Starting phenix.real_space_refine on Wed Aug 27 01:12:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6g4w_4349/08_2025/6g4w_4349.cif Found real_map, /net/cci-nas-00/data/ceres_data/6g4w_4349/08_2025/6g4w_4349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6g4w_4349/08_2025/6g4w_4349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6g4w_4349/08_2025/6g4w_4349.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6g4w_4349/08_2025/6g4w_4349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6g4w_4349/08_2025/6g4w_4349.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians P 1562 5.49 5 C 23571 2.51 5 N 5357 2.21 5 O 14733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45223 Number of models: 1 Model: "" Number of chains: 31 Chain: "2" Number of atoms: 18753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1563, 18753 Inner-chain residues flagged as termini: ['pdbres=" C 21698 "'] Classifications: {'RNA': 1563} Modifications used: {'5*END': 1, 'rna3p_pur': 828, 'rna3p_pyr': 735} Link IDs: {'rna3p': 1562} Chain breaks: 23 Unresolved non-hydrogen bonds: 17009 Unresolved non-hydrogen angles: 26938 Unresolved non-hydrogen dihedrals: 16732 Unresolved non-hydrogen chiralities: 1563 Planarities with less than four sites: {' U%rna3p_pyr:plan': 354, ' A%rna3p_pur:plan': 370, ' A%rna3p_pur:plan2': 370, ' C%rna3p_pyr:plan': 380, ' C%rna3p_pyr:plan2': 380, ' G%rna3p_pur:plan': 458, ' G%rna3p_pur:plan2': 458, ' C%rna3p_pyr%5*END:plan': 1, ' C%rna3p_pyr%5*END:plan2': 1} Unresolved non-hydrogen planarities: 17036 Chain: "R" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 401 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ARG:plan': 12, 'GLU:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 158 Chain: "b" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 405 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 5, 'TRANS': 76} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 3, 'GLU:plan': 4, 'ARG:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 1, 'TYR:plan': 2, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 113 Chain: "B" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1054 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PTRANS': 5, 'TRANS': 207} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 703 Unresolved non-hydrogen angles: 879 Unresolved non-hydrogen dihedrals: 588 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'ASP:plan': 15, 'PHE:plan': 10, 'TRP:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 9, 'ARG:plan': 12, 'GLN:plan1': 11, 'GLU:plan': 10, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 347 Chain: "c" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 300 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ARG:plan': 9, 'GLN:plan1': 3, 'GLU:plan': 5, 'PHE:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 95 Chain: "E" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1287 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 224} Link IDs: {'PTRANS': 14, 'TRANS': 247} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 831 Unresolved non-hydrogen angles: 1050 Unresolved non-hydrogen dihedrals: 695 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'ARG:plan': 22, 'HIS:plan': 8, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 12, 'GLU:plan': 9, 'ASN:plan1': 10, 'TYR:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 401 Chain: "e" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 270 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 3, 'TRANS': 51} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 7, 'GLN:plan1': 3, 'GLU:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 82 Chain: "F" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 935 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PTRANS': 5, 'TRANS': 183} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 581 Unresolved non-hydrogen angles: 732 Unresolved non-hydrogen dihedrals: 480 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'ASP:plan': 9, 'PHE:plan': 4, 'TRP:plan': 2, 'GLN:plan1': 6, 'ASN:plan1': 12, 'TYR:plan': 5, 'GLU:plan': 10, 'HIS:plan': 4, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 309 Chain: "H" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 920 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 9, 'TRANS': 176} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 605 Unresolved non-hydrogen angles: 754 Unresolved non-hydrogen dihedrals: 496 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASN:plan1': 7, 'GLU:plan': 16, 'ASP:plan': 7, 'PHE:plan': 10, 'GLN:plan1': 10, 'ARG:plan': 14, 'HIS:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 303 Chain: "G" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1135 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 751 Unresolved non-hydrogen angles: 923 Unresolved non-hydrogen dihedrals: 625 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'ASN:plan1': 7, 'PHE:plan': 4, 'GLN:plan1': 9, 'GLU:plan': 16, 'ASP:plan': 9, 'ARG:plan': 28, 'TYR:plan': 5, 'TRP:plan': 1, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 371 Chain: "Z" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 358 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 281 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 4, 'PHE:plan': 1, 'TYR:plan': 3, 'GLU:plan': 3, 'ARG:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "Y" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 610 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 4, 'TRANS': 119} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 422 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 359 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 13, 'PHE:plan': 6, 'ASN:plan1': 4, 'GLN:plan1': 3, 'HIS:plan': 4, 'GLU:plan': 5, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 208 Chain: "x" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 865 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PTRANS': 7, 'TRANS': 167} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 685 Unresolved non-hydrogen dihedrals: 441 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 13, 'ASN:plan1': 9, 'TYR:plan': 2, 'TRP:plan': 1, 'PHE:plan': 9, 'HIS:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 260 Chain: "X" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 690 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 5, 'TRANS': 135} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 427 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 12, 'HIS:plan': 5, 'ASP:plan': 5, 'GLN:plan1': 4, 'TRP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 7, 'PHE:plan': 5, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 214 Chain: "w" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1232 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'PTRANS': 13, 'TRANS': 234} Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 835 Unresolved non-hydrogen angles: 1065 Unresolved non-hydrogen dihedrals: 709 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'ARG:plan': 20, 'GLU:plan': 17, 'TYR:plan': 11, 'PHE:plan': 10, 'ASN:plan1': 5, 'TRP:plan': 4, 'GLN:plan1': 9, 'ASP:plan': 6, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 435 Chain: "W" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 634 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ARG:plan': 11, 'ASN:plan1': 7, 'ASP:plan': 6, 'GLU:plan': 6, 'GLN:plan1': 4, 'PHE:plan': 8, 'HIS:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 218 Chain: "u" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 3106 Classifications: {'peptide': 628} Incomplete info: {'truncation_to_alanine': 556} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 585} Chain breaks: 4 Unresolved chain link angles: 42 Unresolved non-hydrogen bonds: 2104 Unresolved non-hydrogen angles: 2677 Unresolved non-hydrogen dihedrals: 1791 Unresolved non-hydrogen chiralities: 168 Planarities with less than four sites: {'ARG:plan': 41, 'ASP:plan': 34, 'GLN:plan1': 34, 'HIS:plan': 21, 'GLU:plan': 37, 'ASN:plan1': 17, 'PHE:plan': 34, 'TRP:plan': 9, 'TYR:plan': 15} Unresolved non-hydrogen planarities: 1137 Chain: "t" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 16} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 2, 'TYR:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "T" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 705 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 4, 'TRANS': 139} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 438 Unresolved non-hydrogen angles: 551 Unresolved non-hydrogen dihedrals: 372 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'ASP:plan': 7, 'ASN:plan1': 4, 'GLN:plan1': 8, 'GLU:plan': 6, 'PHE:plan': 4, 'ARG:plan': 12, 'TRP:plan': 2, 'HIS:plan': 4, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 239 Chain: "S" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 704 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 3, 'TRANS': 139} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 631 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 4, 'GLN:plan1': 6, 'HIS:plan': 5, 'ARG:plan': 20, 'ASN:plan1': 6, 'ASP:plan': 9, 'TYR:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 285 Chain: "Q" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 683 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 5, 'TRANS': 133} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 555 Unresolved non-hydrogen dihedrals: 370 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 8, 'PHE:plan': 3, 'ARG:plan': 14, 'HIS:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 7, 'TYR:plan': 8, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 235 Chain: "P" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 590 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 7, 'TRANS': 112} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 414 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 350 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PHE:plan': 3, 'TYR:plan': 6, 'ARG:plan': 12, 'ASP:plan': 4, 'GLN:plan1': 6, 'GLU:plan': 8, 'ASN:plan1': 3, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 217 Chain: "O" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 659 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 295 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ASN:plan1': 3, 'PHE:plan': 4, 'HIS:plan': 3, 'ASP:plan': 7, 'ARG:plan': 14, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 186 Chain: "N" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 737 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 8, 'TRANS': 140} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 490 Unresolved non-hydrogen angles: 617 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'ARG:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 4, 'TYR:plan': 6, 'TRP:plan': 2, 'ASP:plan': 7, 'GLU:plan': 5, 'PHE:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 233 Chain: "L" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 744 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 6, 'TRANS': 144} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 507 Unresolved non-hydrogen angles: 635 Unresolved non-hydrogen dihedrals: 424 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 6, 'GLU:plan': 7, 'ARG:plan': 14, 'TYR:plan': 7, 'PHE:plan': 6, 'ASN:plan1': 6, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 255 Chain: "J" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 888 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 6, 'TRANS': 173} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 637 Unresolved non-hydrogen angles: 796 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'ARG:plan': 27, 'TRP:plan': 2, 'TYR:plan': 4, 'PHE:plan': 7, 'GLU:plan': 10, 'ASP:plan': 8, 'GLN:plan1': 6, 'ASN:plan1': 4, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 343 Chain: "I" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1009 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 7, 'TRANS': 197} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 703 Unresolved non-hydrogen angles: 875 Unresolved non-hydrogen dihedrals: 603 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'ARG:plan': 23, 'ASP:plan': 6, 'ASN:plan1': 10, 'TRP:plan': 3, 'HIS:plan': 4, 'TYR:plan': 10, 'GLU:plan': 14, 'PHE:plan': 3, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 378 Chain: "s" Number of atoms: 3840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 3840 Classifications: {'peptide': 768} Incomplete info: {'truncation_to_alanine': 768} Link IDs: {'TRANS': 767} Chain breaks: 39 Unresolved non-hydrogen bonds: 1536 Unresolved non-hydrogen angles: 2304 Unresolved non-hydrogen dihedrals: 768 Planarities with less than four sites: {'UNK:plan-1': 768} Unresolved non-hydrogen planarities: 768 Chain: "r" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 582 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 106} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 485 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'HIS:plan': 4, 'ASN:plan1': 6, 'ARG:plan': 9, 'PHE:plan': 6, 'GLN:plan1': 3, 'GLU:plan': 13, 'TRP:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 202 Chain: "q" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 942 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 8, 'TRANS': 183} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 582 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 492 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'PHE:plan': 9, 'TYR:plan': 10, 'ASP:plan': 11, 'GLU:plan': 12, 'ARG:plan': 9, 'ASN:plan1': 7, 'GLN:plan1': 6, 'HIS:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 318 Chain: "k" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Time building chain proxies: 11.69, per 1000 atoms: 0.26 Number of scatterers: 45223 At special positions: 0 Unit cell: (250.404, 247.152, 197.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 1562 15.00 O 14733 8.00 N 5357 7.00 C 23571 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 Atom "ATOM 7636 O5' C 2 829 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10084 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 43 sheets defined 54.8% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.65 Creating SS restraints... Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 27 through 36 Processing helix chain 'R' and resid 43 through 61 Processing helix chain 'R' and resid 73 through 83 removed outlier: 3.676A pdb=" N ASN R 83 " --> pdb=" O GLU R 79 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 18 Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 57 through 64 removed outlier: 4.406A pdb=" N GLY B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 157 through 175 Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 225 through 233 Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.907A pdb=" N TRP E 18 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 50 Processing helix chain 'E' and resid 57 through 66 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 247 through 262 Processing helix chain 'e' and resid 31 through 43 removed outlier: 3.986A pdb=" N ARG e 41 " --> pdb=" O GLN e 37 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL e 43 " --> pdb=" O ASN e 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 67 through 75 Processing helix chain 'F' and resid 85 through 104 removed outlier: 3.665A pdb=" N THR F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 118 removed outlier: 3.740A pdb=" N VAL F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 161 Processing helix chain 'F' and resid 168 through 182 Processing helix chain 'F' and resid 187 through 204 Processing helix chain 'H' and resid 17 through 31 Processing helix chain 'H' and resid 38 through 43 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 68 through 74 Processing helix chain 'H' and resid 75 through 87 removed outlier: 3.532A pdb=" N PHE H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 120 removed outlier: 3.736A pdb=" N ARG H 120 " --> pdb=" O PRO H 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 117 through 120' Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.615A pdb=" N HIS H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 163 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 181 through 229 Processing helix chain 'Z' and resid 51 through 59 Processing helix chain 'Z' and resid 61 through 65 removed outlier: 3.645A pdb=" N TYR Z 65 " --> pdb=" O VAL Z 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 69 through 77 removed outlier: 3.711A pdb=" N LEU Z 77 " --> pdb=" O VAL Z 73 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 95 Processing helix chain 'Y' and resid 36 through 49 removed outlier: 3.612A pdb=" N ILE Y 40 " --> pdb=" O PRO Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 84 Processing helix chain 'Y' and resid 103 through 116 removed outlier: 3.913A pdb=" N ARG Y 107 " --> pdb=" O SER Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 120 through 124 removed outlier: 3.933A pdb=" N ALA Y 123 " --> pdb=" O THR Y 120 " (cutoff:3.500A) Processing helix chain 'x' and resid 84 through 91 Processing helix chain 'x' and resid 91 through 101 Proline residue: x 98 - end of helix Processing helix chain 'x' and resid 127 through 142 removed outlier: 4.088A pdb=" N THR x 131 " --> pdb=" O VAL x 127 " (cutoff:3.500A) Processing helix chain 'x' and resid 145 through 155 removed outlier: 3.718A pdb=" N ALA x 149 " --> pdb=" O GLN x 145 " (cutoff:3.500A) Processing helix chain 'x' and resid 166 through 168 No H-bonds generated for 'chain 'x' and resid 166 through 168' Processing helix chain 'x' and resid 174 through 185 Processing helix chain 'x' and resid 188 through 198 Processing helix chain 'x' and resid 214 through 231 removed outlier: 3.702A pdb=" N GLY x 231 " --> pdb=" O ASN x 227 " (cutoff:3.500A) Processing helix chain 'x' and resid 233 through 245 removed outlier: 3.552A pdb=" N VAL x 237 " --> pdb=" O PRO x 233 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 23 removed outlier: 3.630A pdb=" N LEU X 13 " --> pdb=" O THR X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 32 removed outlier: 3.588A pdb=" N LEU X 32 " --> pdb=" O LYS X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 38 Processing helix chain 'X' and resid 89 through 94 Processing helix chain 'X' and resid 130 through 134 Processing helix chain 'w' and resid 181 through 193 Processing helix chain 'w' and resid 212 through 220 removed outlier: 3.543A pdb=" N TYR w 218 " --> pdb=" O GLU w 214 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL w 219 " --> pdb=" O GLN w 215 " (cutoff:3.500A) Processing helix chain 'w' and resid 221 through 225 removed outlier: 3.657A pdb=" N TRP w 225 " --> pdb=" O PRO w 222 " (cutoff:3.500A) Processing helix chain 'w' and resid 226 through 241 removed outlier: 3.554A pdb=" N LEU w 241 " --> pdb=" O PHE w 237 " (cutoff:3.500A) Processing helix chain 'w' and resid 243 through 253 Processing helix chain 'w' and resid 253 through 266 removed outlier: 3.632A pdb=" N ARG w 257 " --> pdb=" O VAL w 253 " (cutoff:3.500A) Processing helix chain 'w' and resid 269 through 280 Processing helix chain 'w' and resid 282 through 290 Processing helix chain 'w' and resid 290 through 297 Processing helix chain 'w' and resid 302 through 315 Processing helix chain 'w' and resid 318 through 331 removed outlier: 3.604A pdb=" N GLU w 331 " --> pdb=" O LEU w 327 " (cutoff:3.500A) Processing helix chain 'w' and resid 337 through 347 removed outlier: 4.248A pdb=" N PHE w 341 " --> pdb=" O ALA w 337 " (cutoff:3.500A) Processing helix chain 'w' and resid 353 through 367 removed outlier: 3.961A pdb=" N LEU w 357 " --> pdb=" O PRO w 353 " (cutoff:3.500A) Processing helix chain 'w' and resid 375 through 389 Processing helix chain 'w' and resid 390 through 393 removed outlier: 4.182A pdb=" N LEU w 393 " --> pdb=" O LYS w 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 390 through 393' Processing helix chain 'w' and resid 394 through 408 Processing helix chain 'w' and resid 412 through 422 removed outlier: 3.952A pdb=" N GLU w 416 " --> pdb=" O GLN w 412 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 19 removed outlier: 3.629A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 32 through 44 Processing helix chain 'W' and resid 85 through 93 removed outlier: 3.908A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'u' and resid 49 through 74 removed outlier: 3.618A pdb=" N GLN u 53 " --> pdb=" O SER u 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG u 54 " --> pdb=" O ARG u 50 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG u 73 " --> pdb=" O LEU u 69 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN u 74 " --> pdb=" O ALA u 70 " (cutoff:3.500A) Processing helix chain 'u' and resid 95 through 104 Processing helix chain 'u' and resid 142 through 150 Processing helix chain 'u' and resid 167 through 181 Processing helix chain 'u' and resid 191 through 195 removed outlier: 3.634A pdb=" N LEU u 195 " --> pdb=" O ILE u 192 " (cutoff:3.500A) Processing helix chain 'u' and resid 196 through 212 Processing helix chain 'u' and resid 225 through 238 removed outlier: 3.667A pdb=" N ASN u 238 " --> pdb=" O ARG u 234 " (cutoff:3.500A) Processing helix chain 'u' and resid 246 through 250 removed outlier: 3.545A pdb=" N ARG u 249 " --> pdb=" O PHE u 246 " (cutoff:3.500A) Processing helix chain 'u' and resid 398 through 404 Processing helix chain 'u' and resid 465 through 481 Processing helix chain 'u' and resid 532 through 546 removed outlier: 3.592A pdb=" N THR u 536 " --> pdb=" O ASN u 532 " (cutoff:3.500A) Processing helix chain 'u' and resid 566 through 576 removed outlier: 4.245A pdb=" N VAL u 570 " --> pdb=" O PRO u 566 " (cutoff:3.500A) Processing helix chain 'u' and resid 720 through 726 removed outlier: 3.736A pdb=" N LEU u 724 " --> pdb=" O ARG u 720 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 10 through 26 removed outlier: 3.600A pdb=" N GLY T 26 " --> pdb=" O LEU T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 36 removed outlier: 4.386A pdb=" N ASP T 35 " --> pdb=" O GLU T 32 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR T 36 " --> pdb=" O TRP T 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 32 through 36' Processing helix chain 'T' and resid 51 through 67 Processing helix chain 'T' and resid 71 through 79 removed outlier: 3.511A pdb=" N TYR T 79 " --> pdb=" O MET T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 110 removed outlier: 3.566A pdb=" N LEU T 110 " --> pdb=" O ALA T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 144 removed outlier: 3.543A pdb=" N LYS T 144 " --> pdb=" O ALA T 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 30 removed outlier: 3.710A pdb=" N ILE S 30 " --> pdb=" O ILE S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 49 removed outlier: 3.824A pdb=" N ALA S 41 " --> pdb=" O GLY S 37 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS S 47 " --> pdb=" O VAL S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 73 Processing helix chain 'S' and resid 99 through 118 Processing helix chain 'S' and resid 119 through 128 removed outlier: 3.664A pdb=" N LEU S 123 " --> pdb=" O ALA S 119 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG S 124 " --> pdb=" O HIS S 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 52 Processing helix chain 'Q' and resid 52 through 59 removed outlier: 3.782A pdb=" N LEU Q 58 " --> pdb=" O PRO Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 63 Processing helix chain 'Q' and resid 76 through 100 Processing helix chain 'Q' and resid 102 through 116 removed outlier: 3.513A pdb=" N GLN Q 114 " --> pdb=" O ASP Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 Processing helix chain 'P' and resid 22 through 27 Processing helix chain 'P' and resid 29 through 34 removed outlier: 4.155A pdb=" N MET P 34 " --> pdb=" O TYR P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 48 Processing helix chain 'P' and resid 50 through 66 Processing helix chain 'P' and resid 86 through 90 Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.987A pdb=" N ILE P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 119 removed outlier: 3.814A pdb=" N GLU P 118 " --> pdb=" O TYR P 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 88 Processing helix chain 'O' and resid 109 through 122 removed outlier: 4.128A pdb=" N GLN O 113 " --> pdb=" O GLY O 109 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER O 122 " --> pdb=" O ALA O 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 43 Processing helix chain 'N' and resid 46 through 57 Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 103 Processing helix chain 'N' and resid 108 through 132 Processing helix chain 'L' and resid 23 through 30 removed outlier: 3.969A pdb=" N LYS L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 53 removed outlier: 3.891A pdb=" N ILE L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 39 through 60 removed outlier: 4.347A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 83 Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.752A pdb=" N MET J 92 " --> pdb=" O GLU J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 100 removed outlier: 3.520A pdb=" N TYR J 96 " --> pdb=" O LYS J 93 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU J 98 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU J 100 " --> pdb=" O ILE J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 108 removed outlier: 4.291A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 116 Processing helix chain 'J' and resid 122 through 132 Processing helix chain 'J' and resid 151 through 155 Processing helix chain 'J' and resid 172 through 178 Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 88 through 94 removed outlier: 3.550A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 131 through 136 Processing helix chain 'I' and resid 142 through 154 Processing helix chain 'I' and resid 159 through 169 Processing helix chain 'I' and resid 178 through 183 removed outlier: 3.577A pdb=" N CYS I 182 " --> pdb=" O ARG I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 203 Processing helix chain 's' and resid 184 through 199 Processing helix chain 's' and resid 205 through 221 removed outlier: 3.550A pdb=" N UNK s 209 " --> pdb=" O UNK s 205 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N UNK s 210 " --> pdb=" O UNK s 206 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N UNK s 221 " --> pdb=" O UNK s 217 " (cutoff:3.500A) Processing helix chain 's' and resid 230 through 241 Processing helix chain 's' and resid 249 through 262 Processing helix chain 's' and resid 265 through 288 Processing helix chain 's' and resid 292 through 310 Processing helix chain 's' and resid 313 through 335 Processing helix chain 's' and resid 338 through 358 Processing helix chain 's' and resid 361 through 381 removed outlier: 3.683A pdb=" N UNK s 381 " --> pdb=" O UNK s 377 " (cutoff:3.500A) Processing helix chain 's' and resid 384 through 405 Processing helix chain 's' and resid 408 through 426 removed outlier: 3.568A pdb=" N UNK s 426 " --> pdb=" O UNK s 422 " (cutoff:3.500A) Processing helix chain 's' and resid 429 through 450 Processing helix chain 's' and resid 453 through 475 Processing helix chain 's' and resid 478 through 496 Processing helix chain 's' and resid 499 through 517 removed outlier: 3.746A pdb=" N UNK s 517 " --> pdb=" O UNK s 513 " (cutoff:3.500A) Processing helix chain 's' and resid 520 through 538 Processing helix chain 's' and resid 542 through 549 Processing helix chain 's' and resid 556 through 567 removed outlier: 3.781A pdb=" N UNK s 567 " --> pdb=" O UNK s 563 " (cutoff:3.500A) Processing helix chain 's' and resid 572 through 590 removed outlier: 3.899A pdb=" N UNK s 590 " --> pdb=" O UNK s 586 " (cutoff:3.500A) Processing helix chain 's' and resid 593 through 613 Processing helix chain 's' and resid 617 through 634 removed outlier: 3.598A pdb=" N UNK s 634 " --> pdb=" O UNK s 630 " (cutoff:3.500A) Processing helix chain 's' and resid 639 through 647 removed outlier: 3.963A pdb=" N UNK s 647 " --> pdb=" O UNK s 643 " (cutoff:3.500A) Processing helix chain 's' and resid 652 through 671 Processing helix chain 's' and resid 675 through 688 Processing helix chain 's' and resid 693 through 714 removed outlier: 3.978A pdb=" N UNK s 714 " --> pdb=" O UNK s 710 " (cutoff:3.500A) Processing helix chain 's' and resid 717 through 734 Processing helix chain 's' and resid 737 through 756 Processing helix chain 's' and resid 761 through 780 Processing helix chain 's' and resid 785 through 802 Processing helix chain 's' and resid 808 through 824 Processing helix chain 's' and resid 829 through 846 Processing helix chain 's' and resid 851 through 870 Processing helix chain 's' and resid 875 through 894 Processing helix chain 's' and resid 899 through 915 Processing helix chain 's' and resid 920 through 934 Processing helix chain 's' and resid 937 through 953 Processing helix chain 's' and resid 958 through 975 Processing helix chain 's' and resid 981 through 995 Processing helix chain 's' and resid 1000 through 1008 Processing helix chain 's' and resid 1011 through 1028 Processing helix chain 'r' and resid 2 through 9 removed outlier: 3.528A pdb=" N LEU r 9 " --> pdb=" O HIS r 6 " (cutoff:3.500A) Processing helix chain 'r' and resid 38 through 46 Processing helix chain 'r' and resid 47 through 49 No H-bonds generated for 'chain 'r' and resid 47 through 49' Processing helix chain 'r' and resid 50 through 61 Processing helix chain 'r' and resid 77 through 89 removed outlier: 3.579A pdb=" N LEU r 81 " --> pdb=" O ASN r 77 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 29 Processing helix chain 'q' and resid 29 through 47 Processing helix chain 'q' and resid 65 through 74 removed outlier: 3.992A pdb=" N TYR q 70 " --> pdb=" O LEU q 66 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU q 74 " --> pdb=" O TYR q 70 " (cutoff:3.500A) Processing helix chain 'q' and resid 84 through 93 removed outlier: 3.930A pdb=" N ASP q 93 " --> pdb=" O ASP q 89 " (cutoff:3.500A) Processing helix chain 'q' and resid 104 through 108 Processing helix chain 'q' and resid 124 through 130 Processing helix chain 'q' and resid 137 through 152 Processing helix chain 'q' and resid 167 through 182 Processing helix chain 'k' and resid 2 through 19 Processing sheet with id=AA1, first strand: chain 'b' and resid 43 through 47 Processing sheet with id=AA2, first strand: chain 'b' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 49 removed outlier: 8.548A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS B 34 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N PHE B 100 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 13.999A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 14.429A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG B 136 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 70 removed outlier: 13.999A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 14.429A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG B 136 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE B 142 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP B 209 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 20 through 21 Processing sheet with id=AA6, first strand: chain 'c' and resid 20 through 21 removed outlier: 13.515A pdb=" N ILE c 43 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N ASP F 140 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN c 45 " --> pdb=" O ASP F 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR F 126 " --> pdb=" O GLN F 137 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 9 through 10 removed outlier: 4.165A pdb=" N LEU E 9 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AA9, first strand: chain 'E' and resid 140 through 141 removed outlier: 6.540A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP E 158 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 218 through 220 removed outlier: 6.119A pdb=" N LYS E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 47 through 53 removed outlier: 8.995A pdb=" N VAL H 93 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE H 60 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE H 95 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE H 62 " --> pdb=" O ILE H 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 185 through 188 removed outlier: 7.971A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N GLU H 188 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL H 156 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU H 153 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE H 144 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS H 155 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS H 142 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N HIS H 157 " --> pdb=" O VAL H 140 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.708A pdb=" N LEU G 106 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ASP G 57 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL G 108 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY G 55 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASN G 110 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AB6, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AB7, first strand: chain 'Z' and resid 98 through 101 removed outlier: 6.345A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Y' and resid 6 through 15 removed outlier: 5.766A pdb=" N ILE Y 7 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU Y 28 " --> pdb=" O ILE Y 7 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR Y 9 " --> pdb=" O ASP Y 26 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP Y 26 " --> pdb=" O THR Y 9 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS Y 11 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'x' and resid 75 through 78 Processing sheet with id=AC1, first strand: chain 'x' and resid 159 through 164 Processing sheet with id=AC2, first strand: chain 'X' and resid 80 through 84 removed outlier: 5.104A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL X 128 " --> pdb=" O VAL X 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AC4, first strand: chain 'W' and resid 71 through 74 removed outlier: 6.617A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'u' and resid 110 through 112 removed outlier: 7.669A pdb=" N LEU u 157 " --> pdb=" O GLN u 84 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU u 86 " --> pdb=" O LEU u 157 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU u 159 " --> pdb=" O LEU u 86 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL u 88 " --> pdb=" O LEU u 159 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N LEU u 221 " --> pdb=" O TYR u 185 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU u 187 " --> pdb=" O LEU u 221 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'u' and resid 252 through 254 Processing sheet with id=AC7, first strand: chain 'u' and resid 257 through 264 removed outlier: 7.860A pdb=" N VAL u 269 " --> pdb=" O SER u 263 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLY u 270 " --> pdb=" O GLU u 564 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU u 564 " --> pdb=" O GLY u 270 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER u 563 " --> pdb=" O MET u 299 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N MET u 299 " --> pdb=" O SER u 563 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'u' and resid 487 through 488 removed outlier: 6.069A pdb=" N HIS u 638 " --> pdb=" O ILE u 694 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ARG u 696 " --> pdb=" O HIS u 638 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU u 640 " --> pdb=" O ARG u 696 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N VAL u 698 " --> pdb=" O LEU u 640 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE u 629 " --> pdb=" O GLN u 641 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'u' and resid 487 through 488 Processing sheet with id=AD1, first strand: chain 'u' and resid 623 through 625 removed outlier: 6.634A pdb=" N LEU u 667 " --> pdb=" O ILE u 679 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'u' and resid 702 through 707 removed outlier: 7.204A pdb=" N ARG u 714 " --> pdb=" O PRO u 703 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET u 710 " --> pdb=" O PHE u 707 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N HIS u 750 " --> pdb=" O PRO u 744 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LYS u 752 " --> pdb=" O LYS u 742 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 81 through 83 Processing sheet with id=AD4, first strand: chain 'T' and resid 113 through 115 Processing sheet with id=AD5, first strand: chain 'S' and resid 13 through 14 Processing sheet with id=AD6, first strand: chain 'Q' and resid 9 through 15 removed outlier: 6.318A pdb=" N LYS Q 33 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL Q 72 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 16 through 17 Processing sheet with id=AD8, first strand: chain 'P' and resid 76 through 78 Processing sheet with id=AD9, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.643A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY O 29 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LYS O 96 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N CYS O 31 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG O 98 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE O 33 " --> pdb=" O ARG O 98 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU O 93 " --> pdb=" O ILE O 126 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ARG O 128 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE O 95 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 101 through 111 removed outlier: 6.730A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 15.032A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 16.416A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 136 through 137 Processing sheet with id=AE3, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.872A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 37 through 38 removed outlier: 5.383A pdb=" N VAL I 46 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N HIS I 44 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 62 through 67 removed outlier: 7.828A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP I 80 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE I 101 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N CYS I 100 " --> pdb=" O ILE I 175 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE I 175 " --> pdb=" O CYS I 100 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'r' and resid 24 through 32 removed outlier: 6.903A pdb=" N LEU r 25 " --> pdb=" O LEU r 98 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU r 98 " --> pdb=" O LEU r 25 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA r 27 " --> pdb=" O GLY r 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY r 96 " --> pdb=" O ALA r 27 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU r 29 " --> pdb=" O ILE r 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'q' and resid 99 through 102 removed outlier: 6.857A pdb=" N TYR q 56 " --> pdb=" O PHE q 116 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE q 122 " --> pdb=" O ILE q 60 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N PHE q 116 " --> pdb=" O VAL q 154 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLY q 156 " --> pdb=" O PHE q 116 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY q 118 " --> pdb=" O GLY q 156 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG q 158 " --> pdb=" O GLY q 118 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE q 120 " --> pdb=" O ARG q 158 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL q 160 " --> pdb=" O ILE q 120 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILE q 122 " --> pdb=" O VAL q 160 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN q 162 " --> pdb=" O ILE q 122 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE q 200 " --> pdb=" O LEU q 163 " (cutoff:3.500A) 2075 hydrogen bonds defined for protein. 5922 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: 10.85 Time building geometry restraints manager: 5.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.31: 5368 1.31 - 1.39: 5272 1.39 - 1.48: 14353 1.48 - 1.57: 18585 1.57 - 1.65: 3108 Bond restraints: 46686 Sorted by residual: bond pdb=" CA GLY q 118 " pdb=" C GLY q 118 " ideal model delta sigma weight residual 1.516 1.473 0.042 8.90e-03 1.26e+04 2.24e+01 bond pdb=" CA TYR q 191 " pdb=" CB TYR q 191 " ideal model delta sigma weight residual 1.522 1.563 -0.041 8.90e-03 1.26e+04 2.08e+01 bond pdb=" CA ILE r 46 " pdb=" C ILE r 46 " ideal model delta sigma weight residual 1.524 1.569 -0.045 1.05e-02 9.07e+03 1.83e+01 bond pdb=" C GLU r 72 " pdb=" N GLY r 73 " ideal model delta sigma weight residual 1.327 1.368 -0.041 9.60e-03 1.09e+04 1.80e+01 bond pdb=" C ILE W 75 " pdb=" N SER W 76 " ideal model delta sigma weight residual 1.333 1.266 0.067 1.59e-02 3.96e+03 1.77e+01 ... (remaining 46681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 64776 2.43 - 4.85: 2685 4.85 - 7.28: 279 7.28 - 9.71: 46 9.71 - 12.13: 14 Bond angle restraints: 67800 Sorted by residual: angle pdb=" C ILE r 46 " pdb=" N PRO r 47 " pdb=" CA PRO r 47 " ideal model delta sigma weight residual 119.82 127.96 -8.14 9.80e-01 1.04e+00 6.90e+01 angle pdb=" C4' A 21265 " pdb=" C3' A 21265 " pdb=" O3' A 21265 " ideal model delta sigma weight residual 113.00 125.13 -12.13 1.50e+00 4.44e-01 6.54e+01 angle pdb=" C3' G 21330 " pdb=" C2' G 21330 " pdb=" O2' G 21330 " ideal model delta sigma weight residual 110.70 122.16 -11.46 1.50e+00 4.44e-01 5.84e+01 angle pdb=" C4' C 21331 " pdb=" C3' C 21331 " pdb=" O3' C 21331 " ideal model delta sigma weight residual 113.00 123.73 -10.73 1.50e+00 4.44e-01 5.12e+01 angle pdb=" C4' G 21275 " pdb=" C3' G 21275 " pdb=" O3' G 21275 " ideal model delta sigma weight residual 113.00 123.62 -10.62 1.50e+00 4.44e-01 5.01e+01 ... (remaining 67795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 31328 35.37 - 70.73: 3240 70.73 - 106.10: 265 106.10 - 141.46: 13 141.46 - 176.83: 21 Dihedral angle restraints: 34867 sinusoidal: 19501 harmonic: 15366 Sorted by residual: dihedral pdb=" CA PRO u 81 " pdb=" C PRO u 81 " pdb=" N PRO u 82 " pdb=" CA PRO u 82 " ideal model delta harmonic sigma weight residual 180.00 123.48 56.52 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" C5' U 21371 " pdb=" C4' U 21371 " pdb=" C3' U 21371 " pdb=" O3' U 21371 " ideal model delta sinusoidal sigma weight residual 82.00 163.30 -81.30 1 8.00e+00 1.56e-02 1.27e+02 dihedral pdb=" C4' U 21154 " pdb=" C3' U 21154 " pdb=" C2' U 21154 " pdb=" C1' U 21154 " ideal model delta sinusoidal sigma weight residual 36.00 -43.85 79.85 1 8.00e+00 1.56e-02 1.24e+02 ... (remaining 34864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 10183 0.095 - 0.190: 650 0.190 - 0.284: 368 0.284 - 0.379: 86 0.379 - 0.474: 6 Chirality restraints: 11293 Sorted by residual: chirality pdb=" C2' G 21330 " pdb=" C3' G 21330 " pdb=" O2' G 21330 " pdb=" C1' G 21330 " both_signs ideal model delta sigma weight residual False -2.75 -2.28 -0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" C3' G 21330 " pdb=" C4' G 21330 " pdb=" O3' G 21330 " pdb=" C2' G 21330 " both_signs ideal model delta sigma weight residual False -2.48 -2.03 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C2' A 21204 " pdb=" C3' A 21204 " pdb=" O2' A 21204 " pdb=" C1' A 21204 " both_signs ideal model delta sigma weight residual False -2.75 -2.36 -0.40 2.00e-01 2.50e+01 3.95e+00 ... (remaining 11290 not shown) Planarity restraints: 5282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 228 " 0.036 2.00e-02 2.50e+03 7.19e-02 5.18e+01 pdb=" C ILE E 228 " -0.124 2.00e-02 2.50e+03 pdb=" O ILE E 228 " 0.047 2.00e-02 2.50e+03 pdb=" N GLY E 229 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 100 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C PHE B 100 " -0.047 2.00e-02 2.50e+03 pdb=" O PHE B 100 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS B 101 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR Q 46 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C THR Q 46 " -0.047 2.00e-02 2.50e+03 pdb=" O THR Q 46 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU Q 47 " 0.016 2.00e-02 2.50e+03 ... (remaining 5279 not shown) Histogram of nonbonded interaction distances: 0.76 - 1.59: 5 1.59 - 2.42: 104 2.42 - 3.24: 40805 3.24 - 4.07: 91286 4.07 - 4.90: 137251 Warning: very small nonbonded interaction distances. Nonbonded interactions: 269451 Sorted by model distance: nonbonded pdb=" OP1 C 2 829 " pdb=" N LYS E 22 " model vdw 0.760 3.120 nonbonded pdb=" OP2 U 2 406 " pdb=" CB ARG u 50 " model vdw 0.847 3.440 nonbonded pdb=" OP1 G 21526 " pdb=" CB LYS q 196 " model vdw 1.237 3.440 nonbonded pdb=" O VAL F 134 " pdb=" CB ALA q 131 " model vdw 1.456 3.460 nonbonded pdb=" OP1 C 21272 " pdb=" C1' C 21303 " model vdw 1.485 3.470 ... (remaining 269446 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.020 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: 0.040 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 45.490 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5071 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 : 0.006 0.120 46686 Z= 0.387 Angle : 1.114 12.133 67800 Z= 0.737 Chirality : 0.070 0.474 11293 Planarity : 0.005 0.072 5282 Dihedral : 23.585 176.825 24783 Min Nonbonded Distance : 0.760 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.17 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.05 % Twisted Proline : 1.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.51 (0.10), residues: 4519 helix: -2.17 (0.10), residues: 1601 sheet: -1.74 (0.18), residues: 698 loop : -2.63 (0.11), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR R 20 PHE 0.000 0.000 PHE R 28 TRP 0.000 0.000 TRP B 30 Details of bonding type rmsd covalent geometry : bond 0.00569 (46686) covalent geometry : angle 1.11366 (67800) hydrogen bonds : bond 0.13687 ( 2063) hydrogen bonds : angle 7.35839 ( 5922) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.170 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1967 time to fit residues: 35.6516 Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 30.0000 chunk 265 optimal weight: 30.0000 chunk 523 optimal weight: 50.0000 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 50.0000 chunk 310 optimal weight: 0.2980 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 1.9990 chunk 597 optimal weight: 40.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.079897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.067751 restraints weight = 485469.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.067838 restraints weight = 333026.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.068171 restraints weight = 257499.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.068427 restraints weight = 192281.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.068461 restraints weight = 178078.685| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 46686 Z= 0.149 Angle : 0.567 10.132 67800 Z= 0.319 Chirality : 0.034 0.250 11293 Planarity : 0.002 0.027 5282 Dihedral : 20.560 178.777 24783 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.05 % Twisted Proline : 0.50 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.12), residues: 4519 helix: 0.03 (0.12), residues: 1672 sheet: -1.42 (0.18), residues: 771 loop : -2.11 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR R 20 PHE 0.000 0.000 PHE R 28 TRP 0.000 0.000 TRP B 30 Details of bonding type rmsd covalent geometry : bond 0.00226 (46686) covalent geometry : angle 0.56737 (67800) hydrogen bonds : bond 0.03411 ( 2063) hydrogen bonds : angle 5.07282 ( 5922) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.268 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2029 time to fit residues: 36.6915 Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 96 optimal weight: 30.0000 chunk 271 optimal weight: 50.0000 chunk 209 optimal weight: 1.9990 chunk 476 optimal weight: 7.9990 chunk 264 optimal weight: 20.0000 chunk 536 optimal weight: 20.0000 chunk 223 optimal weight: 7.9990 chunk 629 optimal weight: 30.0000 chunk 517 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 211 optimal weight: 40.0000 overall best weight: 11.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.065384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.059760 restraints weight = 926248.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.060138 restraints weight = 712257.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.060412 restraints weight = 592521.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.060551 restraints weight = 519887.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.060706 restraints weight = 479228.070| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.8434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 46686 Z= 0.364 Angle : 1.006 14.792 67800 Z= 0.550 Chirality : 0.049 0.304 11293 Planarity : 0.004 0.026 5282 Dihedral : 23.059 179.083 24783 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.61 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.12), residues: 4519 helix: -0.20 (0.12), residues: 1697 sheet: -1.51 (0.18), residues: 739 loop : -1.91 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR R 20 PHE 0.000 0.000 PHE R 28 TRP 0.000 0.000 TRP B 30 Details of bonding type rmsd covalent geometry : bond 0.00546 (46686) covalent geometry : angle 1.00620 (67800) hydrogen bonds : bond 0.05220 ( 2063) hydrogen bonds : angle 6.17232 ( 5922) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.955 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1583 time to fit residues: 28.4882 Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 528 optimal weight: 20.0000 chunk 542 optimal weight: 0.0870 chunk 374 optimal weight: 5.9990 chunk 475 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 277 optimal weight: 40.0000 chunk 321 optimal weight: 50.0000 chunk 126 optimal weight: 30.0000 chunk 668 optimal weight: 50.0000 chunk 585 optimal weight: 30.0000 chunk 13 optimal weight: 30.0000 overall best weight: 11.2172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.063164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.057179 restraints weight = 889509.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.057542 restraints weight = 687657.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.057808 restraints weight = 575798.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.057996 restraints weight = 507359.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.058148 restraints weight = 463496.411| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6032 moved from start: 1.0160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 46686 Z= 0.259 Angle : 0.733 12.881 67800 Z= 0.397 Chirality : 0.038 0.297 11293 Planarity : 0.004 0.024 5282 Dihedral : 23.730 179.902 24783 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.97 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.12), residues: 4519 helix: 0.47 (0.12), residues: 1718 sheet: -1.51 (0.18), residues: 730 loop : -1.68 (0.14), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR R 20 PHE 0.000 0.000 PHE R 28 TRP 0.000 0.000 TRP B 30 Details of bonding type rmsd covalent geometry : bond 0.00374 (46686) covalent geometry : angle 0.73297 (67800) hydrogen bonds : bond 0.03874 ( 2063) hydrogen bonds : angle 5.43999 ( 5922) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1579 time to fit residues: 28.9117 Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 531 optimal weight: 30.0000 chunk 169 optimal weight: 40.0000 chunk 10 optimal weight: 20.0000 chunk 316 optimal weight: 40.0000 chunk 144 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 503 optimal weight: 30.0000 chunk 207 optimal weight: 20.0000 chunk 428 optimal weight: 50.0000 chunk 394 optimal weight: 0.0670 chunk 256 optimal weight: 0.5980 overall best weight: 12.1330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.059469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.053668 restraints weight = 902230.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.054053 restraints weight = 681199.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.054322 restraints weight = 560802.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.054502 restraints weight = 490336.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.054655 restraints weight = 446598.562| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 1.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 46686 Z= 0.326 Angle : 0.851 11.982 67800 Z= 0.468 Chirality : 0.042 0.270 11293 Planarity : 0.004 0.021 5282 Dihedral : 24.543 179.887 24783 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.65 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.12), residues: 4519 helix: 0.45 (0.12), residues: 1721 sheet: -1.49 (0.19), residues: 719 loop : -1.75 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR R 20 PHE 0.000 0.000 PHE R 28 TRP 0.000 0.000 TRP B 30 Details of bonding type rmsd covalent geometry : bond 0.00498 (46686) covalent geometry : angle 0.85133 (67800) hydrogen bonds : bond 0.04577 ( 2063) hydrogen bonds : angle 5.93727 ( 5922) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.146 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1995 time to fit residues: 35.7697 Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 119 optimal weight: 40.0000 chunk 319 optimal weight: 5.9990 chunk 462 optimal weight: 6.9990 chunk 504 optimal weight: 20.0000 chunk 540 optimal weight: 5.9990 chunk 531 optimal weight: 0.0570 chunk 269 optimal weight: 40.0000 chunk 407 optimal weight: 0.4980 chunk 51 optimal weight: 20.0000 chunk 314 optimal weight: 6.9990 chunk 543 optimal weight: 30.0000 overall best weight: 3.9104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.065866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.054257 restraints weight = 532586.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.054906 restraints weight = 321757.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.054890 restraints weight = 243781.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.055204 restraints weight = 210006.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.055380 restraints weight = 176165.938| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 1.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 46686 Z= 0.118 Angle : 0.431 7.931 67800 Z= 0.240 Chirality : 0.030 0.174 11293 Planarity : 0.002 0.022 5282 Dihedral : 24.019 178.511 24783 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.13), residues: 4519 helix: 1.69 (0.13), residues: 1750 sheet: -1.42 (0.19), residues: 723 loop : -1.48 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR R 20 PHE 0.000 0.000 PHE R 28 TRP 0.000 0.000 TRP B 30 Details of bonding type rmsd covalent geometry : bond 0.00186 (46686) covalent geometry : angle 0.43060 (67800) hydrogen bonds : bond 0.03089 ( 2063) hydrogen bonds : angle 4.86370 ( 5922) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.863 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1682 time to fit residues: 30.5759 Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 108 optimal weight: 50.0000 chunk 568 optimal weight: 3.9990 chunk 287 optimal weight: 0.9990 chunk 507 optimal weight: 7.9990 chunk 52 optimal weight: 30.0000 chunk 643 optimal weight: 50.0000 chunk 226 optimal weight: 50.0000 chunk 357 optimal weight: 8.9990 chunk 138 optimal weight: 30.0000 chunk 460 optimal weight: 50.0000 chunk 178 optimal weight: 50.0000 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.057803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.051894 restraints weight = 887713.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.052257 restraints weight = 673435.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.052481 restraints weight = 560338.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.052603 restraints weight = 495106.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.052771 restraints weight = 461550.932| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 1.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 46686 Z= 0.278 Angle : 0.699 8.258 67800 Z= 0.390 Chirality : 0.037 0.209 11293 Planarity : 0.003 0.017 5282 Dihedral : 24.686 179.522 24783 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.36 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.13), residues: 4519 helix: 1.16 (0.13), residues: 1731 sheet: -1.52 (0.19), residues: 700 loop : -1.71 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR R 20 PHE 0.000 0.000 PHE R 28 TRP 0.000 0.000 TRP B 30 Details of bonding type rmsd covalent geometry : bond 0.00419 (46686) covalent geometry : angle 0.69909 (67800) hydrogen bonds : bond 0.04063 ( 2063) hydrogen bonds : angle 5.56695 ( 5922) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1938 time to fit residues: 35.0138 Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 570 optimal weight: 5.9990 chunk 316 optimal weight: 8.9990 chunk 595 optimal weight: 40.0000 chunk 22 optimal weight: 30.0000 chunk 192 optimal weight: 4.9990 chunk 339 optimal weight: 0.6980 chunk 28 optimal weight: 30.0000 chunk 326 optimal weight: 5.9990 chunk 506 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 345 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.064214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.053199 restraints weight = 541752.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.053736 restraints weight = 342791.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.053748 restraints weight = 237512.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.053849 restraints weight = 197196.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.053886 restraints weight = 183308.601| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 1.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 46686 Z= 0.115 Angle : 0.410 7.849 67800 Z= 0.231 Chirality : 0.029 0.162 11293 Planarity : 0.002 0.022 5282 Dihedral : 24.129 178.284 24783 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.13), residues: 4519 helix: 2.01 (0.13), residues: 1752 sheet: -1.41 (0.19), residues: 718 loop : -1.47 (0.15), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR R 20 PHE 0.000 0.000 PHE R 28 TRP 0.000 0.000 TRP B 30 Details of bonding type rmsd covalent geometry : bond 0.00180 (46686) covalent geometry : angle 0.40976 (67800) hydrogen bonds : bond 0.02969 ( 2063) hydrogen bonds : angle 4.74251 ( 5922) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.290 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1770 time to fit residues: 31.6244 Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 220 optimal weight: 40.0000 chunk 372 optimal weight: 9.9990 chunk 296 optimal weight: 0.0270 chunk 352 optimal weight: 30.0000 chunk 667 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 375 optimal weight: 2.9990 chunk 26 optimal weight: 30.0000 chunk 182 optimal weight: 40.0000 chunk 340 optimal weight: 50.0000 chunk 12 optimal weight: 40.0000 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.063513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.052535 restraints weight = 542272.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.053214 restraints weight = 356136.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.053177 restraints weight = 231085.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.053219 restraints weight = 191899.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.053243 restraints weight = 187927.825| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 1.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 46686 Z= 0.134 Angle : 0.421 7.168 67800 Z= 0.235 Chirality : 0.030 0.166 11293 Planarity : 0.002 0.022 5282 Dihedral : 23.838 174.886 24783 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.14), residues: 4519 helix: 2.34 (0.13), residues: 1753 sheet: -1.34 (0.18), residues: 754 loop : -1.34 (0.15), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR R 20 PHE 0.000 0.000 PHE R 28 TRP 0.000 0.000 TRP B 30 Details of bonding type rmsd covalent geometry : bond 0.00205 (46686) covalent geometry : angle 0.42096 (67800) hydrogen bonds : bond 0.02862 ( 2063) hydrogen bonds : angle 4.43675 ( 5922) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.783 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1651 time to fit residues: 30.4359 Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 134 optimal weight: 30.0000 chunk 346 optimal weight: 30.0000 chunk 232 optimal weight: 20.0000 chunk 163 optimal weight: 0.7980 chunk 364 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 347 optimal weight: 6.9990 chunk 370 optimal weight: 0.3980 chunk 368 optimal weight: 20.0000 chunk 505 optimal weight: 40.0000 chunk 389 optimal weight: 10.0000 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.063170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.052287 restraints weight = 545607.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.052785 restraints weight = 375903.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.052853 restraints weight = 249678.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.052787 restraints weight = 202396.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.052923 restraints weight = 195579.770| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 1.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 46686 Z= 0.120 Angle : 0.386 7.583 67800 Z= 0.219 Chirality : 0.029 0.160 11293 Planarity : 0.002 0.023 5282 Dihedral : 23.732 176.218 24783 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.14), residues: 4519 helix: 2.58 (0.13), residues: 1754 sheet: -1.19 (0.19), residues: 746 loop : -1.18 (0.15), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR R 20 PHE 0.000 0.000 PHE R 28 TRP 0.000 0.000 TRP B 30 Details of bonding type rmsd covalent geometry : bond 0.00184 (46686) covalent geometry : angle 0.38644 (67800) hydrogen bonds : bond 0.02745 ( 2063) hydrogen bonds : angle 4.33617 ( 5922) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9038 Ramachandran restraints generated. 4519 Oldfield, 0 Emsley, 4519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.775 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1669 time to fit residues: 30.0352 Evaluate side-chains 91 residues out of total 3961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 68 optimal weight: 50.0000 chunk 11 optimal weight: 30.0000 chunk 241 optimal weight: 0.4980 chunk 60 optimal weight: 50.0000 chunk 452 optimal weight: 1.9990 chunk 628 optimal weight: 50.0000 chunk 429 optimal weight: 50.0000 chunk 500 optimal weight: 0.0870 chunk 600 optimal weight: 40.0000 chunk 281 optimal weight: 4.9990 chunk 285 optimal weight: 5.9990 overall best weight: 2.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.063251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.052291 restraints weight = 543205.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.052948 restraints weight = 342247.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.052742 restraints weight = 237374.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.052891 restraints weight = 201494.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.052905 restraints weight = 188438.062| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 1.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.027 46686 Z= 0.086 Angle : 0.341 7.056 67800 Z= 0.192 Chirality : 0.028 0.158 11293 Planarity : 0.001 0.024 5282 Dihedral : 23.387 174.352 24783 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.14), residues: 4519 helix: 2.88 (0.13), residues: 1762 sheet: -1.09 (0.19), residues: 751 loop : -1.07 (0.15), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR R 20 PHE 0.000 0.000 PHE R 28 TRP 0.000 0.000 TRP B 30 Details of bonding type rmsd covalent geometry : bond 0.00135 (46686) covalent geometry : angle 0.34092 (67800) hydrogen bonds : bond 0.02460 ( 2063) hydrogen bonds : angle 4.00908 ( 5922) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6443.25 seconds wall clock time: 111 minutes 36.70 seconds (6696.70 seconds total)