O ARG E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 571 removed outlier: 3.530A pdb=" N ALA E 559 " --> pdb=" O ARG E 555 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA E 568 " --> pdb=" O SER E 564 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG E 571 " --> pdb=" O HIS E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 596 removed outlier: 3.615A pdb=" N ALA E 581 " --> pdb=" O THR E 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 622 Processing helix chain 'E' and resid 640 through 651 removed outlier: 3.727A pdb=" N GLU E 645 " --> pdb=" O GLU E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 669 removed outlier: 3.517A pdb=" N LYS E 660 " --> pdb=" O ALA E 656 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP E 668 " --> pdb=" O GLU E 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.880A pdb=" N THR A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.722A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 81 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.567A pdb=" N ILE A 113 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 278 through 287 removed outlier: 4.339A pdb=" N VAL A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 306 Processing helix chain 'A' and resid 334 through 346 removed outlier: 3.609A pdb=" N ALA A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 399 through 411 removed outlier: 3.972A pdb=" N HIS A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 422 removed outlier: 3.921A pdb=" N GLY A 421 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 removed outlier: 3.818A pdb=" N GLN A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 463 removed outlier: 3.654A pdb=" N SER A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 491 Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.722A pdb=" N VAL A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 515 removed outlier: 3.563A pdb=" N ALA A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 534 removed outlier: 3.735A pdb=" N TYR A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 571 removed outlier: 3.548A pdb=" N ALA A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 595 removed outlier: 3.513A pdb=" N ILE A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 590 " --> pdb=" O GLU A 586 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 28 through 36 removed outlier: 4.030A pdb=" N ASP F 32 " --> pdb=" O ASN F 28 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 53 removed outlier: 3.576A pdb=" N SER F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 63 removed outlier: 3.555A pdb=" N ALA F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP F 58 " --> pdb=" O PRO F 54 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 81 removed outlier: 3.581A pdb=" N ALA F 69 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 113 removed outlier: 3.637A pdb=" N ILE F 113 " --> pdb=" O SER F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 263 through 276 removed outlier: 3.529A pdb=" N GLN F 268 " --> pdb=" O PRO F 264 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS F 269 " --> pdb=" O GLU F 265 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA F 274 " --> pdb=" O ILE F 270 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS F 275 " --> pdb=" O ARG F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 287 removed outlier: 3.660A pdb=" N VAL F 284 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 306 Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 337 through 346 removed outlier: 3.951A pdb=" N ALA F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN F 344 " --> pdb=" O ARG F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 385 Processing helix chain 'F' and resid 399 through 410 removed outlier: 4.185A pdb=" N ALA F 405 " --> pdb=" O ARG F 401 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N HIS F 407 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLU F 408 " --> pdb=" O SER F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 456 through 463 removed outlier: 3.791A pdb=" N LEU F 460 " --> pdb=" O PRO F 456 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER F 461 " --> pdb=" O PRO F 457 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG F 462 " --> pdb=" O THR F 458 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE F 463 " --> pdb=" O LEU F 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 456 through 463' Processing helix chain 'F' and resid 474 through 491 removed outlier: 3.774A pdb=" N ASP F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 485 " --> pdb=" O ILE F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 497 removed outlier: 3.984A pdb=" N VAL F 496 " --> pdb=" O GLU F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 515 removed outlier: 3.698A pdb=" N LYS F 507 " --> pdb=" O ASP F 503 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR F 508 " --> pdb=" O LEU F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 537 Processing helix chain 'F' and resid 553 through 571 removed outlier: 3.579A pdb=" N ALA F 559 " --> pdb=" O ARG F 555 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG F 571 " --> pdb=" O HIS F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 596 removed outlier: 3.709A pdb=" N ALA F 596 " --> pdb=" O MET F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 620 removed outlier: 3.918A pdb=" N ILE F 620 " --> pdb=" O LYS F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 650 removed outlier: 3.500A pdb=" N ILE F 644 " --> pdb=" O GLU F 640 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU F 645 " --> pdb=" O GLU F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 667 removed outlier: 3.785A pdb=" N LYS F 660 " --> pdb=" O ALA F 656 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU F 662 " --> pdb=" O ILE F 658 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 665 " --> pdb=" O LEU F 661 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 42 through 44 removed outlier: 6.312A pdb=" N LEU D 42 " --> pdb=" O ARG D 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 103 through 104 removed outlier: 7.079A pdb=" N LEU D 103 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N ILE D 122 " --> pdb=" O LEU D 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 119 through 126 current: chain 'D' and resid 148 through 150 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 148 through 150 current: chain 'D' and resid 203 through 208 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 203 through 208 current: chain 'D' and resid 242 through 249 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 242 through 249 current: chain 'D' and resid 375 through 378 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 388 through 390 removed outlier: 5.990A pdb=" N VAL D 325 " --> pdb=" O ALA D 434 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU D 326 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU D 469 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL D 328 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 352 through 353 removed outlier: 6.704A pdb=" N THR D 352 " --> pdb=" O ASP D 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 414 through 417 Processing sheet with id=AA6, first strand: chain 'D' and resid 519 through 520 removed outlier: 6.995A pdb=" N VAL D 519 " --> pdb=" O VAL D 576 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.118A pdb=" N LEU C 42 " --> pdb=" O ARG C 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 103 through 104 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 116 through 126 current: chain 'C' and resid 147 through 150 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 147 through 150 current: chain 'C' and resid 203 through 209 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 203 through 209 current: chain 'C' and resid 245 through 249 Processing sheet with id=AA9, first strand: chain 'C' and resid 433 through 434 removed outlier: 6.026A pdb=" N VAL C 325 " --> pdb=" O ALA C 434 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 352 through 353 removed outlier: 6.618A pdb=" N THR C 352 " --> pdb=" O ASP C 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 365 through 368 Processing sheet with id=AB3, first strand: chain 'C' and resid 414 through 419 removed outlier: 3.787A pdb=" N ALA C 424 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 519 through 520 removed outlier: 6.928A pdb=" N VAL C 519 " --> pdb=" O VAL C 576 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 44 removed outlier: 3.664A pdb=" N LEU B 42 " --> pdb=" O HIS B 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 103 through 104 removed outlier: 6.937A pdb=" N LEU B 103 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N ILE B 122 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP B 220 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR B 225 " --> pdb=" O ASN B 248 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 242 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LYS B 243 " --> pdb=" O PHE B 203 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP B 205 " --> pdb=" O LYS B 243 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 247 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 188 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N SER B 185 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 126 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 187 " --> pdb=" O THR B 124 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 132 through 135 removed outlier: 7.101A pdb=" N ARG B 179 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AB9, first strand: chain 'B' and resid 388 through 390 removed outlier: 7.309A pdb=" N GLY B 388 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE B 433 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA B 390 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL B 325 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 326 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU B 469 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 328 " --> pdb=" O LEU B 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 352 through 353 removed outlier: 6.806A pdb=" N THR B 352 " --> pdb=" O ASP B 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 365 through 368 Processing sheet with id=AC3, first strand: chain 'B' and resid 414 through 419 Processing sheet with id=AC4, first strand: chain 'B' and resid 519 through 520 removed outlier: 7.092A pdb=" N VAL B 519 " --> pdb=" O VAL B 576 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 43 through 45 removed outlier: 3.526A pdb=" N TYR E 97 " --> pdb=" O ILE E 44 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 103 through 104 removed outlier: 6.921A pdb=" N LEU E 103 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N ILE E 122 " --> pdb=" O LEU E 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 119 through 126 current: chain 'E' and resid 148 through 149 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 148 through 149 current: chain 'E' and resid 203 through 209 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 203 through 209 current: chain 'E' and resid 243 through 249 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 433 through 436 removed outlier: 6.016A pdb=" N VAL E 325 " --> pdb=" O ALA E 434 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA E 436 " --> pdb=" O VAL E 325 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU E 327 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU E 326 " --> pdb=" O PHE E 467 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU E 469 " --> pdb=" O LEU E 326 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL E 328 " --> pdb=" O LEU E 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 352 through 353 removed outlier: 6.744A pdb=" N THR E 352 " --> pdb=" O ASP E 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 365 through 368 Processing sheet with id=AD1, first strand: chain 'E' and resid 388 through 389 removed outlier: 7.301A pdb=" N GLY E 388 " --> pdb=" O THR E 431 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 414 through 417 Processing sheet with id=AD3, first strand: chain 'E' and resid 519 through 520 removed outlier: 6.934A pdb=" N VAL E 519 " --> pdb=" O VAL E 576 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 671 through 672 Processing sheet with id=AD5, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AD6, first strand: chain 'A' and resid 130 through 135 removed outlier: 7.327A pdb=" N ARG A 179 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N LEU A 245 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP A 205 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL A 247 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE A 207 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N HIS A 249 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR A 225 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG A 187 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL A 126 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER A 185 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AD8, first strand: chain 'A' and resid 349 through 353 removed outlier: 3.943A pdb=" N ILE A 350 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 391 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY A 388 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE A 433 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA A 390 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ALA A 435 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE A 392 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 325 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 364 through 368 removed outlier: 3.844A pdb=" N ALA A 365 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 367 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 414 through 417 Processing sheet with id=AE2, first strand: chain 'F' and resid 102 through 104 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 102 through 104 current: chain 'F' and resid 203 through 208 removed outlier: 9.114A pdb=" N LEU F 245 " --> pdb=" O PHE F 203 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP F 205 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL F 247 " --> pdb=" O ASP F 205 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE F 207 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N HIS F 249 " --> pdb=" O ILE F 207 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR F 225 " --> pdb=" O ASN F 248 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY F 121 " --> pdb=" O VAL F 222 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 222 " --> pdb=" O GLY F 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 132 through 140 Processing sheet with id=AE4, first strand: chain 'F' and resid 311 through 312 removed outlier: 3.561A pdb=" N ARG F 311 " --> pdb=" O LEU F 319 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 349 through 353 removed outlier: 6.016A pdb=" N ILE F 350 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP F 393 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR F 352 " --> pdb=" O ASP F 393 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA F 390 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ALA F 435 " --> pdb=" O ALA F 390 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE F 392 " --> pdb=" O ALA F 435 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL F 325 " --> pdb=" O ALA F 434 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU F 326 " --> pdb=" O PHE F 467 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU F 469 " --> pdb=" O LEU F 326 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL F 328 " --> pdb=" O LEU F 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.923A pdb=" N ALA F 365 " --> pdb=" O GLU F 378 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU F 378 " --> pdb=" O ALA F 365 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 414 through 417 removed outlier: 3.878A pdb=" N ILE F 417 " --> pdb=" O ALA F 424 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 519 through 520 removed outlier: 6.903A pdb=" N VAL F 519 " --> pdb=" O VAL F 576 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 1033 hydrogen bonds defined for protein. 3003 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: 11.75 Time building geometry restraints manager: 8.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9714 1.34 - 1.46: 5341 1.46 - 1.58: 14051 1.58 - 1.70: 22 1.70 - 1.82: 142 Bond restraints: 29270 Sorted by residual: bond pdb=" C4 ATP E 701 " pdb=" C5 ATP E 701 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.30e+01 bond pdb=" C4 ATP A 702 " pdb=" C5 ATP A 702 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.07e+01 bond pdb=" C4 ATP D 702 " pdb=" C5 ATP D 702 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.50e+01 bond pdb=" C4 ATP C 702 " pdb=" C5 ATP C 702 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.31e+01 bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.30e+01 ... (remaining 29265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.64: 39624 4.64 - 9.29: 77 9.29 - 13.93: 2 13.93 - 18.58: 2 18.58 - 23.22: 5 Bond angle restraints: 39710 Sorted by residual: angle pdb=" PB ATP D 702 " pdb=" O3B ATP D 702 " pdb=" PG ATP D 702 " ideal model delta sigma weight residual 139.87 116.65 23.22 1.00e+00 1.00e+00 5.39e+02 angle pdb=" PA ATP E 701 " pdb=" O3A ATP E 701 " pdb=" PB ATP E 701 " ideal model delta sigma weight residual 136.83 114.02 22.81 1.00e+00 1.00e+00 5.20e+02 angle pdb=" PA ATP A 702 " pdb=" O3A ATP A 702 " pdb=" PB ATP A 702 " ideal model delta sigma weight residual 136.83 117.48 19.35 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PA ATP B 701 " pdb=" O3A ATP B 701 " pdb=" PB ATP B 701 " ideal model delta sigma weight residual 136.83 117.82 19.01 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PA ATP C 702 " pdb=" O3A ATP C 702 " pdb=" PB ATP C 702 " ideal model delta sigma weight residual 136.83 117.82 19.01 1.00e+00 1.00e+00 3.61e+02 ... (remaining 39705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 16947 17.54 - 35.08: 1010 35.08 - 52.62: 172 52.62 - 70.16: 44 70.16 - 87.70: 17 Dihedral angle restraints: 18190 sinusoidal: 7025 harmonic: 11165 Sorted by residual: dihedral pdb=" CA ASP A 190 " pdb=" CB ASP A 190 " pdb=" CG ASP A 190 " pdb=" OD1 ASP A 190 " ideal model delta sinusoidal sigma weight residual -30.00 -89.49 59.49 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP D 174 " pdb=" CB ASP D 174 " pdb=" CG ASP D 174 " pdb=" OD1 ASP D 174 " ideal model delta sinusoidal sigma weight residual -30.00 -89.44 59.44 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP C 386 " pdb=" CB ASP C 386 " pdb=" CG ASP C 386 " pdb=" OD1 ASP C 386 " ideal model delta sinusoidal sigma weight residual -30.00 -88.99 58.99 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 18187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3109 0.031 - 0.061: 1030 0.061 - 0.092: 401 0.092 - 0.122: 199 0.122 - 0.153: 23 Chirality restraints: 4762 Sorted by residual: chirality pdb=" CB ILE C 291 " pdb=" CA ILE C 291 " pdb=" CG1 ILE C 291 " pdb=" CG2 ILE C 291 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA ASP F 278 " pdb=" N ASP F 278 " pdb=" C ASP F 278 " pdb=" CB ASP F 278 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CB ILE A 231 " pdb=" CA ILE A 231 " pdb=" CG1 ILE A 231 " pdb=" CG2 ILE A 231 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 4759 not shown) Planarity restraints: 5094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 238 " 0.051 5.00e-02 4.00e+02 7.77e-02 9.65e+00 pdb=" N PRO C 239 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 239 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 239 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 130 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO F 131 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO F 131 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 131 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 548 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO F 549 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO F 549 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 549 " -0.018 5.00e-02 4.00e+02 ... (remaining 5091 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 293 2.62 - 3.19: 26002 3.19 - 3.76: 45758 3.76 - 4.33: 63430 4.33 - 4.90: 100812 Nonbonded interactions: 236295 Sorted by model distance: nonbonded pdb="MG MG A 701 " pdb=" O1B ATP A 702 " model vdw 2.050 2.170 nonbonded pdb=" CG GLU F 411 " pdb=" OE1 GLN F 412 " model vdw 2.154 3.440 nonbonded pdb=" OG SER D 336 " pdb="MG MG D 701 " model vdw 2.194 2.170 nonbonded pdb=" O VAL F 610 " pdb=" OG SER F 614 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR F 508 " pdb=" O MET F 570 " model vdw 2.274 3.040 ... (remaining 236290 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 1 through 13 or resid 27 through 54 or (resid 55 and (name \ N or name CA or name C or name O or name CB )) or resid 56 through 71 or (resid \ 72 through 74 and (name N or name CA or name C or name O or name CB )) or resid \ 75 through 89 or (resid 90 through 91 and (name N or name CA or name C or name \ O or name CB )) or resid 92 through 140 or (resid 141 through 142 and (name N or \ name CA or name C or name O or name CB )) or resid 143 through 151 or (resid 15 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 153 through \ 163 or (resid 164 through 165 and (name N or name CA or name C or name O or name \ CB )) or resid 166 through 186 or (resid 187 and (name N or name CA or name C o \ r name O or name CB )) or resid 188 through 194 or (resid 195 and (name N or nam \ e CA or name C or name O or name CB )) or resid 196 through 199 or (resid 200 an \ d (name N or name CA or name C or name O or name CB )) or resid 201 through 213 \ or (resid 214 through 216 and (name N or name CA or name C or name O or name CB \ )) or resid 217 through 219 or (resid 220 through 221 and (name N or name CA or \ name C or name O or name CB )) or resid 222 through 232 or (resid 233 through 23 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 239 through \ 240 or (resid 241 and (name N or name CA or name C or name O or name CB )) or re \ sid 242 or (resid 243 and (name N or name CA or name C or name O or name CB )) o \ r resid 244 through 250 or (resid 251 and (name N or name CA or name C or name O \ or name CB )) or resid 252 through 254 or (resid 255 through 256 and (name N or \ name CA or name C or name O or name CB )) or resid 257 or (resid 258 through 25 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 260 or (resi \ d 261 through 262 and (name N or name CA or name C or name O or name CB )) or re \ sid 263 through 264 or (resid 265 through 267 and (name N or name CA or name C o \ r name O or name CB )) or resid 268 through 314 or (resid 315 and (name N or nam \ e CA or name C or name O or name CB )) or resid 316 through 350 or (resid 351 an \ d (name N or name CA or name C or name O or name CB )) or resid 352 through 369 \ or (resid 370 through 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 392 or (resid 393 through 394 and (name N or name CA or \ name C or name O or name CB )) or resid 395 through 399 or (resid 400 and (name \ N or name CA or name C or name O or name CB )) or resid 401 through 445 or (resi \ d 446 and (name N or name CA or name C or name O or name CB )) or resid 447 thro \ ugh 473 or (resid 474 through 475 and (name N or name CA or name C or name O or \ name CB )) or resid 476 through 482 or (resid 483 and (name N or name CA or name \ C or name O or name CB )) or resid 484 through 491 or (resid 492 through 495 an \ d (name N or name CA or name C or name O or name CB )) or resid 496 through 536 \ or (resid 537 and (name N or name CA or name C or name O or name CB )) or resid \ 538 or (resid 539 through 541 and (name N or name CA or name C or name O or name \ CB )) or resid 542 through 547 or (resid 548 and (name N or name CA or name C o \ r name O or name CB )) or resid 549 through 595)) selection = (chain 'B' and (resid 1 through 13 or resid 27 through 28 or (resid 29 and (name \ N or name CA or name C or name O or name CB )) or resid 30 through 31 or (resid \ 32 and (name N or name CA or name C or name O or name CB )) or resid 33 through \ 65 or (resid 66 through 67 and (name N or name CA or name C or name O or name C \ B )) or resid 68 through 71 or (resid 72 through 74 and (name N or name CA or na \ me C or name O or name CB )) or resid 75 through 79 or (resid 80 through 81 and \ (name N or name CA or name C or name O or name CB )) or resid 82 through 89 or ( \ resid 90 through 91 and (name N or name CA or name C or name O or name CB )) or \ resid 92 through 106 or (resid 107 and (name N or name CA or name C or name O or \ name CB )) or resid 108 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )) or resid 135 through 145 or (resid 146 and (name N o \ r name CA or name C or name O or name CB )) or resid 147 through 148 or (resid 1 \ 49 and (name N or name CA or name C or name O or name CB )) or resid 150 through \ 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or r \ esid 153 through 163 or (resid 164 through 165 and (name N or name CA or name C \ or name O or name CB )) or resid 166 through 186 or (resid 187 and (name N or na \ me CA or name C or name O or name CB )) or resid 188 through 194 or (resid 195 a \ nd (name N or name CA or name C or name O or name CB )) or resid 196 through 199 \ or (resid 200 and (name N or name CA or name C or name O or name CB )) or resid \ 201 through 219 or (resid 220 through 221 and (name N or name CA or name C or n \ ame O or name CB )) or resid 222 through 232 or (resid 233 through 238 and (name \ N or name CA or name C or name O or name CB )) or resid 239 or (resid 240 throu \ gh 241 and (name N or name CA or name C or name O or name CB )) or resid 242 or \ (resid 243 and (name N or name CA or name C or name O or name CB )) or resid 244 \ through 250 or (resid 251 and (name N or name CA or name C or name O or name CB \ )) or resid 252 through 254 or (resid 255 through 256 and (name N or name CA or \ name C or name O or name CB )) or resid 257 or (resid 258 through 259 and (name \ N or name CA or name C or name O or name CB )) or resid 260 or (resid 261 throu \ gh 262 and (name N or name CA or name C or name O or name CB )) or resid 263 thr \ ough 264 or (resid 265 through 267 and (name N or name CA or name C or name O or \ name CB )) or resid 268 through 314 or (resid 315 and (name N or name CA or nam \ e C or name O or name CB )) or resid 316 or (resid 317 and (name N or name CA or \ name C or name O or name CB )) or resid 318 through 350 or (resid 351 and (name \ N or name CA or name C or name O or name CB )) or resid 352 through 368 or (res \ id 369 through 371 and (name N or name CA or name C or name O or name CB )) or r \ esid 372 through 392 or (resid 393 through 394 and (name N or name CA or name C \ or name O or name CB )) or resid 395 through 399 or (resid 400 and (name N or na \ me CA or name C or name O or name CB )) or resid 401 through 407 or (resid 408 t \ hrough 409 and (name N or name CA or name C or name O or name CB )) or resid 410 \ or (resid 411 and (name N or name CA or name C or name O or name CB )) or resid \ 412 through 421 or (resid 422 and (name N or name CA or name C or name O or nam \ e CB )) or resid 423 through 445 or (resid 446 and (name N or name CA or name C \ or name O or name CB )) or resid 447 through 450 or (resid 451 and (name N or na \ me CA or name C or name O or name CB )) or resid 452 through 453 or (resid 454 a \ nd (name N or name CA or name C or name O or name CB )) or resid 455 through 461 \ or (resid 462 and (name N or name CA or name C or name O or name CB )) or resid \ 463 through 474 or (resid 475 and (name N or name CA or name C or name O or nam \ e CB )) or resid 476 through 477 or (resid 478 through 479 and (name N or name C \ A or name C or name O or name CB )) or resid 480 through 482 or (resid 483 and ( \ name N or name CA or name C or name O or name CB )) or resid 484 through 491 or \ (resid 492 through 495 and (name N or name CA or name C or name O or name CB )) \ or resid 496 through 502 or (resid 503 and (name N or name CA or name C or name \ O or name CB )) or resid 504 through 535 or (resid 536 through 537 and (name N o \ r name CA or name C or name O or name CB )) or (resid 538 through 545 and (name \ N or name CA or name C or name O or name CB )) or resid 546 through 547 or (resi \ d 548 and (name N or name CA or name C or name O or name CB )) or resid 549 or ( \ resid 550 and (name N or name CA or name C or name O or name CB )) or resid 551 \ through 557 or (resid 558 through 559 and (name N or name CA or name C or name O \ or name CB )) or resid 560 through 564 or (resid 565 through 566 and (name N or \ name CA or name C or name O or name CB )) or resid 567 through 579 or (resid 58 \ 0 through 581 and (name N or name CA or name C or name O or name CB )) or resid \ 582 through 585 or (resid 586 and (name N or name CA or name C or name O or name \ CB )) or resid 587 through 595)) selection = (chain 'C' and (resid 1 through 13 or resid 27 through 28 or (resid 29 and (name \ N or name CA or name C or name O or name CB )) or resid 30 or (resid 31 through \ 32 and (name N or name CA or name C or name O or name CB )) or resid 33 through \ 65 or (resid 66 through 67 and (name N or name CA or name C or name O or name C \ B )) or resid 68 through 71 or (resid 72 through 74 and (name N or name CA or na \ me C or name O or name CB )) or resid 75 through 79 or (resid 80 through 81 and \ (name N or name CA or name C or name O or name CB )) or resid 82 through 89 or ( \ resid 90 through 91 and (name N or name CA or name C or name O or name CB )) or \ resid 92 through 106 or (resid 107 and (name N or name CA or name C or name O or \ name CB )) or resid 108 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )) or resid 135 through 140 or (resid 141 through 142 a \ nd (name N or name CA or name C or name O or name CB )) or resid 143 through 145 \ or (resid 146 and (name N or name CA or name C or name O or name CB )) or resid \ 147 through 148 or (resid 149 and (name N or name CA or name C or name O or nam \ e CB )) or resid 150 through 163 or (resid 164 through 165 and (name N or name C \ A or name C or name O or name CB )) or resid 166 through 186 or (resid 187 and ( \ name N or name CA or name C or name O or name CB )) or resid 188 through 194 or \ (resid 195 and (name N or name CA or name C or name O or name CB )) or resid 196 \ through 199 or (resid 200 and (name N or name CA or name C or name O or name CB \ )) or resid 201 through 213 or (resid 214 through 216 and (name N or name CA or \ name C or name O or name CB )) or resid 217 through 219 or (resid 220 through 2 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 222 through \ 233 or (resid 234 through 238 and (name N or name CA or name C or name O or nam \ e CB )) or resid 239 or (resid 240 through 241 and (name N or name CA or name C \ or name O or name CB )) or resid 242 or (resid 243 and (name N or name CA or nam \ e C or name O or name CB )) or resid 244 through 250 or (resid 251 and (name N o \ r name CA or name C or name O or name CB )) or resid 252 through 254 or (resid 2 \ 55 through 256 and (name N or name CA or name C or name O or name CB )) or resid \ 257 or (resid 258 through 259 and (name N or name CA or name C or name O or nam \ e CB )) or resid 260 or (resid 261 through 262 and (name N or name CA or name C \ or name O or name CB )) or resid 263 through 265 or (resid 266 through 267 and ( \ name N or name CA or name C or name O or name CB )) or resid 268 through 314 or \ (resid 315 and (name N or name CA or name C or name O or name CB )) or resid 316 \ or (resid 317 and (name N or name CA or name C or name O or name CB )) or resid \ 318 through 350 or (resid 351 and (name N or name CA or name C or name O or nam \ e CB )) or resid 352 through 368 or (resid 369 through 371 and (name N or name C \ A or name C or name O or name CB )) or resid 372 through 392 or (resid 393 throu \ gh 394 and (name N or name CA or name C or name O or name CB )) or resid 395 thr \ ough 399 or (resid 400 and (name N or name CA or name C or name O or name CB )) \ or resid 401 through 407 or (resid 408 through 409 and (name N or name CA or nam \ e C or name O or name CB )) or resid 410 or (resid 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 418 or (resid 419 through 4 \ 20 and (name N or name CA or name C or name O or name CB )) or resid 421 or (res \ id 422 and (name N or name CA or name C or name O or name CB )) or resid 423 thr \ ough 445 or (resid 446 and (name N or name CA or name C or name O or name CB )) \ or resid 447 through 450 or (resid 451 and (name N or name CA or name C or name \ O or name CB )) or resid 452 through 453 or (resid 454 and (name N or name CA or \ name C or name O or name CB )) or resid 455 through 461 or (resid 462 and (name \ N or name CA or name C or name O or name CB )) or resid 463 through 473 or (res \ id 474 through 475 and (name N or name CA or name C or name O or name CB )) or r \ esid 476 through 477 or (resid 478 through 479 and (name N or name CA or name C \ or name O or name CB )) or resid 480 through 482 or (resid 483 and (name N or na \ me CA or name C or name O or name CB )) or resid 484 through 491 or (resid 492 t \ hrough 495 and (name N or name CA or name C or name O or name CB )) or resid 496 \ through 502 or (resid 503 and (name N or name CA or name C or name O or name CB \ )) or resid 504 through 535 or (resid 536 through 537 and (name N or name CA or \ name C or name O or name CB )) or resid 538 or (resid 539 through 541 and (name \ N or name CA or name C or name O or name CB )) or (resid 542 through 545 and (n \ ame N or name CA or name C or name O or name CB )) or resid 546 through 549 or ( \ resid 550 and (name N or name CA or name C or name O or name CB )) or resid 551 \ through 557 or (resid 558 through 559 and (name N or name CA or name C or name O \ or name CB )) or resid 560 through 564 or (resid 565 through 566 and (name N or \ name CA or name C or name O or name CB )) or resid 567 through 579 or (resid 58 \ 0 through 581 and (name N or name CA or name C or name O or name CB )) or resid \ 582 through 585 or (resid 586 and (name N or name CA or name C or name O or name \ CB )) or resid 587 through 595)) selection = (chain 'D' and (resid 1 through 13 or resid 27 through 28 or (resid 29 and (name \ N or name CA or name C or name O or name CB )) or resid 30 through 54 or (resid \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 through \ 65 or (resid 66 through 67 and (name N or name CA or name C or name O or name C \ B )) or resid 68 through 71 or (resid 72 through 74 and (name N or name CA or na \ me C or name O or name CB )) or resid 75 through 79 or (resid 80 through 81 and \ (name N or name CA or name C or name O or name CB )) or resid 82 through 89 or ( \ resid 90 through 91 and (name N or name CA or name C or name O or name CB )) or \ resid 92 through 106 or (resid 107 and (name N or name CA or name C or name O or \ name CB )) or resid 108 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )) or resid 135 through 145 or (resid 146 and (name N o \ r name CA or name C or name O or name CB )) or resid 147 through 148 or (resid 1 \ 49 and (name N or name CA or name C or name O or name CB )) or resid 150 through \ 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or r \ esid 153 through 163 or (resid 164 through 165 and (name N or name CA or name C \ or name O or name CB )) or resid 166 through 194 or (resid 195 and (name N or na \ me CA or name C or name O or name CB )) or resid 196 through 213 or (resid 214 t \ hrough 216 and (name N or name CA or name C or name O or name CB )) or resid 217 \ through 219 or (resid 220 through 221 and (name N or name CA or name C or name \ O or name CB )) or resid 222 through 232 or (resid 233 through 238 and (name N o \ r name CA or name C or name O or name CB )) or resid 239 or (resid 240 through 2 \ 41 and (name N or name CA or name C or name O or name CB )) or resid 242 or (res \ id 243 and (name N or name CA or name C or name O or name CB )) or resid 244 thr \ ough 250 or (resid 251 and (name N or name CA or name C or name O or name CB )) \ or resid 252 through 254 or (resid 255 through 256 and (name N or name CA or nam \ e C or name O or name CB )) or resid 257 or (resid 258 through 259 and (name N o \ r name CA or name C or name O or name CB )) or resid 260 or (resid 261 through 2 \ 62 and (name N or name CA or name C or name O or name CB )) or resid 263 through \ 264 or (resid 265 through 267 and (name N or name CA or name C or name O or nam \ e CB )) or resid 268 through 314 or (resid 315 and (name N or name CA or name C \ or name O or name CB )) or resid 316 or (resid 317 and (name N or name CA or nam \ e C or name O or name CB )) or resid 318 through 350 or (resid 351 and (name N o \ r name CA or name C or name O or name CB )) or resid 352 through 367 or (resid 3 \ 68 through 371 and (name N or name CA or name C or name O or name CB )) or resid \ 372 through 392 or (resid 393 through 394 and (name N or name CA or name C or n \ ame O or name CB )) or resid 395 through 399 or (resid 400 and (name N or name C \ A or name C or name O or name CB )) or resid 401 through 407 or (resid 408 throu \ gh 409 and (name N or name CA or name C or name O or name CB )) or resid 410 or \ (resid 411 and (name N or name CA or name C or name O or name CB )) or resid 412 \ through 421 or (resid 422 and (name N or name CA or name C or name O or name CB \ )) or resid 423 through 445 or (resid 446 and (name N or name CA or name C or n \ ame O or name CB )) or resid 447 through 450 or (resid 451 and (name N or name C \ A or name C or name O or name CB )) or resid 452 through 453 or (resid 454 and ( \ name N or name CA or name C or name O or name CB )) or resid 455 through 461 or \ (resid 462 and (name N or name CA or name C or name O or name CB )) or resid 463 \ through 473 or (resid 474 through 475 and (name N or name CA or name C or name \ O or name CB )) or resid 476 through 477 or (resid 478 through 479 and (name N o \ r name CA or name C or name O or name CB )) or resid 480 through 482 or (resid 4 \ 83 and (name N or name CA or name C or name O or name CB )) or resid 484 through \ 491 or (resid 492 through 495 and (name N or name CA or name C or name O or nam \ e CB )) or resid 496 through 502 or (resid 503 and (name N or name CA or name C \ or name O or name CB )) or resid 504 through 535 or (resid 536 through 537 and ( \ name N or name CA or name C or name O or name CB )) or resid 538 or (resid 539 t \ hrough 541 and (name N or name CA or name C or name O or name CB )) or (resid 54 \ 2 through 545 and (name N or name CA or name C or name O or name CB )) or resid \ 546 through 547 or (resid 548 and (name N or name CA or name C or name O or name \ CB )) or resid 549 or (resid 550 and (name N or name CA or name C or name O or \ name CB )) or resid 551 through 557 or (resid 558 through 559 and (name N or nam \ e CA or name C or name O or name CB )) or resid 560 through 564 or (resid 565 th \ rough 566 and (name N or name CA or name C or name O or name CB )) or resid 567 \ through 579 or (resid 580 through 581 and (name N or name CA or name C or name O \ or name CB )) or resid 582 through 585 or (resid 586 and (name N or name CA or \ name C or name O or name CB )) or resid 587 through 595)) selection = (chain 'E' and (resid 1 through 13 or resid 27 through 28 or (resid 29 and (name \ N or name CA or name C or name O or name CB )) or resid 30 through 31 or (resid \ 32 and (name N or name CA or name C or name O or name CB )) or resid 33 through \ 54 or (resid 55 and (name N or name CA or name C or name O or name CB )) or res \ id 56 through 65 or (resid 66 through 67 and (name N or name CA or name C or nam \ e O or name CB )) or resid 68 through 71 or (resid 72 through 74 and (name N or \ name CA or name C or name O or name CB )) or resid 75 through 106 or (resid 107 \ and (name N or name CA or name C or name O or name CB )) or resid 108 through 13 \ 3 or (resid 134 and (name N or name CA or name C or name O or name CB )) or resi \ d 135 through 140 or (resid 141 through 142 and (name N or name CA or name C or \ name O or name CB )) or resid 143 through 151 or (resid 152 and (name N or name \ CA or name C or name O or name CB )) or resid 153 through 155 or (resid 156 and \ (name N or name CA or name C or name O or name CB )) or resid 157 through 199 or \ (resid 200 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 1 through 213 or (resid 214 through 216 and (name N or name CA or name C or name \ O or name CB )) or resid 217 through 219 or (resid 220 through 221 and (name N \ or name CA or name C or name O or name CB )) or resid 222 through 233 or (resid \ 234 through 238 and (name N or name CA or name C or name O or name CB )) or resi \ d 239 through 240 or (resid 241 and (name N or name CA or name C or name O or na \ me CB )) or resid 242 or (resid 243 and (name N or name CA or name C or name O o \ r name CB )) or resid 244 through 250 or (resid 251 and (name N or name CA or na \ me C or name O or name CB )) or resid 252 through 255 or (resid 256 and (name N \ or name CA or name C or name O or name CB )) or resid 257 or (resid 258 through \ 259 and (name N or name CA or name C or name O or name CB )) or resid 260 throug \ h 261 or (resid 262 and (name N or name CA or name C or name O or name CB )) or \ resid 263 through 264 or (resid 265 through 267 and (name N or name CA or name C \ or name O or name CB )) or resid 268 through 314 or (resid 315 and (name N or n \ ame CA or name C or name O or name CB )) or resid 316 or (resid 317 and (name N \ or name CA or name C or name O or name CB )) or resid 318 through 350 or (resid \ 351 and (name N or name CA or name C or name O or name CB )) or resid 352 throug \ h 368 or (resid 369 through 371 and (name N or name CA or name C or name O or na \ me CB )) or resid 372 through 392 or (resid 393 through 394 and (name N or name \ CA or name C or name O or name CB )) or resid 395 through 399 or (resid 400 and \ (name N or name CA or name C or name O or name CB )) or resid 401 through 407 or \ (resid 408 through 409 and (name N or name CA or name C or name O or name CB )) \ or resid 410 or (resid 411 and (name N or name CA or name C or name O or name C \ B )) or resid 412 through 421 or (resid 422 and (name N or name CA or name C or \ name O or name CB )) or resid 423 through 450 or (resid 451 and (name N or name \ CA or name C or name O or name CB )) or resid 452 through 453 or (resid 454 and \ (name N or name CA or name C or name O or name CB )) or resid 455 through 461 or \ (resid 462 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 3 through 473 or (resid 474 through 475 and (name N or name CA or name C or name \ O or name CB )) or resid 476 through 477 or (resid 478 through 479 and (name N \ or name CA or name C or name O or name CB )) or resid 480 through 491 or (resid \ 492 through 495 and (name N or name CA or name C or name O or name CB )) or resi \ d 496 through 535 or (resid 536 through 537 and (name N or name CA or name C or \ name O or name CB )) or resid 538 or (resid 539 through 541 and (name N or name \ CA or name C or name O or name CB )) or (resid 542 through 545 and (name N or na \ me CA or name C or name O or name CB )) or resid 546 through 547 or (resid 548 a \ nd (name N or name CA or name C or name O or name CB )) or resid 549 or (resid 5 \ 50 and (name N or name CA or name C or name O or name CB )) or resid 551 through \ 557 or (resid 558 through 559 and (name N or name CA or name C or name O or nam \ e CB )) or resid 560 through 564 or (resid 565 through 566 and (name N or name C \ A or name C or name O or name CB )) or resid 567 through 579 or (resid 580 throu \ gh 581 and (name N or name CA or name C or name O or name CB )) or resid 582 thr \ ough 585 or (resid 586 and (name N or name CA or name C or name O or name CB )) \ or resid 587 through 595)) selection = (chain 'F' and (resid 1 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 86 or (resid 87 through 91 and (nam \ e N or name CA or name C or name O or name CB )) or resid 92 through 106 or (res \ id 107 and (name N or name CA or name C or name O or name CB )) or resid 108 thr \ ough 140 or (resid 141 through 142 and (name N or name CA or name C or name O or \ name CB )) or resid 143 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 148 or (resid 149 and (name N o \ r name CA or name C or name O or name CB )) or resid 150 through 151 or (resid 1 \ 52 and (name N or name CA or name C or name O or name CB )) or resid 153 through \ 171 or (resid 172 and (name N or name CA or name C or name O or name CB )) or r \ esid 173 through 186 or (resid 187 and (name N or name CA or name C or name O or \ name CB )) or resid 188 through 194 or (resid 195 and (name N or name CA or nam \ e C or name O or name CB )) or resid 196 through 199 or (resid 200 and (name N o \ r name CA or name C or name O or name CB )) or resid 201 through 213 or (resid 2 \ 14 through 216 and (name N or name CA or name C or name O or name CB )) or resid \ 217 through 220 or (resid 221 and (name N or name CA or name C or name O or nam \ e CB )) or resid 222 through 233 or (resid 234 through 238 and (name N or name C \ A or name C or name O or name CB )) or resid 239 or (resid 240 through 241 and ( \ name N or name CA or name C or name O or name CB )) or resid 242 through 254 or \ (resid 255 through 256 and (name N or name CA or name C or name O or name CB )) \ or resid 257 through 260 or (resid 261 through 262 and (name N or name CA or nam \ e C or name O or name CB )) or resid 263 through 265 or (resid 266 through 267 a \ nd (name N or name CA or name C or name O or name CB )) or resid 268 through 368 \ or (resid 369 through 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 407 or (resid 408 through 409 and (name N or name CA or \ name C or name O or name CB )) or resid 410 or (resid 411 and (name N or name C \ A or name C or name O or name CB )) or resid 412 through 421 or (resid 422 and ( \ name N or name CA or name C or name O or name CB )) or resid 423 through 445 or \ (resid 446 and (name N or name CA or name C or name O or name CB )) or resid 447 \ through 450 or (resid 451 and (name N or name CA or name C or name O or name CB \ )) or resid 452 through 453 or (resid 454 and (name N or name CA or name C or n \ ame O or name CB )) or resid 455 through 461 or (resid 462 and (name N or name C \ A or name C or name O or name CB )) or resid 463 through 473 or (resid 474 throu \ gh 475 and (name N or name CA or name C or name O or name CB )) or resid 476 thr \ ough 477 or (resid 478 through 479 and (name N or name CA or name C or name O or \ name CB )) or resid 480 through 535 or (resid 536 through 537 and (name N or na \ me CA or name C or name O or name CB )) or resid 538 or (resid 539 through 541 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 542 through 54 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 546 through \ 547 or (resid 548 and (name N or name CA or name C or name O or name CB )) or re \ sid 549 or (resid 550 and (name N or name CA or name C or name O or name CB )) o \ r resid 551 through 557 or (resid 558 through 559 and (name N or name CA or name \ C or name O or name CB )) or resid 560 through 564 or (resid 565 through 566 an \ d (name N or name CA or name C or name O or name CB )) or resid 567 through 579 \ or (resid 580 through 581 and (name N or name CA or name C or name O or name CB \ )) or resid 582 through 585 or (resid 586 and (name N or name CA or name C or na \ me O or name CB )) or resid 587 through 595)) } 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.260 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 68.400 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.130 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 29270 Z= 0.226 Angle : 0.663 23.224 39710 Z= 0.469 Chirality : 0.040 0.153 4762 Planarity : 0.003 0.078 5094 Dihedral : 11.875 87.697 10904 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.52 % Favored : 97.37 % Rotamer: Outliers : 0.31 % Allowed : 3.10 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.11), residues: 3806 helix: -2.60 (0.10), residues: 1423 sheet: -2.96 (0.16), residues: 670 loop : -1.99 (0.13), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 46 HIS 0.003 0.000 HIS F 249 PHE 0.008 0.001 PHE D 132 TYR 0.012 0.001 TYR D 508 ARG 0.003 0.000 ARG A 522 Details of bonding type rmsd hydrogen bonds : bond 0.25757 ( 1033) hydrogen bonds : angle 8.24040 ( 3003) covalent geometry : bond 0.00297 (29270) covalent geometry : angle 0.66323 (39710) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 427 time to evaluate : 3.524 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: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7410 (mpt-90) cc_final: 0.6433 (mmm160) REVERT: D 202 ARG cc_start: 0.6268 (OUTLIER) cc_final: 0.5637 (mpp80) REVERT: D 246 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7058 (tm-30) REVERT: D 255 LYS cc_start: 0.7368 (mmmt) cc_final: 0.6525 (mmmt) REVERT: D 355 LYS cc_start: 0.7568 (mmtm) cc_final: 0.7310 (mmtp) REVERT: D 483 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7390 (tm-30) REVERT: D 612 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8288 (tttt) REVERT: C 46 TRP cc_start: 0.8317 (t60) cc_final: 0.7942 (t60) REVERT: C 119 VAL cc_start: 0.8985 (p) cc_final: 0.8652 (m) REVERT: C 470 LEU cc_start: 0.8259 (tp) cc_final: 0.8059 (tt) REVERT: B 525 MET cc_start: 0.8228 (mtp) cc_final: 0.8002 (mtp) REVERT: B 552 ILE cc_start: 0.8145 (tt) cc_final: 0.6998 (tt) REVERT: B 570 MET cc_start: 0.8831 (ttp) cc_final: 0.8625 (ttm) REVERT: E 52 PHE cc_start: 0.6874 (t80) cc_final: 0.6413 (m-80) REVERT: E 200 MET cc_start: 0.1746 (mmp) cc_final: 0.1325 (ptt) REVERT: E 217 LEU cc_start: 0.8103 (mm) cc_final: 0.7271 (mm) REVERT: A 1 MET cc_start: 0.6643 (ptp) cc_final: 0.6051 (pmm) REVERT: A 195 LEU cc_start: 0.7904 (mp) cc_final: 0.7459 (tp) REVERT: F 42 LEU cc_start: 0.7233 (tt) cc_final: 0.6723 (tp) REVERT: F 525 MET cc_start: 0.7772 (mtp) cc_final: 0.7383 (mtt) REVERT: F 548 GLN cc_start: 0.6609 (tp-100) cc_final: 0.6094 (tm-30) REVERT: F 572 LEU cc_start: 0.8457 (mt) cc_final: 0.8027 (mt) REVERT: F 591 MET cc_start: 0.8428 (tmm) cc_final: 0.7517 (tmm) REVERT: F 592 MET cc_start: 0.7471 (mmm) cc_final: 0.7182 (mmm) outliers start: 9 outliers final: 3 residues processed: 434 average time/residue: 0.5257 time to fit residues: 332.0547 Evaluate side-chains 240 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 236 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain E residue 318 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 6.9990 chunk 289 optimal weight: 20.0000 chunk 160 optimal weight: 0.0040 chunk 98 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 299 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 182 optimal weight: 0.6980 chunk 222 optimal weight: 2.9990 chunk 346 optimal weight: 5.9990 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 HIS D 344 ASN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN C 294 HIS C 412 GLN C 649 GLN B 199 GLN B 344 ASN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN E 98 ASN E 151 GLN ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN E 618 ASN A 170 ASN A 344 ASN A 407 HIS ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.136414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.107868 restraints weight = 78232.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.106521 restraints weight = 62486.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.107490 restraints weight = 65470.583| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29270 Z= 0.180 Angle : 0.594 9.740 39710 Z= 0.302 Chirality : 0.043 0.169 4762 Planarity : 0.004 0.044 5094 Dihedral : 7.060 85.118 4295 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.03 % Rotamer: Outliers : 1.81 % Allowed : 9.60 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.12), residues: 3806 helix: -0.78 (0.12), residues: 1472 sheet: -2.61 (0.18), residues: 640 loop : -1.63 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 46 HIS 0.006 0.001 HIS B 294 PHE 0.018 0.002 PHE D 443 TYR 0.024 0.002 TYR B 531 ARG 0.009 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 1033) hydrogen bonds : angle 5.05677 ( 3003) covalent geometry : bond 0.00421 (29270) covalent geometry : angle 0.59394 (39710) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 247 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7511 (mpt-90) cc_final: 0.6609 (mmm160) REVERT: D 202 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.5960 (mpp80) REVERT: D 241 PHE cc_start: 0.6742 (m-80) cc_final: 0.6254 (m-80) REVERT: D 246 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7319 (tm-30) REVERT: D 355 LYS cc_start: 0.7640 (mmtm) cc_final: 0.7374 (mmtp) REVERT: D 483 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7532 (tm-30) REVERT: D 612 LYS cc_start: 0.8528 (ttmt) cc_final: 0.8102 (pttp) REVERT: C 225 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8600 (t) REVERT: B 552 ILE cc_start: 0.7764 (tt) cc_final: 0.6110 (tt) REVERT: E 200 MET cc_start: 0.2095 (mmp) cc_final: 0.1571 (ptt) REVERT: E 225 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8568 (t) REVERT: E 340 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7163 (mmt90) REVERT: A 1 MET cc_start: 0.7194 (ptp) cc_final: 0.6547 (pmm) REVERT: A 535 MET cc_start: 0.8713 (mtp) cc_final: 0.8467 (mtp) REVERT: F 42 LEU cc_start: 0.6581 (tt) cc_final: 0.6202 (tp) REVERT: F 303 LEU cc_start: 0.8197 (mt) cc_final: 0.7827 (mp) REVERT: F 548 GLN cc_start: 0.6071 (tp-100) cc_final: 0.5868 (tm-30) REVERT: F 591 MET cc_start: 0.8385 (tmm) cc_final: 0.7457 (tmm) outliers start: 52 outliers final: 27 residues processed: 288 average time/residue: 0.4332 time to fit residues: 195.9548 Evaluate side-chains 233 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 266 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 212 optimal weight: 0.0370 chunk 90 optimal weight: 0.9980 chunk 379 optimal weight: 30.0000 chunk 196 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 296 optimal weight: 6.9990 chunk 78 optimal weight: 0.0670 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN ** D 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 GLN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 412 GLN F 437 ASN F 446 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.134126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105084 restraints weight = 76807.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.103420 restraints weight = 58044.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.104241 restraints weight = 64899.108| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29270 Z= 0.148 Angle : 0.542 10.355 39710 Z= 0.272 Chirality : 0.042 0.153 4762 Planarity : 0.004 0.040 5094 Dihedral : 6.876 88.436 4291 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.76 % Favored : 97.21 % Rotamer: Outliers : 2.02 % Allowed : 12.70 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 3806 helix: 0.05 (0.13), residues: 1470 sheet: -2.46 (0.18), residues: 612 loop : -1.34 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 46 HIS 0.008 0.001 HIS F 249 PHE 0.018 0.001 PHE D 10 TYR 0.018 0.002 TYR B 531 ARG 0.006 0.000 ARG B 536 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 1033) hydrogen bonds : angle 4.61412 ( 3003) covalent geometry : bond 0.00347 (29270) covalent geometry : angle 0.54213 (39710) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7519 (mpt-90) cc_final: 0.6638 (mmm160) REVERT: D 202 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.6217 (mpp80) REVERT: D 241 PHE cc_start: 0.6903 (m-80) cc_final: 0.6314 (m-80) REVERT: D 246 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7288 (tm-30) REVERT: D 355 LYS cc_start: 0.7724 (mmtm) cc_final: 0.7484 (mmtp) REVERT: D 483 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7490 (tm-30) REVERT: D 612 LYS cc_start: 0.8595 (ttmt) cc_final: 0.8132 (pttp) REVERT: C 189 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8062 (pt0) REVERT: C 225 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8620 (t) REVERT: C 603 LEU cc_start: 0.5334 (mt) cc_final: 0.5012 (pt) REVERT: B 97 TYR cc_start: 0.7179 (p90) cc_final: 0.6931 (p90) REVERT: B 525 MET cc_start: 0.7701 (mtp) cc_final: 0.7304 (mtm) REVERT: B 535 MET cc_start: 0.8022 (mmm) cc_final: 0.7820 (mmm) REVERT: E 200 MET cc_start: 0.2318 (mmp) cc_final: 0.1654 (ptt) REVERT: E 369 ASP cc_start: 0.6487 (p0) cc_final: 0.6256 (t70) REVERT: E 603 LEU cc_start: 0.5812 (OUTLIER) cc_final: 0.5598 (mp) REVERT: A 1 MET cc_start: 0.7200 (ptp) cc_final: 0.6552 (pmm) REVERT: A 195 LEU cc_start: 0.7440 (mt) cc_final: 0.7023 (tp) REVERT: A 591 MET cc_start: 0.7182 (tmm) cc_final: 0.6245 (tmm) REVERT: F 42 LEU cc_start: 0.7049 (tt) cc_final: 0.6703 (tp) REVERT: F 548 GLN cc_start: 0.6128 (tp-100) cc_final: 0.5706 (tm-30) REVERT: F 591 MET cc_start: 0.8389 (tmm) cc_final: 0.7764 (tmm) REVERT: F 592 MET cc_start: 0.7177 (mmm) cc_final: 0.6754 (mmm) outliers start: 58 outliers final: 32 residues processed: 264 average time/residue: 0.4216 time to fit residues: 179.2473 Evaluate side-chains 232 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 603 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 326 optimal weight: 9.9990 chunk 338 optimal weight: 8.9990 chunk 145 optimal weight: 0.0370 chunk 12 optimal weight: 0.9980 chunk 293 optimal weight: 0.0000 chunk 119 optimal weight: 0.5980 chunk 341 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 345 optimal weight: 6.9990 overall best weight: 0.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 HIS ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 248 ASN B 437 ASN B 556 GLN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 444 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.136613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.107253 restraints weight = 77376.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.105937 restraints weight = 62849.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.106982 restraints weight = 60749.818| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29270 Z= 0.102 Angle : 0.507 10.250 39710 Z= 0.254 Chirality : 0.041 0.182 4762 Planarity : 0.003 0.048 5094 Dihedral : 6.680 88.035 4291 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 2.16 % Allowed : 13.47 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3806 helix: 0.44 (0.14), residues: 1478 sheet: -2.31 (0.19), residues: 600 loop : -1.13 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 375 HIS 0.005 0.001 HIS F 249 PHE 0.024 0.001 PHE B 10 TYR 0.015 0.001 TYR B 531 ARG 0.006 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.02999 ( 1033) hydrogen bonds : angle 4.30369 ( 3003) covalent geometry : bond 0.00223 (29270) covalent geometry : angle 0.50743 (39710) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 208 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7590 (mpt-90) cc_final: 0.6708 (mmm160) REVERT: D 202 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.5969 (mpp80) REVERT: D 246 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7180 (tm-30) REVERT: D 355 LYS cc_start: 0.7613 (mmtm) cc_final: 0.7387 (mmtp) REVERT: D 612 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8142 (pttp) REVERT: C 189 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8203 (pt0) REVERT: C 603 LEU cc_start: 0.5168 (mt) cc_final: 0.4929 (pt) REVERT: E 200 MET cc_start: 0.2479 (mmt) cc_final: 0.1710 (ptt) REVERT: E 340 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7174 (mmt90) REVERT: E 369 ASP cc_start: 0.6673 (p0) cc_final: 0.6420 (t70) REVERT: E 525 MET cc_start: 0.8233 (mtp) cc_final: 0.7964 (mtp) REVERT: A 1 MET cc_start: 0.7087 (ptp) cc_final: 0.6417 (pmm) REVERT: A 195 LEU cc_start: 0.7351 (mt) cc_final: 0.7016 (tp) REVERT: F 212 LEU cc_start: 0.7099 (mt) cc_final: 0.6731 (mp) REVERT: F 548 GLN cc_start: 0.5971 (tp-100) cc_final: 0.5654 (tm-30) outliers start: 62 outliers final: 33 residues processed: 255 average time/residue: 0.5181 time to fit residues: 220.5780 Evaluate side-chains 220 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 556 GLN Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 230 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 6 optimal weight: 0.5980 chunk 279 optimal weight: 20.0000 chunk 136 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 GLN B 556 GLN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.134801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.105874 restraints weight = 76826.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.104039 restraints weight = 64456.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.104856 restraints weight = 73950.922| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 29270 Z= 0.160 Angle : 0.552 12.329 39710 Z= 0.275 Chirality : 0.042 0.173 4762 Planarity : 0.004 0.045 5094 Dihedral : 6.740 84.528 4291 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 2.57 % Allowed : 14.20 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 3806 helix: 0.54 (0.14), residues: 1489 sheet: -2.23 (0.19), residues: 605 loop : -1.14 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 375 HIS 0.005 0.001 HIS F 249 PHE 0.027 0.002 PHE E 132 TYR 0.021 0.002 TYR B 532 ARG 0.019 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 1033) hydrogen bonds : angle 4.28416 ( 3003) covalent geometry : bond 0.00385 (29270) covalent geometry : angle 0.55156 (39710) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 195 time to evaluate : 3.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7618 (mpt-90) cc_final: 0.6789 (mmm160) REVERT: D 202 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.6361 (mpp80) REVERT: D 246 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7422 (tm-30) REVERT: D 355 LYS cc_start: 0.7605 (mmtm) cc_final: 0.7373 (mmtp) REVERT: D 612 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8167 (pttp) REVERT: C 189 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8330 (pt0) REVERT: C 603 LEU cc_start: 0.5465 (mt) cc_final: 0.5206 (pt) REVERT: B 97 TYR cc_start: 0.7211 (p90) cc_final: 0.6858 (p90) REVERT: A 1 MET cc_start: 0.7022 (ptp) cc_final: 0.6375 (pmm) REVERT: A 195 LEU cc_start: 0.7461 (mt) cc_final: 0.7089 (tp) REVERT: A 591 MET cc_start: 0.7319 (tmm) cc_final: 0.6521 (tmm) REVERT: F 548 GLN cc_start: 0.6084 (tp-100) cc_final: 0.5647 (tm-30) REVERT: F 591 MET cc_start: 0.8350 (tmm) cc_final: 0.7683 (tmm) outliers start: 74 outliers final: 46 residues processed: 254 average time/residue: 0.4005 time to fit residues: 166.8232 Evaluate side-chains 225 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 309 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 83 optimal weight: 1.9990 chunk 29 optimal weight: 0.0770 chunk 18 optimal weight: 0.3980 chunk 128 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 349 optimal weight: 7.9990 chunk 286 optimal weight: 10.0000 chunk 272 optimal weight: 50.0000 chunk 20 optimal weight: 0.0870 chunk 235 optimal weight: 3.9990 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.132636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.104317 restraints weight = 76384.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.102654 restraints weight = 61605.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.103343 restraints weight = 72591.527| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29270 Z= 0.136 Angle : 0.532 10.941 39710 Z= 0.265 Chirality : 0.042 0.183 4762 Planarity : 0.004 0.042 5094 Dihedral : 6.661 83.198 4291 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.85 % Rotamer: Outliers : 2.23 % Allowed : 15.31 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3806 helix: 0.64 (0.14), residues: 1490 sheet: -2.16 (0.19), residues: 597 loop : -1.02 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 375 HIS 0.009 0.001 HIS F 249 PHE 0.024 0.001 PHE D 10 TYR 0.016 0.001 TYR F 531 ARG 0.020 0.000 ARG F 578 Details of bonding type rmsd hydrogen bonds : bond 0.02958 ( 1033) hydrogen bonds : angle 4.14138 ( 3003) covalent geometry : bond 0.00322 (29270) covalent geometry : angle 0.53187 (39710) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 198 time to evaluate : 3.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.7023 (p0) REVERT: D 152 ARG cc_start: 0.7614 (mpt-90) cc_final: 0.6791 (mmm160) REVERT: D 202 ARG cc_start: 0.6747 (OUTLIER) cc_final: 0.6224 (mpp80) REVERT: D 612 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8200 (pttp) REVERT: C 92 VAL cc_start: 0.6228 (OUTLIER) cc_final: 0.5878 (p) REVERT: C 189 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8402 (pt0) REVERT: C 422 ILE cc_start: 0.7668 (mm) cc_final: 0.7334 (tp) REVERT: C 488 VAL cc_start: 0.8667 (t) cc_final: 0.8363 (p) REVERT: B 97 TYR cc_start: 0.7191 (p90) cc_final: 0.6710 (p90) REVERT: B 425 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8160 (p) REVERT: E 42 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6582 (tt) REVERT: E 200 MET cc_start: 0.2752 (mmt) cc_final: 0.1166 (ptt) REVERT: A 1 MET cc_start: 0.7063 (ptp) cc_final: 0.6376 (pmm) REVERT: A 195 LEU cc_start: 0.7291 (mt) cc_final: 0.7026 (tp) REVERT: A 592 MET cc_start: 0.8163 (mpp) cc_final: 0.7911 (mpp) REVERT: F 97 TYR cc_start: 0.7210 (p90) cc_final: 0.6906 (p90) REVERT: F 212 LEU cc_start: 0.7428 (mt) cc_final: 0.7135 (mp) REVERT: F 548 GLN cc_start: 0.5876 (tp-100) cc_final: 0.5539 (tm-30) outliers start: 64 outliers final: 49 residues processed: 252 average time/residue: 0.3915 time to fit residues: 161.6439 Evaluate side-chains 233 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 367 optimal weight: 0.0770 chunk 229 optimal weight: 0.8980 chunk 358 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 213 optimal weight: 0.5980 chunk 315 optimal weight: 20.0000 chunk 316 optimal weight: 5.9990 chunk 267 optimal weight: 0.8980 chunk 306 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN E 618 ASN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.133703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.105567 restraints weight = 76343.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.104049 restraints weight = 63172.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105216 restraints weight = 64082.912| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29270 Z= 0.112 Angle : 0.531 11.096 39710 Z= 0.262 Chirality : 0.042 0.189 4762 Planarity : 0.003 0.044 5094 Dihedral : 6.542 82.534 4291 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.93 % Rotamer: Outliers : 2.16 % Allowed : 15.83 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3806 helix: 0.71 (0.14), residues: 1495 sheet: -2.09 (0.19), residues: 580 loop : -0.99 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 375 HIS 0.002 0.001 HIS A 567 PHE 0.017 0.001 PHE E 132 TYR 0.016 0.001 TYR B 532 ARG 0.010 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.02823 ( 1033) hydrogen bonds : angle 4.06289 ( 3003) covalent geometry : bond 0.00257 (29270) covalent geometry : angle 0.53116 (39710) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 188 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7696 (mpt-90) cc_final: 0.6725 (mmm160) REVERT: D 202 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.6131 (mpp80) REVERT: D 612 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8183 (pttp) REVERT: C 92 VAL cc_start: 0.6236 (OUTLIER) cc_final: 0.5859 (p) REVERT: C 189 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8462 (pt0) REVERT: C 200 MET cc_start: 0.5499 (tpp) cc_final: 0.5296 (mmt) REVERT: C 422 ILE cc_start: 0.7664 (mm) cc_final: 0.7372 (tp) REVERT: C 488 VAL cc_start: 0.8661 (t) cc_final: 0.8361 (p) REVERT: B 97 TYR cc_start: 0.7142 (p90) cc_final: 0.6699 (p90) REVERT: B 592 MET cc_start: 0.7273 (mmm) cc_final: 0.7043 (mpp) REVERT: E 42 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6518 (tt) REVERT: E 200 MET cc_start: 0.2567 (mmt) cc_final: 0.1082 (ptt) REVERT: A 1 MET cc_start: 0.7033 (ptp) cc_final: 0.6367 (pmm) REVERT: A 195 LEU cc_start: 0.7249 (mt) cc_final: 0.7010 (tp) REVERT: F 97 TYR cc_start: 0.7230 (p90) cc_final: 0.7017 (p90) REVERT: F 548 GLN cc_start: 0.5852 (tp-100) cc_final: 0.5551 (tm-30) outliers start: 62 outliers final: 45 residues processed: 238 average time/residue: 0.3967 time to fit residues: 155.2473 Evaluate side-chains 226 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 177 time to evaluate : 3.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 92 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 303 optimal weight: 0.0870 chunk 371 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 320 optimal weight: 10.0000 chunk 183 optimal weight: 0.2980 chunk 241 optimal weight: 1.9990 chunk 290 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 GLN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.133334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.104744 restraints weight = 76448.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.102709 restraints weight = 59175.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.103575 restraints weight = 62674.025| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29270 Z= 0.116 Angle : 0.531 11.763 39710 Z= 0.262 Chirality : 0.042 0.179 4762 Planarity : 0.004 0.044 5094 Dihedral : 6.369 81.248 4289 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 2.26 % Allowed : 16.08 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3806 helix: 0.78 (0.14), residues: 1497 sheet: -2.07 (0.19), residues: 593 loop : -0.96 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 375 HIS 0.003 0.001 HIS C 93 PHE 0.016 0.001 PHE D 10 TYR 0.022 0.001 TYR F 341 ARG 0.012 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.02756 ( 1033) hydrogen bonds : angle 4.01923 ( 3003) covalent geometry : bond 0.00270 (29270) covalent geometry : angle 0.53062 (39710) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7710 (mpt-90) cc_final: 0.6570 (mmm160) REVERT: D 612 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8175 (pttp) REVERT: C 92 VAL cc_start: 0.6347 (OUTLIER) cc_final: 0.5938 (p) REVERT: C 189 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8472 (pt0) REVERT: C 422 ILE cc_start: 0.7620 (mm) cc_final: 0.7374 (tp) REVERT: C 488 VAL cc_start: 0.8655 (t) cc_final: 0.8350 (p) REVERT: B 97 TYR cc_start: 0.7162 (p90) cc_final: 0.6725 (p90) REVERT: E 42 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6496 (tt) REVERT: E 200 MET cc_start: 0.2427 (mmt) cc_final: 0.0945 (ptt) REVERT: A 1 MET cc_start: 0.7058 (ptp) cc_final: 0.6378 (pmm) REVERT: A 195 LEU cc_start: 0.7411 (mt) cc_final: 0.7068 (tp) REVERT: A 591 MET cc_start: 0.7500 (tmm) cc_final: 0.6572 (tmm) REVERT: F 97 TYR cc_start: 0.7408 (p90) cc_final: 0.7188 (p90) REVERT: F 548 GLN cc_start: 0.5894 (tp-100) cc_final: 0.5600 (tm-30) outliers start: 65 outliers final: 52 residues processed: 241 average time/residue: 0.3644 time to fit residues: 145.7413 Evaluate side-chains 224 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 154 optimal weight: 0.7980 chunk 332 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 346 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 258 optimal weight: 0.2980 chunk 343 optimal weight: 0.9980 chunk 269 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.132536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.104737 restraints weight = 76211.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.103081 restraints weight = 61144.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.103975 restraints weight = 66973.431| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29270 Z= 0.124 Angle : 0.541 14.594 39710 Z= 0.266 Chirality : 0.042 0.180 4762 Planarity : 0.004 0.043 5094 Dihedral : 6.285 80.372 4285 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.72 % Rotamer: Outliers : 2.26 % Allowed : 16.25 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3806 helix: 0.86 (0.14), residues: 1490 sheet: -2.02 (0.19), residues: 612 loop : -0.93 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 375 HIS 0.003 0.001 HIS F 249 PHE 0.014 0.001 PHE E 132 TYR 0.018 0.001 TYR F 341 ARG 0.009 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.02791 ( 1033) hydrogen bonds : angle 4.01582 ( 3003) covalent geometry : bond 0.00293 (29270) covalent geometry : angle 0.54128 (39710) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 180 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7741 (mpt-90) cc_final: 0.7018 (mmm160) REVERT: D 612 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8194 (pttp) REVERT: C 92 VAL cc_start: 0.6349 (OUTLIER) cc_final: 0.5943 (p) REVERT: C 422 ILE cc_start: 0.7642 (mm) cc_final: 0.7420 (tp) REVERT: C 470 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8507 (mp) REVERT: C 488 VAL cc_start: 0.8698 (t) cc_final: 0.8407 (p) REVERT: B 97 TYR cc_start: 0.7116 (p90) cc_final: 0.6650 (p90) REVERT: E 200 MET cc_start: 0.2472 (mmt) cc_final: 0.0946 (ptt) REVERT: A 1 MET cc_start: 0.7003 (ptp) cc_final: 0.6387 (pmm) REVERT: A 195 LEU cc_start: 0.7266 (mt) cc_final: 0.6975 (tp) REVERT: A 592 MET cc_start: 0.8305 (mpp) cc_final: 0.7999 (mpp) REVERT: F 1 MET cc_start: 0.2391 (tmm) cc_final: 0.2181 (tmm) outliers start: 65 outliers final: 50 residues processed: 234 average time/residue: 0.3701 time to fit residues: 144.9559 Evaluate side-chains 227 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 175 time to evaluate : 3.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 48 optimal weight: 2.9990 chunk 231 optimal weight: 0.5980 chunk 216 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 262 optimal weight: 9.9990 chunk 285 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 118 optimal weight: 0.0980 chunk 302 optimal weight: 4.9990 chunk 374 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 GLN E 344 ASN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.133734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.105343 restraints weight = 76641.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.103385 restraints weight = 59646.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.104357 restraints weight = 65488.694| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29270 Z= 0.111 Angle : 0.533 13.749 39710 Z= 0.262 Chirality : 0.042 0.169 4762 Planarity : 0.004 0.044 5094 Dihedral : 6.170 79.829 4285 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 1.98 % Allowed : 16.35 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3806 helix: 0.90 (0.14), residues: 1490 sheet: -1.98 (0.19), residues: 630 loop : -0.89 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 375 HIS 0.003 0.001 HIS F 249 PHE 0.015 0.001 PHE E 132 TYR 0.026 0.001 TYR F 97 ARG 0.010 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.02724 ( 1033) hydrogen bonds : angle 3.94597 ( 3003) covalent geometry : bond 0.00258 (29270) covalent geometry : angle 0.53276 (39710) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 183 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7773 (mpt-90) cc_final: 0.6933 (mmm160) REVERT: D 612 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8176 (pttp) REVERT: C 6 MET cc_start: 0.7017 (mtm) cc_final: 0.6504 (ttm) REVERT: C 92 VAL cc_start: 0.6304 (OUTLIER) cc_final: 0.5917 (p) REVERT: C 422 ILE cc_start: 0.7666 (mm) cc_final: 0.7455 (tp) REVERT: C 470 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8462 (mp) REVERT: C 488 VAL cc_start: 0.8661 (t) cc_final: 0.8366 (p) REVERT: B 97 TYR cc_start: 0.7147 (p90) cc_final: 0.6667 (p90) REVERT: E 200 MET cc_start: 0.2511 (mmt) cc_final: 0.0962 (ptt) REVERT: A 1 MET cc_start: 0.7088 (ptp) cc_final: 0.6400 (pmm) REVERT: A 195 LEU cc_start: 0.7399 (mt) cc_final: 0.7072 (tp) outliers start: 57 outliers final: 50 residues processed: 230 average time/residue: 0.3771 time to fit residues: 143.7973 Evaluate side-chains 224 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 183 optimal weight: 0.3980 chunk 363 optimal weight: 0.0030 chunk 240 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 347 optimal weight: 0.8980 chunk 129 optimal weight: 0.0970 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.135766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.106225 restraints weight = 76630.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.104284 restraints weight = 64951.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.105367 restraints weight = 59319.595| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29270 Z= 0.098 Angle : 0.531 14.524 39710 Z= 0.261 Chirality : 0.042 0.160 4762 Planarity : 0.003 0.044 5094 Dihedral : 6.030 78.784 4285 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.98 % Rotamer: Outliers : 1.91 % Allowed : 16.70 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3806 helix: 0.96 (0.14), residues: 1488 sheet: -1.87 (0.19), residues: 621 loop : -0.84 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 375 HIS 0.003 0.000 HIS F 249 PHE 0.015 0.001 PHE E 132 TYR 0.034 0.001 TYR F 341 ARG 0.007 0.000 ARG A 522 Details of bonding type rmsd hydrogen bonds : bond 0.02625 ( 1033) hydrogen bonds : angle 3.91372 ( 3003) covalent geometry : bond 0.00220 (29270) covalent geometry : angle 0.53095 (39710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8914.83 seconds wall clock time: 156 minutes 51.34 seconds (9411.34 seconds total)