Starting phenix.real_space_refine on Fri Mar 6 22:17:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ln6_23450/03_2026/7ln6_23450.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ln6_23450/03_2026/7ln6_23450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ln6_23450/03_2026/7ln6_23450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ln6_23450/03_2026/7ln6_23450.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ln6_23450/03_2026/7ln6_23450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ln6_23450/03_2026/7ln6_23450.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 31 5.49 5 Mg 7 5.21 5 S 178 5.16 5 C 21962 2.51 5 N 6222 2.21 5 O 6672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35072 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5693 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 690} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 5766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5766 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 700} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 5866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5866 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 710} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 5869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5869 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 710} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 5800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5800 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 5604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5604 Classifications: {'peptide': 714} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 672} Chain breaks: 4 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 115 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 90 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.12, per 1000 atoms: 0.26 Number of scatterers: 35072 At special positions: 0 Unit cell: (166.891, 170.08, 147.757, 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 178 16.00 P 31 15.00 Mg 7 11.99 O 6672 8.00 N 6222 7.00 C 21962 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.3 seconds 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8332 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 30 sheets defined 51.3% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 129 through 140 removed outlier: 4.737A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 190 through 199 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.462A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.757A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.552A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.313A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 335 removed outlier: 3.936A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.780A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 438 through 445 removed outlier: 3.549A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 3.780A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 523 through 536 removed outlier: 4.193A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 removed outlier: 4.117A pdb=" N LEU A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 544 through 548' Processing helix chain 'A' and resid 553 through 569 Processing helix chain 'A' and resid 578 through 583 removed outlier: 4.303A pdb=" N ILE A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 609 removed outlier: 3.518A pdb=" N ALA A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 714 removed outlier: 4.090A pdb=" N ARG A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 743 Processing helix chain 'A' and resid 748 through 766 removed outlier: 3.769A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 85 through 93 removed outlier: 3.634A pdb=" N ARG B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 129 through 140 removed outlier: 4.450A pdb=" N LYS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 190 through 200 removed outlier: 4.071A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.543A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.162A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.291A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 280 through 296 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.550A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 336 removed outlier: 3.932A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.695A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 427 Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.570A pdb=" N LEU B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 482 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.970A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 532 removed outlier: 3.875A pdb=" N ILE B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 547 removed outlier: 4.015A pdb=" N LEU B 547 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 569 removed outlier: 3.539A pdb=" N ALA B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 583 removed outlier: 4.153A pdb=" N ILE B 582 " --> pdb=" O GLN B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 609 removed outlier: 3.557A pdb=" N ASN B 602 " --> pdb=" O ASP B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.653A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 714 Processing helix chain 'B' and resid 732 through 741 removed outlier: 3.821A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 766 Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 129 through 140 removed outlier: 4.692A pdb=" N LYS C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix Processing helix chain 'C' and resid 190 through 199 removed outlier: 3.668A pdb=" N GLU C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.302A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.011A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 272 through 275 Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.772A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.709A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 426 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.531A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 3.806A pdb=" N VAL C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 4.082A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 545 through 547 No H-bonds generated for 'chain 'C' and resid 545 through 547' Processing helix chain 'C' and resid 553 through 569 Processing helix chain 'C' and resid 578 through 583 removed outlier: 4.131A pdb=" N ILE C 582 " --> pdb=" O GLN C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 609 removed outlier: 3.756A pdb=" N ASN C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.775A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 714 removed outlier: 3.671A pdb=" N ARG C 713 " --> pdb=" O ARG C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 741 removed outlier: 3.628A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 766 removed outlier: 3.698A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 120 through 123 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.613A pdb=" N GLU D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.561A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 228 through 234 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 272 through 275 Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 318 through 333 removed outlier: 3.553A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.834A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.572A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 426 removed outlier: 3.568A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.539A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 499 removed outlier: 3.672A pdb=" N VAL D 493 " --> pdb=" O LEU D 489 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.940A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.578A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 548 Processing helix chain 'D' and resid 553 through 569 removed outlier: 3.683A pdb=" N VAL D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 583 removed outlier: 4.021A pdb=" N ILE D 582 " --> pdb=" O GLN D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 609 Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.906A pdb=" N ILE D 628 " --> pdb=" O ARG D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.788A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 714 Processing helix chain 'D' and resid 732 through 741 removed outlier: 3.524A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 765 removed outlier: 4.076A pdb=" N TYR D 755 " --> pdb=" O ASP D 751 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE D 758 " --> pdb=" O LYS D 754 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 762 " --> pdb=" O PHE D 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 120 through 123 Processing helix chain 'E' and resid 129 through 140 removed outlier: 4.693A pdb=" N LYS E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Proline residue: E 137 - end of helix Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.847A pdb=" N GLU E 194 " --> pdb=" O LYS E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.906A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.808A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 272 through 275 Processing helix chain 'E' and resid 280 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.175A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 339 removed outlier: 4.296A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN E 337 " --> pdb=" O ASP E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.672A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 427 Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.504A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.479A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.918A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 534 removed outlier: 3.582A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 547 No H-bonds generated for 'chain 'E' and resid 545 through 547' Processing helix chain 'E' and resid 553 through 569 removed outlier: 3.632A pdb=" N VAL E 559 " --> pdb=" O SER E 555 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA E 569 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 595 through 611 Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.882A pdb=" N ILE E 628 " --> pdb=" O ARG E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.905A pdb=" N LEU E 634 " --> pdb=" O ASP E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 662 removed outlier: 3.584A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.595A pdb=" N ALA E 676 " --> pdb=" O LEU E 672 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 714 Processing helix chain 'E' and resid 732 through 742 removed outlier: 3.948A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 766 removed outlier: 3.766A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR E 755 " --> pdb=" O ASP E 751 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA E 759 " --> pdb=" O TYR E 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 129 through 139 removed outlier: 4.901A pdb=" N LYS F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Proline residue: F 137 - end of helix Processing helix chain 'F' and resid 190 through 200 removed outlier: 3.503A pdb=" N GLU F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.022A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 removed outlier: 3.648A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 271 through 277 Processing helix chain 'F' and resid 280 through 296 Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.547A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 387 removed outlier: 4.228A pdb=" N ASN F 387 " --> pdb=" O ILE F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.739A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 426 Processing helix chain 'F' and resid 438 through 445 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.662A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 494 Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 499 through 506 Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.767A pdb=" N CYS F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 548 removed outlier: 4.129A pdb=" N LEU F 548 " --> pdb=" O GLY F 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 544 through 548' Processing helix chain 'F' and resid 553 through 569 Processing helix chain 'F' and resid 578 through 583 removed outlier: 3.564A pdb=" N ILE F 582 " --> pdb=" O GLN F 578 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA F 583 " --> pdb=" O LEU F 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 578 through 583' Processing helix chain 'F' and resid 599 through 611 Processing helix chain 'F' and resid 612 through 614 No H-bonds generated for 'chain 'F' and resid 612 through 614' Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.644A pdb=" N LEU F 634 " --> pdb=" O ASP F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 664 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 714 Processing helix chain 'F' and resid 732 through 743 Processing helix chain 'F' and resid 748 through 762 removed outlier: 3.840A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 762 " --> pdb=" O PHE F 758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 29 removed outlier: 7.416A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 39 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS A 69 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 154 removed outlier: 5.839A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 167 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 146 removed outlier: 3.818A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.212A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 543 removed outlier: 6.120A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 30 removed outlier: 6.253A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 40 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL B 39 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG B 65 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 151 through 154 removed outlier: 6.391A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE B 114 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 147 removed outlier: 3.659A pdb=" N CYS B 174 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.709A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.393A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 26 through 29 removed outlier: 5.998A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 151 through 154 removed outlier: 3.624A pdb=" N VAL C 154 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 167 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 113 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 114 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS C 183 " --> pdb=" O ILE C 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.809A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.384A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 538 through 543 removed outlier: 6.724A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 25 through 29 removed outlier: 7.687A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 109 through 110 removed outlier: 6.760A pdb=" N LYS D 109 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG D 144 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 151 through 154 removed outlier: 6.596A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.454A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.516A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 26 through 29 removed outlier: 6.084A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 151 through 154 removed outlier: 6.283A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS E 183 " --> pdb=" O ILE E 114 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 145 through 147 removed outlier: 3.775A pdb=" N ILE E 146 " --> pdb=" O CYS E 174 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N CYS E 174 " --> pdb=" O ILE E 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.391A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 538 through 543 removed outlier: 3.658A pdb=" N GLY E 621 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 25 through 29 removed outlier: 5.751A pdb=" N VAL F 39 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS F 69 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL F 57 " --> pdb=" O CYS F 69 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 151 through 154 removed outlier: 3.501A pdb=" N VAL F 154 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS F 183 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 145 through 147 removed outlier: 3.603A pdb=" N CYS F 174 " --> pdb=" O ILE F 146 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.954A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE F 241 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR F 347 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU F 243 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 538 through 543 removed outlier: 3.557A pdb=" N VAL F 573 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA F 622 " --> pdb=" O PHE F 576 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) 1581 hydrogen bonds defined for protein. 4581 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: 8.90 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 35321 1.57 - 1.92: 333 1.92 - 2.27: 0 2.27 - 2.62: 0 2.62 - 2.96: 3 Bond restraints: 35657 Sorted by residual: bond pdb=" C LEU B 464 " pdb=" N ARG B 465 " ideal model delta sigma weight residual 1.332 2.953 -1.620 1.40e-02 5.10e+03 1.34e+04 bond pdb=" C LEU E 464 " pdb=" N ARG E 465 " ideal model delta sigma weight residual 1.332 2.888 -1.556 1.40e-02 5.10e+03 1.24e+04 bond pdb=" C LEU D 464 " pdb=" N ARG D 465 " ideal model delta sigma weight residual 1.333 2.965 -1.632 1.73e-02 3.34e+03 8.90e+03 bond pdb=" CG PRO A 137 " pdb=" CD PRO A 137 " ideal model delta sigma weight residual 1.503 1.234 0.269 3.40e-02 8.65e+02 6.27e+01 bond pdb=" CB PRO A 137 " pdb=" CG PRO A 137 " ideal model delta sigma weight residual 1.492 1.614 -0.122 5.00e-02 4.00e+02 5.95e+00 ... (remaining 35652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.40: 48214 13.40 - 26.79: 1 26.79 - 40.19: 2 40.19 - 53.58: 0 53.58 - 66.98: 2 Bond angle restraints: 48219 Sorted by residual: angle pdb=" O LEU E 464 " pdb=" C LEU E 464 " pdb=" N ARG E 465 " ideal model delta sigma weight residual 122.12 55.14 66.98 1.06e+00 8.90e-01 3.99e+03 angle pdb=" O LEU B 464 " pdb=" C LEU B 464 " pdb=" N ARG B 465 " ideal model delta sigma weight residual 122.46 56.33 66.13 1.38e+00 5.25e-01 2.30e+03 angle pdb=" O LEU D 464 " pdb=" C LEU D 464 " pdb=" N ARG D 465 " ideal model delta sigma weight residual 122.34 85.90 36.44 1.80e+00 3.09e-01 4.10e+02 angle pdb=" C LEU D 464 " pdb=" N ARG D 465 " pdb=" CA ARG D 465 " ideal model delta sigma weight residual 122.55 91.47 31.08 2.03e+00 2.43e-01 2.34e+02 angle pdb=" N PRO A 137 " pdb=" CD PRO A 137 " pdb=" CG PRO A 137 " ideal model delta sigma weight residual 103.20 87.39 15.81 1.50e+00 4.44e-01 1.11e+02 ... (remaining 48214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.61: 21502 32.61 - 65.22: 631 65.22 - 97.83: 83 97.83 - 130.44: 5 130.44 - 163.06: 6 Dihedral angle restraints: 22227 sinusoidal: 9392 harmonic: 12835 Sorted by residual: dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 103.06 -163.06 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O1B ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PB ADP B 902 " pdb=" PA ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 96.01 -156.01 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 95.87 -155.87 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 22224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3875 0.040 - 0.080: 1036 0.080 - 0.119: 455 0.119 - 0.159: 55 0.159 - 0.199: 5 Chirality restraints: 5426 Sorted by residual: chirality pdb=" CB THR F 509 " pdb=" CA THR F 509 " pdb=" OG1 THR F 509 " pdb=" CG2 THR F 509 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" CB ILE A 303 " pdb=" CA ILE A 303 " pdb=" CG1 ILE A 303 " pdb=" CG2 ILE A 303 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CB VAL A 235 " pdb=" CA VAL A 235 " pdb=" CG1 VAL A 235 " pdb=" CG2 VAL A 235 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.92e-01 ... (remaining 5423 not shown) Planarity restraints: 6314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 464 " 0.184 2.00e-02 2.50e+03 2.74e-01 7.48e+02 pdb=" C LEU E 464 " -0.441 2.00e-02 2.50e+03 pdb=" O LEU E 464 " 0.266 2.00e-02 2.50e+03 pdb=" N ARG E 465 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 464 " -0.187 2.00e-02 2.50e+03 2.73e-01 7.48e+02 pdb=" C LEU B 464 " 0.444 2.00e-02 2.50e+03 pdb=" O LEU B 464 " -0.258 2.00e-02 2.50e+03 pdb=" N ARG B 465 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 464 " 0.169 2.00e-02 2.50e+03 2.35e-01 5.51e+02 pdb=" C LEU D 464 " -0.396 2.00e-02 2.50e+03 pdb=" O LEU D 464 " 0.181 2.00e-02 2.50e+03 pdb=" N ARG D 465 " 0.045 2.00e-02 2.50e+03 ... (remaining 6311 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 261 2.57 - 3.15: 28761 3.15 - 3.74: 55842 3.74 - 4.32: 76086 4.32 - 4.90: 125603 Nonbonded interactions: 286553 Sorted by model distance: nonbonded pdb=" O3G ATP D 901 " pdb="MG MG D 904 " model vdw 1.989 2.170 nonbonded pdb=" O1G ATP D 902 " pdb="MG MG D 903 " model vdw 2.023 2.170 nonbonded pdb=" OG1 THR C 525 " pdb="MG MG C 902 " model vdw 2.060 2.170 nonbonded pdb=" OG1 THR E 525 " pdb="MG MG E 903 " model vdw 2.061 2.170 nonbonded pdb=" O3B ATP F 901 " pdb="MG MG F 903 " model vdw 2.073 2.170 ... (remaining 286548 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 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 388 or (resid 389 and (name N or name CA or name C or name O or name CB )) or r \ esid 390 through 533 or (resid 534 and (name N or name CA or name C or name O or \ name CB )) or resid 535 through 545 or (resid 546 through 549 and (name N or na \ me CA or name C or name O or name CB )) or resid 550 through 555 or (resid 556 t \ hrough 557 and (name N or name CA or name C or name O or name CB )) or resid 558 \ through 583 or resid 597 through 762)) selection = (chain 'B' and (resid 23 through 231 or (resid 232 and (name N or name CA or nam \ e C or name O or name CB )) or resid 233 through 441 or (resid 442 and (name N o \ r name CA or name C or name O or name CB )) or resid 443 through 461 or resid 47 \ 2 through 507 or (resid 508 and (name N or name CA or name C or name O or name C \ B )) or resid 509 through 545 or (resid 546 through 549 and (name N or name CA o \ r name C or name O or name CB )) or resid 550 through 553 or (resid 554 and (nam \ e N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 thro \ ugh 557 and (name N or name CA or name C or name O or name CB )) or resid 558 th \ rough 583 or resid 597 through 743 or (resid 744 and (name N or name CA or name \ C or name O or name CB )) or resid 745 through 754 or (resid 755 and (name N or \ name CA or name C or name O or name CB )) or resid 756 through 762)) selection = (chain 'C' and (resid 23 through 231 or (resid 232 and (name N or name CA or nam \ e C or name O or name CB )) or resid 233 through 238 or (resid 239 and (name N o \ r name CA or name C or name O or name CB )) or resid 240 through 335 or (resid 3 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 337 or (res \ id 338 through 339 and (name N or name CA or name C or name O or name CB )) or r \ esid 340 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 441 or (resid 442 and (name N or name CA or nam \ e C or name O or name CB )) or resid 443 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or (resid 546 through 549 and (name N or name CA o \ r name C or name O or name CB )) or resid 550 through 553 or (resid 554 and (nam \ e N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 thro \ ugh 557 and (name N or name CA or name C or name O or name CB )) or resid 558 th \ rough 583 or resid 597 through 743 or (resid 744 and (name N or name CA or name \ C or name O or name CB )) or resid 745 through 754 or (resid 755 and (name N or \ name CA or name C or name O or name CB )) or resid 756 through 762)) selection = (chain 'D' and (resid 23 through 231 or (resid 232 and (name N or name CA or nam \ e C or name O or name CB )) or resid 233 through 238 or (resid 239 and (name N o \ r name CA or name C or name O or name CB )) or resid 240 through 335 or (resid 3 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 337 or (res \ id 338 through 339 and (name N or name CA or name C or name O or name CB )) or r \ esid 340 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 441 or (resid 442 and (name N or name CA or nam \ e C or name O or name CB )) or resid 443 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or (resid 546 through 549 and (name N or name CA o \ r name C or name O or name CB )) or resid 550 through 553 or (resid 554 and (nam \ e N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 thro \ ugh 557 and (name N or name CA or name C or name O or name CB )) or resid 558 th \ rough 583 or resid 597 through 743 or (resid 744 and (name N or name CA or name \ C or name O or name CB )) or resid 745 through 754 or (resid 755 and (name N or \ name CA or name C or name O or name CB )) or resid 756 through 762)) selection = (chain 'E' and (resid 23 through 231 or (resid 232 and (name N or name CA or nam \ e C or name O or name CB )) or resid 233 through 238 or (resid 239 and (name N o \ r name CA or name C or name O or name CB )) or resid 240 through 335 or (resid 3 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 337 or (res \ id 338 through 339 and (name N or name CA or name C or name O or name CB )) or r \ esid 340 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 441 or (resid 442 and (name N or name CA or nam \ e C or name O or name CB )) or resid 443 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or (resid 546 through 549 and (name N or name CA o \ r name C or name O or name CB )) or resid 550 through 553 or (resid 554 and (nam \ e N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 thro \ ugh 557 and (name N or name CA or name C or name O or name CB )) or resid 558 th \ rough 583 or resid 597 through 743 or (resid 744 and (name N or name CA or name \ C or name O or name CB )) or resid 745 through 754 or (resid 755 and (name N or \ name CA or name C or name O or name CB )) or resid 756 through 762)) selection = (chain 'F' and (resid 23 through 231 or (resid 232 and (name N or name CA or nam \ e C or name O or name CB )) or resid 233 through 238 or (resid 239 and (name N o \ r name CA or name C or name O or name CB )) or resid 240 through 335 or (resid 3 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 337 or (res \ id 338 through 339 and (name N or name CA or name C or name O or name CB )) or r \ esid 340 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 441 or (resid 442 and (name N or name CA or nam \ e C or name O or name CB )) or resid 443 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 743 or (resid 744 and (name N or name CA or name C or \ name O or name CB )) or resid 745 through 754 or (resid 755 and (name N or name \ CA or name C or name O or name CB )) or resid 756 through 762)) } 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: 2.390 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: 0.050 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 34.220 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 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 : 0.015 1.632 35658 Z= 1.000 Angle : 0.823 66.977 48219 Z= 0.526 Chirality : 0.044 0.199 5426 Planarity : 0.008 0.274 6314 Dihedral : 15.442 163.055 13895 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.64 % Favored : 97.34 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.13), residues: 4393 helix: 0.85 (0.12), residues: 1936 sheet: 0.86 (0.21), residues: 671 loop : 0.18 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 453 TYR 0.019 0.002 TYR E 755 PHE 0.029 0.002 PHE B 682 TRP 0.040 0.003 TRP A 454 HIS 0.008 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.01523 (35657) covalent geometry : angle 0.82311 (48219) hydrogen bonds : bond 0.21371 ( 1581) hydrogen bonds : angle 6.69167 ( 4581) Misc. bond : bond 0.00982 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 336 time to evaluate : 1.334 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.2470 time to fit residues: 130.7843 Evaluate side-chains 183 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 692 GLN B 660 ASN C 43 GLN C 624 ASN C 660 ASN ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.077783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.055448 restraints weight = 157015.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.054754 restraints weight = 85440.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.054870 restraints weight = 70154.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.055158 restraints weight = 56495.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.055191 restraints weight = 51505.735| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 35658 Z= 0.237 Angle : 0.663 12.362 48219 Z= 0.336 Chirality : 0.046 0.165 5426 Planarity : 0.005 0.066 6314 Dihedral : 10.861 150.536 5131 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.61 % Favored : 97.36 % Rotamer: Outliers : 0.86 % Allowed : 5.85 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.13), residues: 4399 helix: 1.12 (0.12), residues: 1968 sheet: 0.43 (0.20), residues: 715 loop : 0.25 (0.16), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 191 TYR 0.023 0.002 TYR B 138 PHE 0.017 0.002 PHE B 265 TRP 0.020 0.002 TRP A 476 HIS 0.009 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00535 (35657) covalent geometry : angle 0.66256 (48219) hydrogen bonds : bond 0.04984 ( 1581) hydrogen bonds : angle 5.11225 ( 4581) Misc. bond : bond 0.00113 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 1.373 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: symmetry clash REVERT: C 442 MET cc_start: 0.8938 (ptm) cc_final: 0.8692 (ptm) REVERT: D 46 MET cc_start: 0.7989 (mtt) cc_final: 0.7786 (mtt) REVERT: E 332 MET cc_start: 0.8616 (mmm) cc_final: 0.8159 (mmm) REVERT: F 46 MET cc_start: 0.2845 (tpp) cc_final: 0.2265 (tmm) REVERT: F 611 MET cc_start: 0.5944 (ppp) cc_final: 0.5725 (ppp) outliers start: 32 outliers final: 16 residues processed: 217 average time/residue: 0.2215 time to fit residues: 79.4469 Evaluate side-chains 188 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 752 ILE Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 627 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 40 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 chunk 431 optimal weight: 6.9990 chunk 425 optimal weight: 0.4980 chunk 161 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 369 optimal weight: 2.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN B 183 HIS B 458 GLN C 212 GLN C 533 ASN D 183 HIS D 624 ASN E 43 GLN E 421 GLN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 603 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.077151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054489 restraints weight = 157051.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.054004 restraints weight = 85420.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.054702 restraints weight = 65145.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.054920 restraints weight = 50199.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.054949 restraints weight = 48832.221| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 35658 Z= 0.240 Angle : 0.638 11.623 48219 Z= 0.320 Chirality : 0.045 0.170 5426 Planarity : 0.005 0.060 6314 Dihedral : 10.328 149.590 5131 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.80 % Favored : 97.16 % Rotamer: Outliers : 1.26 % Allowed : 8.48 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.13), residues: 4399 helix: 1.25 (0.12), residues: 1970 sheet: 0.31 (0.20), residues: 697 loop : 0.23 (0.16), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 191 TYR 0.017 0.002 TYR F 138 PHE 0.021 0.002 PHE B 682 TRP 0.017 0.002 TRP A 476 HIS 0.008 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00539 (35657) covalent geometry : angle 0.63756 (48219) hydrogen bonds : bond 0.04221 ( 1581) hydrogen bonds : angle 4.83570 ( 4581) Misc. bond : bond 0.00142 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.4995 (pmm) cc_final: 0.4753 (pmm) REVERT: A 219 MET cc_start: 0.8665 (mmm) cc_final: 0.8448 (mmm) REVERT: A 550 MET cc_start: 0.8739 (ptm) cc_final: 0.8127 (ttp) REVERT: C 151 ILE cc_start: 0.8355 (mm) cc_final: 0.8139 (tp) REVERT: C 190 LYS cc_start: 0.7690 (tppt) cc_final: 0.7470 (tppt) REVERT: C 442 MET cc_start: 0.8968 (ptm) cc_final: 0.8721 (ptm) REVERT: D 46 MET cc_start: 0.8211 (mtt) cc_final: 0.7977 (mtt) REVERT: D 449 MET cc_start: 0.8774 (tpt) cc_final: 0.8544 (tpp) REVERT: F 449 MET cc_start: 0.8879 (tpp) cc_final: 0.8630 (tpp) outliers start: 47 outliers final: 23 residues processed: 212 average time/residue: 0.2101 time to fit residues: 75.3347 Evaluate side-chains 184 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 627 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 355 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 288 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 ASN D 296 ASN E 421 GLN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 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 = 0.3759 r_free = 0.3759 target = 0.077327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.053167 restraints weight = 155006.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.054583 restraints weight = 82659.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.055014 restraints weight = 55002.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.055274 restraints weight = 42727.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.055412 restraints weight = 41503.154| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35658 Z= 0.179 Angle : 0.579 10.873 48219 Z= 0.289 Chirality : 0.044 0.155 5426 Planarity : 0.004 0.054 6314 Dihedral : 9.969 144.021 5131 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Rotamer: Outliers : 1.34 % Allowed : 9.98 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.13), residues: 4399 helix: 1.36 (0.12), residues: 1976 sheet: 0.33 (0.20), residues: 679 loop : 0.27 (0.16), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 191 TYR 0.042 0.001 TYR A 495 PHE 0.016 0.001 PHE B 682 TRP 0.011 0.001 TRP A 476 HIS 0.008 0.001 HIS E 226 Details of bonding type rmsd covalent geometry : bond 0.00406 (35657) covalent geometry : angle 0.57929 (48219) hydrogen bonds : bond 0.03723 ( 1581) hydrogen bonds : angle 4.64070 ( 4581) Misc. bond : bond 0.00098 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.5299 (pmm) cc_final: 0.5086 (pmm) REVERT: B 768 PHE cc_start: 0.7236 (m-80) cc_final: 0.6945 (m-10) REVERT: C 102 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9068 (mp) REVERT: C 151 ILE cc_start: 0.8328 (mm) cc_final: 0.8127 (tp) REVERT: C 442 MET cc_start: 0.8975 (ptm) cc_final: 0.8724 (ptm) REVERT: D 49 LEU cc_start: 0.8850 (tp) cc_final: 0.8211 (mp) REVERT: E 332 MET cc_start: 0.8925 (mmm) cc_final: 0.8262 (mmm) REVERT: F 46 MET cc_start: 0.3780 (tmm) cc_final: 0.3211 (tmm) REVERT: F 449 MET cc_start: 0.8882 (tpp) cc_final: 0.8607 (tpp) outliers start: 50 outliers final: 27 residues processed: 216 average time/residue: 0.1946 time to fit residues: 72.4230 Evaluate side-chains 190 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 627 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 379 optimal weight: 40.0000 chunk 217 optimal weight: 0.4980 chunk 27 optimal weight: 20.0000 chunk 332 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 373 optimal weight: 7.9990 chunk 385 optimal weight: 20.0000 chunk 324 optimal weight: 8.9990 chunk 400 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 ASN B 568 GLN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 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 = 0.3748 r_free = 0.3748 target = 0.076905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.052782 restraints weight = 155516.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.054338 restraints weight = 84548.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.054581 restraints weight = 62223.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.054941 restraints weight = 43541.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.055083 restraints weight = 41736.352| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35658 Z= 0.192 Angle : 0.586 10.554 48219 Z= 0.292 Chirality : 0.044 0.175 5426 Planarity : 0.004 0.052 6314 Dihedral : 9.808 141.331 5131 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 1.56 % Allowed : 11.35 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.13), residues: 4399 helix: 1.42 (0.12), residues: 1975 sheet: 0.27 (0.20), residues: 680 loop : 0.26 (0.16), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.031 0.001 TYR A 495 PHE 0.018 0.001 PHE B 682 TRP 0.010 0.001 TRP D 551 HIS 0.007 0.001 HIS E 226 Details of bonding type rmsd covalent geometry : bond 0.00434 (35657) covalent geometry : angle 0.58560 (48219) hydrogen bonds : bond 0.03681 ( 1581) hydrogen bonds : angle 4.61673 ( 4581) Misc. bond : bond 0.00097 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 169 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8935 (ttm) cc_final: 0.8514 (tpt) REVERT: A 506 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: A 550 MET cc_start: 0.8548 (ptm) cc_final: 0.8112 (ttp) REVERT: B 678 MET cc_start: 0.8142 (tmm) cc_final: 0.7819 (tmm) REVERT: B 768 PHE cc_start: 0.7261 (m-80) cc_final: 0.6959 (m-10) REVERT: C 102 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.9059 (mp) REVERT: C 151 ILE cc_start: 0.8343 (mm) cc_final: 0.8110 (tp) REVERT: C 319 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: C 442 MET cc_start: 0.9001 (ptm) cc_final: 0.8739 (ptm) REVERT: D 46 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7908 (mtt) REVERT: F 46 MET cc_start: 0.3924 (tmm) cc_final: 0.3345 (tmm) REVERT: F 442 MET cc_start: 0.8932 (mpp) cc_final: 0.8665 (mpp) REVERT: F 449 MET cc_start: 0.8892 (tpp) cc_final: 0.8613 (tpp) outliers start: 58 outliers final: 37 residues processed: 215 average time/residue: 0.2011 time to fit residues: 73.3955 Evaluate side-chains 196 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 627 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 387 optimal weight: 40.0000 chunk 44 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 320 optimal weight: 1.9990 chunk 336 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 175 optimal weight: 0.6980 chunk 354 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 255 optimal weight: 0.0070 overall best weight: 2.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 GLN ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN B 460 ASN B 568 GLN C 460 ASN D 602 ASN D 624 ASN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.077252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.054569 restraints weight = 155685.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.054880 restraints weight = 84354.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.055156 restraints weight = 54382.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.055250 restraints weight = 51435.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.055361 restraints weight = 46432.011| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35658 Z= 0.148 Angle : 0.558 15.760 48219 Z= 0.276 Chirality : 0.043 0.194 5426 Planarity : 0.004 0.052 6314 Dihedral : 9.590 140.283 5131 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Rotamer: Outliers : 1.34 % Allowed : 12.32 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.13), residues: 4399 helix: 1.53 (0.12), residues: 1974 sheet: 0.27 (0.20), residues: 680 loop : 0.29 (0.16), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.022 0.001 TYR A 495 PHE 0.026 0.001 PHE F 742 TRP 0.009 0.001 TRP D 551 HIS 0.006 0.001 HIS E 226 Details of bonding type rmsd covalent geometry : bond 0.00336 (35657) covalent geometry : angle 0.55772 (48219) hydrogen bonds : bond 0.03430 ( 1581) hydrogen bonds : angle 4.47749 ( 4581) Misc. bond : bond 0.00073 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8009 (m-80) REVERT: A 550 MET cc_start: 0.8611 (ptm) cc_final: 0.8141 (ttp) REVERT: B 768 PHE cc_start: 0.7457 (m-80) cc_final: 0.7033 (m-10) REVERT: C 151 ILE cc_start: 0.8407 (mm) cc_final: 0.8177 (tp) REVERT: C 319 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: C 427 MET cc_start: 0.8839 (tpp) cc_final: 0.8293 (ppp) REVERT: C 456 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9447 (mt) REVERT: D 46 MET cc_start: 0.8215 (mtt) cc_final: 0.7836 (mtt) REVERT: D 49 LEU cc_start: 0.8750 (tt) cc_final: 0.7971 (mp) REVERT: D 192 GLU cc_start: 0.7891 (tp30) cc_final: 0.7602 (tp30) REVERT: D 678 MET cc_start: 0.8814 (mmp) cc_final: 0.8574 (mmp) REVERT: D 740 MET cc_start: 0.8483 (mmm) cc_final: 0.8137 (mmm) REVERT: E 332 MET cc_start: 0.8846 (mmm) cc_final: 0.8194 (mmm) REVERT: F 46 MET cc_start: 0.3660 (tmm) cc_final: 0.3392 (tmm) REVERT: F 442 MET cc_start: 0.8986 (mpp) cc_final: 0.8769 (mpp) REVERT: F 449 MET cc_start: 0.8939 (tpp) cc_final: 0.8653 (tpp) outliers start: 50 outliers final: 35 residues processed: 206 average time/residue: 0.1897 time to fit residues: 67.5767 Evaluate side-chains 194 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 627 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 416 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 278 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 425 optimal weight: 9.9990 chunk 304 optimal weight: 0.9990 chunk 380 optimal weight: 40.0000 chunk 28 optimal weight: 0.8980 chunk 336 optimal weight: 9.9990 chunk 227 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN D 21 ASN D 458 GLN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 760 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.077315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.054858 restraints weight = 155325.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.055087 restraints weight = 84861.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.055103 restraints weight = 58451.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.055211 restraints weight = 53010.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.055323 restraints weight = 50049.264| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35658 Z= 0.135 Angle : 0.552 13.911 48219 Z= 0.272 Chirality : 0.043 0.216 5426 Planarity : 0.004 0.052 6314 Dihedral : 9.481 139.451 5131 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.23 % Rotamer: Outliers : 1.42 % Allowed : 12.74 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.13), residues: 4399 helix: 1.59 (0.12), residues: 1975 sheet: 0.24 (0.20), residues: 679 loop : 0.30 (0.16), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.019 0.001 TYR A 495 PHE 0.012 0.001 PHE B 682 TRP 0.010 0.001 TRP D 551 HIS 0.005 0.001 HIS E 226 Details of bonding type rmsd covalent geometry : bond 0.00307 (35657) covalent geometry : angle 0.55229 (48219) hydrogen bonds : bond 0.03334 ( 1581) hydrogen bonds : angle 4.41033 ( 4581) Misc. bond : bond 0.00070 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 163 time to evaluate : 1.295 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: A 344 MET cc_start: 0.8744 (ttm) cc_final: 0.8493 (tpt) REVERT: A 506 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: A 550 MET cc_start: 0.8581 (ptm) cc_final: 0.8079 (ttp) REVERT: B 768 PHE cc_start: 0.7441 (m-80) cc_final: 0.7025 (m-10) REVERT: C 151 ILE cc_start: 0.8524 (mm) cc_final: 0.8260 (tp) REVERT: C 319 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: D 46 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7912 (mtt) REVERT: D 49 LEU cc_start: 0.8715 (tt) cc_final: 0.7970 (mp) REVERT: D 678 MET cc_start: 0.8771 (mmp) cc_final: 0.8549 (mmp) REVERT: D 689 GLU cc_start: 0.8722 (tp30) cc_final: 0.8140 (tp30) REVERT: D 740 MET cc_start: 0.8449 (mmm) cc_final: 0.8067 (mmm) REVERT: E 332 MET cc_start: 0.8878 (mmm) cc_final: 0.8237 (mmm) REVERT: E 442 MET cc_start: 0.9034 (tpp) cc_final: 0.8811 (tpp) REVERT: F 46 MET cc_start: 0.3582 (tmm) cc_final: 0.3306 (tmm) REVERT: F 158 MET cc_start: 0.3184 (pmm) cc_final: 0.2911 (pmm) REVERT: F 449 MET cc_start: 0.8954 (tpp) cc_final: 0.8661 (tpp) REVERT: F 740 MET cc_start: 0.6986 (tmm) cc_final: 0.6058 (ptp) outliers start: 53 outliers final: 36 residues processed: 207 average time/residue: 0.1938 time to fit residues: 69.3153 Evaluate side-chains 194 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 627 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 135 optimal weight: 0.9990 chunk 297 optimal weight: 9.9990 chunk 430 optimal weight: 2.9990 chunk 420 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 chunk 341 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 236 optimal weight: 0.0040 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN C 624 ASN E 494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.077276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.053226 restraints weight = 155469.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.055289 restraints weight = 82108.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.055529 restraints weight = 47555.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.055546 restraints weight = 39597.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.055711 restraints weight = 42027.063| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35658 Z= 0.135 Angle : 0.562 13.678 48219 Z= 0.275 Chirality : 0.043 0.240 5426 Planarity : 0.004 0.051 6314 Dihedral : 9.348 138.331 5131 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.36 % Rotamer: Outliers : 1.48 % Allowed : 13.07 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.13), residues: 4399 helix: 1.62 (0.12), residues: 1973 sheet: 0.23 (0.20), residues: 671 loop : 0.29 (0.16), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.018 0.001 TYR A 495 PHE 0.012 0.001 PHE B 682 TRP 0.010 0.001 TRP D 551 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00307 (35657) covalent geometry : angle 0.56242 (48219) hydrogen bonds : bond 0.03271 ( 1581) hydrogen bonds : angle 4.37896 ( 4581) Misc. bond : bond 0.00077 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 166 time to evaluate : 1.479 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: A 84 MET cc_start: 0.3414 (pmm) cc_final: 0.2690 (pmm) REVERT: A 506 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: A 550 MET cc_start: 0.8643 (ptm) cc_final: 0.8231 (ttp) REVERT: B 768 PHE cc_start: 0.7159 (m-80) cc_final: 0.6726 (m-10) REVERT: C 151 ILE cc_start: 0.8433 (mm) cc_final: 0.8032 (tt) REVERT: C 319 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: C 379 GLU cc_start: 0.8237 (tt0) cc_final: 0.7954 (tt0) REVERT: C 456 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9395 (mt) REVERT: D 46 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7933 (mtt) REVERT: D 49 LEU cc_start: 0.8732 (tt) cc_final: 0.8063 (mp) REVERT: D 192 GLU cc_start: 0.7950 (tp30) cc_final: 0.7684 (tp30) REVERT: D 442 MET cc_start: 0.8397 (mmt) cc_final: 0.8089 (mmm) REVERT: D 678 MET cc_start: 0.8762 (mmp) cc_final: 0.8548 (mmp) REVERT: D 689 GLU cc_start: 0.8707 (tp30) cc_final: 0.8147 (tp30) REVERT: D 740 MET cc_start: 0.8449 (mmm) cc_final: 0.8047 (mmm) REVERT: E 332 MET cc_start: 0.8954 (mmm) cc_final: 0.8427 (mmm) REVERT: E 442 MET cc_start: 0.8965 (tpp) cc_final: 0.8736 (tpp) REVERT: F 46 MET cc_start: 0.3333 (tmm) cc_final: 0.3050 (tmm) REVERT: F 449 MET cc_start: 0.8933 (tpp) cc_final: 0.8612 (tpp) REVERT: F 740 MET cc_start: 0.6848 (tmm) cc_final: 0.6053 (ptp) outliers start: 55 outliers final: 40 residues processed: 212 average time/residue: 0.2082 time to fit residues: 75.2688 Evaluate side-chains 199 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 627 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 161 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 254 optimal weight: 8.9990 chunk 304 optimal weight: 0.9990 chunk 422 optimal weight: 0.9990 chunk 427 optimal weight: 6.9990 chunk 368 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 379 optimal weight: 7.9990 chunk 229 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN C 624 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.076895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.053361 restraints weight = 155060.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.054983 restraints weight = 80563.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.055306 restraints weight = 45352.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.055514 restraints weight = 42480.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.055497 restraints weight = 37080.594| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35658 Z= 0.158 Angle : 0.572 12.401 48219 Z= 0.281 Chirality : 0.043 0.200 5426 Planarity : 0.004 0.051 6314 Dihedral : 9.315 137.698 5131 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.25 % Rotamer: Outliers : 1.37 % Allowed : 13.15 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.13), residues: 4399 helix: 1.60 (0.12), residues: 1980 sheet: 0.22 (0.20), residues: 673 loop : 0.33 (0.16), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.017 0.001 TYR A 495 PHE 0.014 0.001 PHE B 682 TRP 0.010 0.001 TRP D 551 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00360 (35657) covalent geometry : angle 0.57215 (48219) hydrogen bonds : bond 0.03341 ( 1581) hydrogen bonds : angle 4.41478 ( 4581) Misc. bond : bond 0.00109 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 1.459 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: A 84 MET cc_start: 0.3403 (pmm) cc_final: 0.2674 (pmm) REVERT: A 344 MET cc_start: 0.8939 (ttm) cc_final: 0.8479 (tpt) REVERT: A 506 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: A 550 MET cc_start: 0.8677 (ptm) cc_final: 0.8175 (ttp) REVERT: B 768 PHE cc_start: 0.7024 (m-80) cc_final: 0.6642 (m-10) REVERT: C 190 LYS cc_start: 0.7667 (tppt) cc_final: 0.7448 (tppt) REVERT: C 319 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: C 379 GLU cc_start: 0.8316 (tt0) cc_final: 0.8057 (tt0) REVERT: C 456 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9415 (mt) REVERT: D 46 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7985 (mtt) REVERT: D 192 GLU cc_start: 0.7920 (tp30) cc_final: 0.7645 (tp30) REVERT: D 442 MET cc_start: 0.8391 (mmt) cc_final: 0.8039 (mmm) REVERT: D 678 MET cc_start: 0.8788 (mmp) cc_final: 0.8579 (mmp) REVERT: D 689 GLU cc_start: 0.8701 (tp30) cc_final: 0.8169 (tp30) REVERT: E 332 MET cc_start: 0.9013 (mmm) cc_final: 0.8337 (mmm) REVERT: F 46 MET cc_start: 0.3347 (tmm) cc_final: 0.3050 (tmm) REVERT: F 449 MET cc_start: 0.8918 (tpp) cc_final: 0.8593 (tpp) REVERT: F 740 MET cc_start: 0.6874 (tmm) cc_final: 0.6074 (ptp) outliers start: 51 outliers final: 45 residues processed: 201 average time/residue: 0.2075 time to fit residues: 70.9320 Evaluate side-chains 203 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 627 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 344 optimal weight: 7.9990 chunk 398 optimal weight: 0.0070 chunk 208 optimal weight: 5.9990 chunk 305 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 224 optimal weight: 0.0980 chunk 56 optimal weight: 5.9990 chunk 318 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 364 optimal weight: 0.9980 chunk 277 optimal weight: 0.8980 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS B 460 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN C 90 ASN C 624 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.077575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.054677 restraints weight = 156478.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.055760 restraints weight = 81727.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.055640 restraints weight = 50677.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.055966 restraints weight = 51280.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.055979 restraints weight = 42059.116| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35658 Z= 0.110 Angle : 0.567 15.615 48219 Z= 0.277 Chirality : 0.043 0.230 5426 Planarity : 0.004 0.062 6314 Dihedral : 9.184 136.762 5131 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.55 % Favored : 97.41 % Rotamer: Outliers : 1.21 % Allowed : 13.55 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.13), residues: 4399 helix: 1.62 (0.12), residues: 1981 sheet: 0.29 (0.20), residues: 665 loop : 0.37 (0.16), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 86 TYR 0.016 0.001 TYR A 495 PHE 0.009 0.001 PHE B 506 TRP 0.011 0.001 TRP F 454 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00247 (35657) covalent geometry : angle 0.56719 (48219) hydrogen bonds : bond 0.03213 ( 1581) hydrogen bonds : angle 4.34288 ( 4581) Misc. bond : bond 0.00062 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8798 Ramachandran restraints generated. 4399 Oldfield, 0 Emsley, 4399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 1.431 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: A 84 MET cc_start: 0.3384 (pmm) cc_final: 0.2721 (pmm) REVERT: A 305 GLU cc_start: 0.9048 (tp30) cc_final: 0.8791 (tp30) REVERT: A 344 MET cc_start: 0.8949 (ttm) cc_final: 0.8443 (tpt) REVERT: A 506 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: A 550 MET cc_start: 0.8619 (ptm) cc_final: 0.8187 (ttp) REVERT: A 564 ASP cc_start: 0.8820 (t0) cc_final: 0.8617 (t0) REVERT: B 768 PHE cc_start: 0.7148 (m-80) cc_final: 0.6715 (m-10) REVERT: C 84 MET cc_start: 0.8313 (tmm) cc_final: 0.7984 (tmm) REVERT: C 379 GLU cc_start: 0.8264 (tt0) cc_final: 0.8004 (tt0) REVERT: C 456 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9392 (mt) REVERT: C 611 MET cc_start: 0.7793 (mtp) cc_final: 0.7557 (mtp) REVERT: D 46 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8012 (mtt) REVERT: D 49 LEU cc_start: 0.8841 (tp) cc_final: 0.8148 (mp) REVERT: D 442 MET cc_start: 0.8400 (mmt) cc_final: 0.8060 (mmm) REVERT: D 689 GLU cc_start: 0.8662 (tp30) cc_final: 0.8119 (tp30) REVERT: D 740 MET cc_start: 0.8450 (mmm) cc_final: 0.8055 (mmm) REVERT: E 332 MET cc_start: 0.8992 (mmm) cc_final: 0.8336 (mmm) REVERT: E 442 MET cc_start: 0.8984 (tpp) cc_final: 0.8780 (tpp) REVERT: F 46 MET cc_start: 0.2832 (tmm) cc_final: 0.2536 (tmm) REVERT: F 158 MET cc_start: 0.3527 (pmm) cc_final: 0.3309 (pmm) REVERT: F 449 MET cc_start: 0.8957 (tpp) cc_final: 0.8633 (tpp) REVERT: F 740 MET cc_start: 0.6854 (tmm) cc_final: 0.6121 (ptp) outliers start: 45 outliers final: 37 residues processed: 204 average time/residue: 0.1991 time to fit residues: 69.7515 Evaluate side-chains 203 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 635 ARG Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 627 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 268 optimal weight: 0.7980 chunk 269 optimal weight: 0.9990 chunk 247 optimal weight: 10.0000 chunk 270 optimal weight: 0.0870 chunk 178 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 395 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 333 optimal weight: 6.9990 chunk 334 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS B 460 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN C 624 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.077664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.055692 restraints weight = 154869.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.055233 restraints weight = 82364.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.055517 restraints weight = 59042.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.055736 restraints weight = 54781.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.055765 restraints weight = 45388.724| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35658 Z= 0.102 Angle : 0.562 15.256 48219 Z= 0.275 Chirality : 0.043 0.225 5426 Planarity : 0.004 0.051 6314 Dihedral : 9.130 136.271 5131 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.50 % Rotamer: Outliers : 1.15 % Allowed : 13.79 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.13), residues: 4399 helix: 1.63 (0.12), residues: 1981 sheet: 0.23 (0.20), residues: 676 loop : 0.38 (0.16), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 86 TYR 0.016 0.001 TYR A 110 PHE 0.008 0.001 PHE B 506 TRP 0.011 0.001 TRP F 454 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00227 (35657) covalent geometry : angle 0.56234 (48219) hydrogen bonds : bond 0.03130 ( 1581) hydrogen bonds : angle 4.31516 ( 4581) Misc. bond : bond 0.00044 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5713.32 seconds wall clock time: 99 minutes 36.89 seconds (5976.89 seconds total)