Starting phenix.real_space_refine on Fri Nov 17 20:58:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqa_11357/11_2023/6zqa_11357_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqa_11357/11_2023/6zqa_11357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqa_11357/11_2023/6zqa_11357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqa_11357/11_2023/6zqa_11357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqa_11357/11_2023/6zqa_11357_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqa_11357/11_2023/6zqa_11357_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1488 5.49 5 Mg 2 5.21 5 C 70351 2.51 5 N 24699 2.21 5 O 29449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 125991 Number of models: 1 Model: "" Number of chains: 63 Chain: "UA" Number of atoms: 4121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 4121 Classifications: {'peptide': 834} Incomplete info: {'truncation_to_alanine': 730} Link IDs: {'PTRANS': 22, 'TRANS': 811} Chain breaks: 1 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 2661 Unresolved non-hydrogen angles: 3419 Unresolved non-hydrogen dihedrals: 2236 Unresolved non-hydrogen chiralities: 235 Planarities with less than four sites: {'GLN:plan1': 33, 'HIS:plan': 18, 'TYR:plan': 22, 'ASN:plan1': 45, 'TRP:plan': 13, 'ASP:plan': 53, 'PHE:plan': 59, 'GLU:plan': 41, 'ARG:plan': 44} Unresolved non-hydrogen planarities: 1525 Chain: "UB" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 2512 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 468} Link IDs: {'PTRANS': 16, 'TRANS': 487} Chain breaks: 5 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1718 Unresolved non-hydrogen angles: 2152 Unresolved non-hydrogen dihedrals: 1425 Unresolved non-hydrogen chiralities: 139 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 11, 'TYR:plan': 17, 'ASN:plan1': 25, 'TRP:plan': 1, 'ASP:plan': 31, 'PHE:plan': 22, 'GLU:plan': 46, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 911 Chain: "UC" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 628 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 408 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 8, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 218 Chain: "UD" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 3339 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 615} Link IDs: {'PTRANS': 19, 'TRANS': 655} Chain breaks: 5 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 2128 Unresolved non-hydrogen angles: 2742 Unresolved non-hydrogen dihedrals: 1768 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 11, 'TYR:plan': 10, 'ASN:plan1': 55, 'TRP:plan': 17, 'ASP:plan': 46, 'PHE:plan': 32, 'GLU:plan': 28, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 1120 Chain: "UE" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 2353 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 428} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 4 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1492 Unresolved non-hydrogen angles: 1928 Unresolved non-hydrogen dihedrals: 1229 Unresolved non-hydrogen chiralities: 158 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 11, 'TYR:plan': 14, 'ASN:plan1': 33, 'TRP:plan': 9, 'ASP:plan': 29, 'PHE:plan': 16, 'GLU:plan': 21, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 780 Chain: "UF" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 1456 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 6, 'TRANS': 286} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1087 Unresolved non-hydrogen angles: 1382 Unresolved non-hydrogen dihedrals: 932 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 7, 'TYR:plan': 19, 'ASN:plan1': 27, 'TRP:plan': 5, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 15, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 607 Chain: "UG" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 2629 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 462} Link IDs: {'PTRANS': 23, 'TRANS': 509} Chain breaks: 1 Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1675 Unresolved non-hydrogen angles: 2129 Unresolved non-hydrogen dihedrals: 1405 Unresolved non-hydrogen chiralities: 140 Planarities with less than four sites: {'GLN:plan1': 23, 'HIS:plan': 19, 'TYR:plan': 17, 'ASN:plan1': 31, 'TRP:plan': 6, 'ASP:plan': 29, 'PHE:plan': 15, 'GLU:plan': 33, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 892 Chain: "UH" Number of atoms: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 2190 Classifications: {'peptide': 442} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 407} Link IDs: {'PTRANS': 17, 'TRANS': 424} Chain breaks: 7 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1424 Unresolved non-hydrogen angles: 1837 Unresolved non-hydrogen dihedrals: 1152 Unresolved non-hydrogen chiralities: 165 Planarities with less than four sites: {'GLN:plan1': 20, 'ARG:plan': 11, 'TYR:plan': 18, 'ASN:plan1': 27, 'TRP:plan': 2, 'ASP:plan': 27, 'PHE:plan': 22, 'GLU:plan': 26, 'HIS:plan': 6} Unresolved non-hydrogen planarities: 711 Chain: "UI" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 517 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 9, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 163 Chain: "UJ" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 3621 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 667} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 701} Chain breaks: 2 Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 2302 Unresolved non-hydrogen angles: 2937 Unresolved non-hydrogen dihedrals: 1897 Unresolved non-hydrogen chiralities: 245 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 34, 'TYR:plan': 26, 'ASN:plan1': 46, 'TRP:plan': 5, 'HIS:plan': 9, 'PHE:plan': 38, 'GLU:plan': 41, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 1126 Chain: "UK" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1203 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PTRANS': 3, 'TRANS': 238} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 846 Unresolved non-hydrogen angles: 1034 Unresolved non-hydrogen dihedrals: 719 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 9, 'GLU:plan': 18, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 457 Chain: "UL" Number of atoms: 4163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 4163 Classifications: {'peptide': 842} Incomplete info: {'truncation_to_alanine': 747} Link IDs: {'PTRANS': 18, 'TRANS': 823} Chain breaks: 6 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 2701 Unresolved non-hydrogen angles: 3457 Unresolved non-hydrogen dihedrals: 2281 Unresolved non-hydrogen chiralities: 258 Planarities with less than four sites: {'GLN:plan1': 30, 'HIS:plan': 23, 'TYR:plan': 21, 'ASN:plan1': 30, 'TRP:plan': 19, 'ASP:plan': 61, 'PHE:plan': 38, 'GLU:plan': 50, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 1399 Chain: "UM" Number of atoms: 3763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 3763 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 668} Link IDs: {'PTRANS': 19, 'TRANS': 742} Chain breaks: 5 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 2313 Unresolved non-hydrogen angles: 2976 Unresolved non-hydrogen dihedrals: 1907 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 29, 'ASP:plan': 52, 'TYR:plan': 20, 'ASN:plan1': 42, 'TRP:plan': 14, 'HIS:plan': 19, 'PHE:plan': 21, 'GLU:plan': 42, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 1168 Chain: "UN" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 733 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PTRANS': 10, 'TRANS': 136} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 521 Unresolved non-hydrogen angles: 659 Unresolved non-hydrogen dihedrals: 436 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 12, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 315 Chain: "UO" Number of atoms: 2441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 2441 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 437} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain breaks: 1 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1554 Unresolved non-hydrogen angles: 1995 Unresolved non-hydrogen dihedrals: 1296 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 26, 'TYR:plan': 15, 'ASN:plan1': 24, 'TRP:plan': 7, 'HIS:plan': 15, 'PHE:plan': 19, 'GLU:plan': 22, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 851 Chain: "UP" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 298 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 80 Chain: "UQ" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 4122 Classifications: {'peptide': 832} Incomplete info: {'truncation_to_alanine': 769} Link IDs: {'PTRANS': 22, 'TRANS': 809} Chain breaks: 5 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 2678 Unresolved non-hydrogen angles: 3451 Unresolved non-hydrogen dihedrals: 2219 Unresolved non-hydrogen chiralities: 258 Planarities with less than four sites: {'GLN:plan1': 42, 'HIS:plan': 23, 'TYR:plan': 24, 'ASN:plan1': 79, 'TRP:plan': 12, 'ASP:plan': 51, 'PHE:plan': 45, 'GLU:plan': 34, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 1450 Chain: "UR" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 2377 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 425} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 461} Chain breaks: 3 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1510 Unresolved non-hydrogen angles: 1949 Unresolved non-hydrogen dihedrals: 1270 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 15, 'TYR:plan': 14, 'ASN:plan1': 32, 'TRP:plan': 10, 'ASP:plan': 25, 'PHE:plan': 18, 'GLU:plan': 17, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 798 Chain: "US" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 2357 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 439} Link IDs: {'PTRANS': 22, 'TRANS': 450} Chain breaks: 6 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1619 Unresolved non-hydrogen angles: 2078 Unresolved non-hydrogen dihedrals: 1373 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 15, 'TYR:plan': 19, 'ASN:plan1': 32, 'TRP:plan': 6, 'ASP:plan': 24, 'PHE:plan': 31, 'GLU:plan': 28, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 860 Chain: "UU" Number of atoms: 4181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 4181 Classifications: {'peptide': 848} Incomplete info: {'truncation_to_alanine': 743} Link IDs: {'PTRANS': 26, 'TRANS': 821} Chain breaks: 2 Unresolved chain link angles: 26 Unresolved non-hydrogen bonds: 2637 Unresolved non-hydrogen angles: 3378 Unresolved non-hydrogen dihedrals: 2203 Unresolved non-hydrogen chiralities: 252 Planarities with less than four sites: {'GLN:plan1': 28, 'HIS:plan': 22, 'TYR:plan': 23, 'ASN:plan1': 40, 'TRP:plan': 10, 'ASP:plan': 54, 'PHE:plan': 49, 'GLU:plan': 39, 'ARG:plan': 41} Unresolved non-hydrogen planarities: 1410 Chain: "UV" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 5442 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 1000} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1044} Chain breaks: 5 Unresolved chain link angles: 53 Unresolved non-hydrogen bonds: 3645 Unresolved non-hydrogen angles: 4659 Unresolved non-hydrogen dihedrals: 3081 Unresolved non-hydrogen chiralities: 331 Planarities with less than four sites: {'GLN:plan1': 34, 'ASP:plan': 54, 'TYR:plan': 45, 'ASN:plan1': 69, 'TRP:plan': 8, 'HIS:plan': 26, 'PHE:plan': 77, 'GLU:plan': 57, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 1887 Chain: "UX" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 862 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 164} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 558 Unresolved non-hydrogen angles: 701 Unresolved non-hydrogen dihedrals: 462 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 9, 'ASP:plan': 10, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 267 Chain: "UZ" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1224 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 230} Link IDs: {'PTRANS': 12, 'TRANS': 234} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 818 Unresolved non-hydrogen angles: 1029 Unresolved non-hydrogen dihedrals: 677 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 13, 'TYR:plan': 10, 'ASN:plan1': 14, 'HIS:plan': 6, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 388 Chain: "CA" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1190 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 202} Link IDs: {'PTRANS': 15, 'TRANS': 226} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 729 Unresolved non-hydrogen angles: 925 Unresolved non-hydrogen dihedrals: 605 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 7, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 19, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 374 Chain: "CB" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1122 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 192} Link IDs: {'PTRANS': 12, 'TRANS': 215} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 695 Unresolved non-hydrogen angles: 882 Unresolved non-hydrogen dihedrals: 577 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 7, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 361 Chain: "CD" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 1880 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 326} Link IDs: {'PTRANS': 9, 'TRANS': 370} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1163 Unresolved non-hydrogen angles: 1475 Unresolved non-hydrogen dihedrals: 957 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 7, 'TYR:plan': 12, 'ASN:plan1': 21, 'TRP:plan': 2, 'ASP:plan': 25, 'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 631 Chain: "CE" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 2155 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 358} Link IDs: {'PTRANS': 8, 'TRANS': 426} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1230 Unresolved non-hydrogen angles: 1552 Unresolved non-hydrogen dihedrals: 1000 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 16, 'TRP:plan': 2, 'ASP:plan': 27, 'PHE:plan': 8, 'GLU:plan': 34, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 594 Chain: "CF" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 611 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 427 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 146 Chain: "CG" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 611 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 114} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 423 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 146 Chain: "CH" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 2158 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 382} Link IDs: {'PTRANS': 14, 'TRANS': 423} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1418 Unresolved non-hydrogen angles: 1805 Unresolved non-hydrogen dihedrals: 1204 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 8, 'TYR:plan': 15, 'ASN:plan1': 15, 'TRP:plan': 8, 'ASP:plan': 26, 'PHE:plan': 21, 'GLU:plan': 29, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 773 Chain: "CI" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 905 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PTRANS': 6, 'TRANS': 175} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 830 Unresolved non-hydrogen dihedrals: 547 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 8, 'TYR:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 8, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 362 Chain: "CJ" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 1397 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 12, 'TRANS': 269} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 942 Unresolved non-hydrogen angles: 1194 Unresolved non-hydrogen dihedrals: 774 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 9, 'TYR:plan': 7, 'ASN:plan1': 13, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 13, 'GLU:plan': 18, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 546 Chain: "CK" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1031 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 187} Link IDs: {'PTRANS': 8, 'TRANS': 198} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 656 Unresolved non-hydrogen angles: 818 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 27, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 352 Chain: "CL" Number of atoms: 3859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 3859 Classifications: {'peptide': 781} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 691} Link IDs: {'PTRANS': 44, 'TRANS': 736} Chain breaks: 4 Unresolved chain link angles: 45 Unresolved non-hydrogen bonds: 2621 Unresolved non-hydrogen angles: 3308 Unresolved non-hydrogen dihedrals: 2228 Unresolved non-hydrogen chiralities: 212 Planarities with less than four sites: {'GLN:plan1': 28, 'ASP:plan': 39, 'TYR:plan': 25, 'ASN:plan1': 26, 'TRP:plan': 9, 'HIS:plan': 17, 'PHE:plan': 39, 'GLU:plan': 50, 'ARG:plan': 55} Unresolved non-hydrogen planarities: 1357 Chain: "CM" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 1767 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 307} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 342} Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1066 Unresolved non-hydrogen angles: 1357 Unresolved non-hydrogen dihedrals: 883 Unresolved non-hydrogen chiralities: 114 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 13, 'TRP:plan': 4, 'ASP:plan': 15, 'PHE:plan': 13, 'GLU:plan': 24, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 498 Chain: "CN" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1154 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 212} Link IDs: {'PTRANS': 8, 'TRANS': 223} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 784 Unresolved non-hydrogen angles: 997 Unresolved non-hydrogen dihedrals: 666 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 14, 'TYR:plan': 7, 'ASN:plan1': 16, 'TRP:plan': 2, 'HIS:plan': 10, 'PHE:plan': 16, 'GLU:plan': 16, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 434 Chain: "JF" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1071 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 658 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 17, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 304 Chain: "JG" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1141 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 217} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 689 Unresolved non-hydrogen angles: 872 Unresolved non-hydrogen dihedrals: 564 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 17, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 312 Chain: "JH" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1295 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 233} Link IDs: {'PTRANS': 14, 'TRANS': 246} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 886 Unresolved non-hydrogen angles: 1141 Unresolved non-hydrogen dihedrals: 753 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 12, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 15, 'GLU:plan': 14, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 472 Chain: "JJ" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 898 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PTRANS': 9, 'TRANS': 172} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 578 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 479 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 11, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 273 Chain: "JM" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 671 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 488 Unresolved non-hydrogen angles: 602 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 252 Chain: "JN" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 918 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 5, 'TRANS': 180} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 745 Unresolved non-hydrogen dihedrals: 498 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 8, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 306 Chain: "JO" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 933 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PTRANS': 9, 'TRANS': 178} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 616 Unresolved non-hydrogen angles: 778 Unresolved non-hydrogen dihedrals: 512 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 297 Chain: "JP" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 2283 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 416} Link IDs: {'PTRANS': 14, 'TRANS': 446} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1563 Unresolved non-hydrogen angles: 1983 Unresolved non-hydrogen dihedrals: 1332 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 16, 'TYR:plan': 20, 'ASN:plan1': 31, 'TRP:plan': 7, 'ASP:plan': 30, 'PHE:plan': 17, 'GLU:plan': 28, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 901 Chain: "JQ" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 312 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "DA" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1187 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 212} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 752 Unresolved non-hydrogen angles: 940 Unresolved non-hydrogen dihedrals: 621 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 10, 'GLU:plan': 13, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 362 Chain: "DF" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1055 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 8, 'TRANS': 204} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 636 Unresolved non-hydrogen angles: 809 Unresolved non-hydrogen dihedrals: 505 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 13, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 341 Chain: "DH" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 913 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 173} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 747 Unresolved non-hydrogen dihedrals: 485 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 9, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 297 Chain: "DJ" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 915 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 8, 'TRANS': 176} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 605 Unresolved non-hydrogen angles: 755 Unresolved non-hydrogen dihedrals: 504 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 12, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 326 Chain: "DN" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 742 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PTRANS': 7, 'TRANS': 142} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 600 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 239 Chain: "DO" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 587 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 144 Chain: "DQ" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 616 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 6, 'TRANS': 118} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 375 Unresolved non-hydrogen angles: 475 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 177 Chain: "DS" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 521 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 189 Chain: "DW" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 634 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 405 Unresolved non-hydrogen angles: 514 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 212 Chain: "DX" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 503 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 249 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 128 Chain: "Db" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 400 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 4, 'TRANS': 76} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "Dc" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 310 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 96 Chain: "D2" Number of atoms: 11160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 11160 Classifications: {'RNA': 523} Modifications used: {'rna2p_pur': 37, 'rna2p_pyr': 37, 'rna3p_pur': 243, 'rna3p_pyr': 206} Link IDs: {'rna2p': 74, 'rna3p': 448} Chain breaks: 3 Chain: "D3" Number of atoms: 16806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 16806 Classifications: {'RNA': 787} Modifications used: {'rna2p_pur': 49, 'rna2p_pyr': 51, 'rna3p_pur': 377, 'rna3p_pyr': 310} Link IDs: {'rna2p': 100, 'rna3p': 686} Chain breaks: 16 Chain: "D4" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 3712 Classifications: {'RNA': 175} Modifications used: {'rna2p_pur': 19, 'rna2p_pyr': 16, 'rna3p_pur': 67, 'rna3p_pyr': 72} Link IDs: {'rna2p': 35, 'rna3p': 139} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "UX" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "CL" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Db" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 52.24, per 1000 atoms: 0.41 Number of scatterers: 125991 At special positions: 0 Unit cell: (307.11, 308.169, 306.051, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 P 1488 15.00 Mg 2 11.99 O 29449 8.00 N 24699 7.00 C 70351 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 46.61 Conformation dependent library (CDL) restraints added in 18.8 seconds 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 36180 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 582 helices and 223 sheets defined 41.9% alpha, 20.3% beta 491 base pairs and 734 stacking pairs defined. Time for finding SS restraints: 95.53 Creating SS restraints... Processing helix chain 'UA' and resid 176 through 184 removed outlier: 4.565A pdb=" N ASNUA 181 " --> pdb=" O SERUA 177 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEUUA 182 " --> pdb=" O GLUUA 178 " (cutoff:3.500A) Processing helix chain 'UA' and resid 631 through 636 removed outlier: 5.529A pdb=" N THRUA 636 " --> pdb=" O SERUA 632 " (cutoff:3.500A) Processing helix chain 'UA' and resid 652 through 658 removed outlier: 6.109A pdb=" N ASPUA 658 " --> pdb=" O GLUUA 654 " (cutoff:3.500A) Processing helix chain 'UA' and resid 669 through 674 removed outlier: 5.053A pdb=" N ARGUA 673 " --> pdb=" O ASPUA 669 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYSUA 674 " --> pdb=" O LEUUA 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'UA' and resid 669 through 674' Processing helix chain 'UA' and resid 707 through 712 removed outlier: 4.753A pdb=" N PHEUA 712 " --> pdb=" O ASPUA 708 " (cutoff:3.500A) Processing helix chain 'UA' and resid 722 through 733 Processing helix chain 'UA' and resid 734 through 746 Processing helix chain 'UA' and resid 747 through 758 Processing helix chain 'UA' and resid 759 through 770 removed outlier: 3.812A pdb=" N ILEUA 763 " --> pdb=" O PROUA 759 " (cutoff:3.500A) Proline residue: UA 764 - end of helix Processing helix chain 'UA' and resid 771 through 789 Proline residue: UA 776 - end of helix Processing helix chain 'UA' and resid 791 through 807 Processing helix chain 'UA' and resid 808 through 814 Processing helix chain 'UA' and resid 815 through 831 removed outlier: 5.291A pdb=" N THRUA 819 " --> pdb=" O TYRUA 815 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ALAUA 820 " --> pdb=" O LEUUA 816 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARGUA 822 " --> pdb=" O SERUA 818 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SERUA 823 " --> pdb=" O THRUA 819 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VALUA 829 " --> pdb=" O GLNUA 825 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VALUA 831 " --> pdb=" O PHEUA 827 " (cutoff:3.500A) Processing helix chain 'UA' and resid 832 through 852 Processing helix chain 'UB' and resid 201 through 250 removed outlier: 4.692A pdb=" N LEUUB 239 " --> pdb=" O GLNUB 235 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASPUB 240 " --> pdb=" O ILEUB 236 " (cutoff:3.500A) Processing helix chain 'UB' and resid 264 through 281 Processing helix chain 'UB' and resid 291 through 316 Processing helix chain 'UB' and resid 385 through 396 Processing helix chain 'UB' and resid 398 through 413 removed outlier: 5.803A pdb=" N ILEUB 402 " --> pdb=" O ASPUB 398 " (cutoff:3.500A) Proline residue: UB 412 - end of helix Processing helix chain 'UB' and resid 419 through 440 Processing helix chain 'UB' and resid 446 through 466 removed outlier: 4.480A pdb=" N ARGUB 450 " --> pdb=" O GLNUB 446 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THRUB 451 " --> pdb=" O SERUB 447 " (cutoff:3.500A) Processing helix chain 'UB' and resid 467 through 488 Processing helix chain 'UB' and resid 494 through 508 Processing helix chain 'UB' and resid 515 through 531 Proline residue: UB 520 - end of helix Processing helix chain 'UB' and resid 536 through 558 Processing helix chain 'UB' and resid 561 through 578 removed outlier: 4.309A pdb=" N GLUUB 578 " --> pdb=" O THRUB 574 " (cutoff:3.500A) Processing helix chain 'UB' and resid 616 through 624 removed outlier: 4.005A pdb=" N SERUB 620 " --> pdb=" O LEUUB 616 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASPUB 623 " --> pdb=" O LEUUB 619 " (cutoff:3.500A) Processing helix chain 'UB' and resid 628 through 650 removed outlier: 3.963A pdb=" N CYSUB 632 " --> pdb=" O PROUB 628 " (cutoff:3.500A) Processing helix chain 'UB' and resid 656 through 675 Proline residue: UB 663 - end of helix Processing helix chain 'UB' and resid 678 through 695 removed outlier: 4.264A pdb=" N ARGUB 682 " --> pdb=" O PHEUB 678 " (cutoff:3.500A) Processing helix chain 'UB' and resid 731 through 806 removed outlier: 3.582A pdb=" N LEUUB 805 " --> pdb=" O ARGUB 801 " (cutoff:3.500A) Processing helix chain 'UC' and resid 493 through 530 removed outlier: 5.464A pdb=" N GLNUC 497 " --> pdb=" O ASPUC 493 " (cutoff:3.500A) Processing helix chain 'UC' and resid 541 through 547 Processing helix chain 'UC' and resid 555 through 561 removed outlier: 5.152A pdb=" N SERUC 561 " --> pdb=" O ASPUC 557 " (cutoff:3.500A) Processing helix chain 'UC' and resid 562 through 580 removed outlier: 3.783A pdb=" N LYSUC 574 " --> pdb=" O GLNUC 570 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYSUC 575 " --> pdb=" O LYSUC 571 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYSUC 577 " --> pdb=" O GLNUC 573 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERUC 578 " --> pdb=" O LYSUC 574 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VALUC 579 " --> pdb=" O LYSUC 575 " (cutoff:3.500A) Processing helix chain 'UD' and resid 311 through 318 Processing helix chain 'UD' and resid 467 through 473 Processing helix chain 'UD' and resid 519 through 526 Proline residue: UD 526 - end of helix Processing helix chain 'UD' and resid 612 through 619 Processing helix chain 'UD' and resid 623 through 629 Processing helix chain 'UE' and resid 318 through 323 Proline residue: UE 323 - end of helix Processing helix chain 'UE' and resid 437 through 448 Processing helix chain 'UE' and resid 449 through 460 removed outlier: 6.119A pdb=" N ARGUE 460 " --> pdb=" O VALUE 456 " (cutoff:3.500A) Processing helix chain 'UE' and resid 461 through 472 Processing helix chain 'UE' and resid 473 through 492 Processing helix chain 'UE' and resid 493 through 499 Proline residue: UE 497 - end of helix No H-bonds generated for 'chain 'UE' and resid 493 through 499' Processing helix chain 'UE' and resid 500 through 510 removed outlier: 3.808A pdb=" N LEUUE 506 " --> pdb=" O VALUE 502 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILEUE 507 " --> pdb=" O LYSUE 503 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILEUE 508 " --> pdb=" O TRPUE 504 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLYUE 510 " --> pdb=" O LEUUE 506 " (cutoff:3.500A) Processing helix chain 'UE' and resid 511 through 517 Proline residue: UE 517 - end of helix Processing helix chain 'UE' and resid 518 through 524 Processing helix chain 'UE' and resid 525 through 556 Proline residue: UE 538 - end of helix Processing helix chain 'UF' and resid 2 through 22 Proline residue: UF 13 - end of helix removed outlier: 4.532A pdb=" N GLYUF 22 " --> pdb=" O LEUUF 18 " (cutoff:3.500A) Processing helix chain 'UF' and resid 25 through 46 removed outlier: 5.881A pdb=" N ARGUF 46 " --> pdb=" O ARGUF 42 " (cutoff:3.500A) Processing helix chain 'UF' and resid 49 through 75 Processing helix chain 'UF' and resid 84 through 104 Proline residue: UF 104 - end of helix Processing helix chain 'UF' and resid 106 through 121 removed outlier: 4.299A pdb=" N GLYUF 121 " --> pdb=" O METUF 117 " (cutoff:3.500A) Processing helix chain 'UF' and resid 125 through 140 Processing helix chain 'UF' and resid 143 through 156 Processing helix chain 'UF' and resid 160 through 176 Proline residue: UF 176 - end of helix Processing helix chain 'UF' and resid 178 through 207 Processing helix chain 'UF' and resid 264 through 290 removed outlier: 4.958A pdb=" N HISUF 289 " --> pdb=" O TYRUF 285 " (cutoff:3.500A) Processing helix chain 'UF' and resid 297 through 323 Processing helix chain 'UF' and resid 330 through 344 Processing helix chain 'UF' and resid 356 through 372 Processing helix chain 'UG' and resid 17 through 22 Processing helix chain 'UG' and resid 39 through 67 removed outlier: 4.879A pdb=" N TYRUG 65 " --> pdb=" O ALAUG 61 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LEUUG 66 " --> pdb=" O ALAUG 62 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEUUG 67 " --> pdb=" O THRUG 63 " (cutoff:3.500A) Processing helix chain 'UG' and resid 87 through 95 Processing helix chain 'UG' and resid 96 through 104 removed outlier: 5.631A pdb=" N LEUUG 104 " --> pdb=" O ALAUG 100 " (cutoff:3.500A) Processing helix chain 'UG' and resid 421 through 436 Processing helix chain 'UG' and resid 447 through 452 removed outlier: 5.318A pdb=" N VALUG 452 " --> pdb=" O SERUG 448 " (cutoff:3.500A) Processing helix chain 'UG' and resid 462 through 480 removed outlier: 4.933A pdb=" N ALAUG 477 " --> pdb=" O ALAUG 473 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LYSUG 478 " --> pdb=" O ASNUG 474 " (cutoff:3.500A) Processing helix chain 'UG' and resid 495 through 505 removed outlier: 4.792A pdb=" N THRUG 505 " --> pdb=" O LEUUG 501 " (cutoff:3.500A) Processing helix chain 'UG' and resid 510 through 536 Processing helix chain 'UG' and resid 544 through 552 removed outlier: 4.430A pdb=" N ARGUG 552 " --> pdb=" O GLUUG 548 " (cutoff:3.500A) Processing helix chain 'UH' and resid 520 through 530 Proline residue: UH 530 - end of helix Processing helix chain 'UH' and resid 534 through 540 Processing helix chain 'UH' and resid 548 through 557 Processing helix chain 'UH' and resid 562 through 572 Processing helix chain 'UH' and resid 577 through 590 Processing helix chain 'UH' and resid 591 through 603 removed outlier: 5.540A pdb=" N SERUH 603 " --> pdb=" O METUH 599 " (cutoff:3.500A) Processing helix chain 'UH' and resid 604 through 617 Processing helix chain 'UH' and resid 631 through 646 Processing helix chain 'UH' and resid 651 through 681 Processing helix chain 'UI' and resid 413 through 426 Processing helix chain 'UI' and resid 428 through 445 Proline residue: UI 445 - end of helix Processing helix chain 'UI' and resid 450 through 463 removed outlier: 4.957A pdb=" N LEUUI 454 " --> pdb=" O ASNUI 450 " (cutoff:3.500A) Processing helix chain 'UI' and resid 464 through 470 Processing helix chain 'UI' and resid 473 through 515 removed outlier: 4.709A pdb=" N ASNUI 478 " --> pdb=" O HISUI 474 " (cutoff:3.500A) Proline residue: UI 494 - end of helix Processing helix chain 'UJ' and resid 3 through 16 Processing helix chain 'UJ' and resid 21 through 32 removed outlier: 5.453A pdb=" N SERUJ 32 " --> pdb=" O LEUUJ 28 " (cutoff:3.500A) Processing helix chain 'UJ' and resid 37 through 43 Processing helix chain 'UJ' and resid 44 through 63 Processing helix chain 'UJ' and resid 66 through 73 Processing helix chain 'UJ' and resid 75 through 81 Processing helix chain 'UJ' and resid 87 through 106 Processing helix chain 'UJ' and resid 111 through 125 Processing helix chain 'UJ' and resid 126 through 131 Processing helix chain 'UJ' and resid 132 through 140 Processing helix chain 'UJ' and resid 145 through 155 Processing helix chain 'UJ' and resid 161 through 168 Processing helix chain 'UJ' and resid 175 through 186 removed outlier: 5.554A pdb=" N METUJ 186 " --> pdb=" O LEUUJ 182 " (cutoff:3.500A) Processing helix chain 'UJ' and resid 187 through 203 Processing helix chain 'UJ' and resid 206 through 225 Processing helix chain 'UJ' and resid 227 through 249 Proline residue: UJ 236 - end of helix removed outlier: 5.537A pdb=" N LYSUJ 249 " --> pdb=" O LEUUJ 245 " (cutoff:3.500A) Processing helix chain 'UJ' and resid 250 through 269 Proline residue: UJ 269 - end of helix Processing helix chain 'UJ' and resid 271 through 286 Processing helix chain 'UJ' and resid 288 through 307 removed outlier: 5.335A pdb=" N LYSUJ 307 " --> pdb=" O PHEUJ 303 " (cutoff:3.500A) Processing helix chain 'UJ' and resid 316 through 328 Processing helix chain 'UJ' and resid 329 through 339 removed outlier: 5.651A pdb=" N GLUUJ 339 " --> pdb=" O PHEUJ 335 " (cutoff:3.500A) Processing helix chain 'UJ' and resid 344 through 358 Processing helix chain 'UJ' and resid 362 through 374 removed outlier: 5.264A pdb=" N ARGUJ 374 " --> pdb=" O LEUUJ 370 " (cutoff:3.500A) Processing helix chain 'UJ' and resid 376 through 394 Processing helix chain 'UJ' and resid 397 through 411 Processing helix chain 'UJ' and resid 412 through 423 Processing helix chain 'UJ' and resid 488 through 503 Processing helix chain 'UJ' and resid 522 through 533 Proline residue: UJ 533 - end of helix Processing helix chain 'UJ' and resid 536 through 554 Processing helix chain 'UJ' and resid 560 through 574 removed outlier: 5.001A pdb=" N VALUJ 564 " --> pdb=" O ILEUJ 560 " (cutoff:3.500A) Proline residue: UJ 565 - end of helix removed outlier: 5.481A pdb=" N ALAUJ 574 " --> pdb=" O ALAUJ 570 " (cutoff:3.500A) Processing helix chain 'UJ' and resid 575 through 593 Proline residue: UJ 593 - end of helix Processing helix chain 'UJ' and resid 615 through 630 Processing helix chain 'UJ' and resid 637 through 643 Proline residue: UJ 643 - end of helix Processing helix chain 'UJ' and resid 646 through 662 Proline residue: UJ 662 - end of helix Processing helix chain 'UJ' and resid 663 through 676 removed outlier: 5.427A pdb=" N LYSUJ 676 " --> pdb=" O ASPUJ 672 " (cutoff:3.500A) Processing helix chain 'UJ' and resid 679 through 689 Processing helix chain 'UJ' and resid 690 through 699 Processing helix chain 'UJ' and resid 700 through 710 removed outlier: 3.709A pdb=" N LYSUJ 704 " --> pdb=" O SERUJ 700 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SERUJ 705 " --> pdb=" O SERUJ 701 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILEUJ 707 " --> pdb=" O GLUUJ 703 " (cutoff:3.500A) Processing helix chain 'UJ' and resid 712 through 724 removed outlier: 5.582A pdb=" N VALUJ 724 " --> pdb=" O LEUUJ 720 " (cutoff:3.500A) Processing helix chain 'UJ' and resid 732 through 742 removed outlier: 5.185A pdb=" N ASNUJ 742 " --> pdb=" O LEUUJ 738 " (cutoff:3.500A) Processing helix chain 'UJ' and resid 745 through 763 Processing helix chain 'UJ' and resid 765 through 782 Processing helix chain 'UJ' and resid 784 through 796 Proline residue: UJ 796 - end of helix Processing helix chain 'UJ' and resid 798 through 808 Processing helix chain 'UK' and resid 6 through 11 Processing helix chain 'UK' and resid 19 through 24 removed outlier: 3.722A pdb=" N SERUK 23 " --> pdb=" O LEUUK 19 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ARGUK 24 " --> pdb=" O THRUK 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'UK' and resid 19 through 24' Processing helix chain 'UK' and resid 30 through 58 Processing helix chain 'UK' and resid 64 through 70 removed outlier: 4.720A pdb=" N HISUK 68 " --> pdb=" O TYRUK 64 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SERUK 69 " --> pdb=" O HISUK 65 " (cutoff:3.500A) Processing helix chain 'UK' and resid 92 through 125 Processing helix chain 'UK' and resid 139 through 146 Processing helix chain 'UK' and resid 147 through 153 Processing helix chain 'UK' and resid 155 through 162 removed outlier: 5.001A pdb=" N SERUK 162 " --> pdb=" O METUK 158 " (cutoff:3.500A) Processing helix chain 'UK' and resid 167 through 172 Processing helix chain 'UK' and resid 189 through 226 removed outlier: 4.181A pdb=" N LEUUK 225 " --> pdb=" O GLNUK 221 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LYSUK 226 " --> pdb=" O ARGUK 222 " (cutoff:3.500A) Processing helix chain 'UL' and resid 288 through 305 Processing helix chain 'UL' and resid 311 through 327 removed outlier: 5.443A pdb=" N SERUL 322 " --> pdb=" O LYSUL 318 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N SERUL 323 " --> pdb=" O GLUUL 319 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N HISUL 327 " --> pdb=" O SERUL 323 " (cutoff:3.500A) Processing helix chain 'UL' and resid 747 through 777 removed outlier: 6.182A pdb=" N LEUUL 752 " --> pdb=" O ALAUL 748 " (cutoff:3.500A) Processing helix chain 'UL' and resid 791 through 798 Processing helix chain 'UL' and resid 800 through 813 removed outlier: 5.288A pdb=" N ARGUL 813 " --> pdb=" O LEUUL 809 " (cutoff:3.500A) Processing helix chain 'UL' and resid 814 through 825 removed outlier: 6.974A pdb=" N GLUUL 818 " --> pdb=" O METUL 814 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASPUL 819 " --> pdb=" O SERUL 815 " (cutoff:3.500A) Proline residue: UL 825 - end of helix Processing helix chain 'UL' and resid 826 through 843 Processing helix chain 'UL' and resid 844 through 850 removed outlier: 4.522A pdb=" N SERUL 848 " --> pdb=" O THRUL 844 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N HISUL 849 " --> pdb=" O LEUUL 845 " (cutoff:3.500A) Processing helix chain 'UL' and resid 851 through 865 Processing helix chain 'UL' and resid 866 through 872 removed outlier: 5.572A pdb=" N LYSUL 872 " --> pdb=" O LEUUL 868 " (cutoff:3.500A) Processing helix chain 'UL' and resid 873 through 917 Processing helix chain 'UL' and resid 922 through 934 Processing helix chain 'UM' and resid 647 through 676 Processing helix chain 'UM' and resid 677 through 689 Processing helix chain 'UM' and resid 690 through 706 Processing helix chain 'UM' and resid 721 through 731 Processing helix chain 'UM' and resid 732 through 750 removed outlier: 5.400A pdb=" N ALAUM 750 " --> pdb=" O TRPUM 746 " (cutoff:3.500A) Processing helix chain 'UM' and resid 752 through 767 Processing helix chain 'UM' and resid 768 through 776 Proline residue: UM 776 - end of helix Processing helix chain 'UM' and resid 777 through 817 Proline residue: UM 787 - end of helix removed outlier: 3.955A pdb=" N ILEUM 805 " --> pdb=" O GLUUM 801 " (cutoff:3.500A) Processing helix chain 'UN' and resid 276 through 308 removed outlier: 4.575A pdb=" N GLNUN 280 " --> pdb=" O GLNUN 276 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLNUN 304 " --> pdb=" O ASPUN 300 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASNUN 305 " --> pdb=" O ILEUN 301 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARGUN 306 " --> pdb=" O VALUN 302 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARGUN 307 " --> pdb=" O GLNUN 303 " (cutoff:3.500A) Processing helix chain 'UN' and resid 336 through 349 Processing helix chain 'UN' and resid 836 through 844 removed outlier: 5.494A pdb=" N SERUN 844 " --> pdb=" O LEUUN 840 " (cutoff:3.500A) Processing helix chain 'UN' and resid 853 through 862 Processing helix chain 'UN' and resid 871 through 880 Processing helix chain 'UO' and resid 21 through 31 removed outlier: 5.993A pdb=" N THRUO 31 " --> pdb=" O TRPUO 27 " (cutoff:3.500A) Processing helix chain 'UO' and resid 354 through 362 Processing helix chain 'UO' and resid 386 through 395 Processing helix chain 'UO' and resid 396 through 406 Processing helix chain 'UO' and resid 410 through 425 Processing helix chain 'UO' and resid 426 through 432 Processing helix chain 'UO' and resid 437 through 450 Proline residue: UO 441 - end of helix Processing helix chain 'UO' and resid 453 through 471 removed outlier: 4.772A pdb=" N ILEUO 458 " --> pdb=" O ARGUO 454 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLYUO 471 " --> pdb=" O LEUUO 467 " (cutoff:3.500A) Processing helix chain 'UO' and resid 472 through 477 Processing helix chain 'UO' and resid 478 through 512 removed outlier: 3.700A pdb=" N GLNUO 502 " --> pdb=" O SERUO 498 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARGUO 503 " --> pdb=" O LYSUO 499 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILEUO 504 " --> pdb=" O GLUUO 500 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEUUO 511 " --> pdb=" O METUO 507 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THRUO 512 " --> pdb=" O LEUUO 508 " (cutoff:3.500A) Processing helix chain 'UP' and resid 155 through 168 Processing helix chain 'UP' and resid 183 through 190 Processing helix chain 'UP' and resid 195 through 208 Processing helix chain 'UQ' and resid 67 through 72 removed outlier: 4.113A pdb=" N ASNUQ 71 " --> pdb=" O LYSUQ 67 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SERUQ 72 " --> pdb=" O PHEUQ 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'UQ' and resid 67 through 72' Processing helix chain 'UQ' and resid 73 through 78 Processing helix chain 'UQ' and resid 213 through 219 Processing helix chain 'UQ' and resid 240 through 246 removed outlier: 6.099A pdb=" N SERUQ 246 " --> pdb=" O GLYUQ 242 " (cutoff:3.500A) Processing helix chain 'UQ' and resid 247 through 253 removed outlier: 4.543A pdb=" N SERUQ 251 " --> pdb=" O SERUQ 247 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEUUQ 252 " --> pdb=" O GLNUQ 248 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N SERUQ 253 " --> pdb=" O THRUQ 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'UQ' and resid 247 through 253' Processing helix chain 'UQ' and resid 414 through 431 Processing helix chain 'UQ' and resid 485 through 491 removed outlier: 5.317A pdb=" N GLNUQ 491 " --> pdb=" O GLUUQ 487 " (cutoff:3.500A) Processing helix chain 'UQ' and resid 564 through 569 removed outlier: 4.624A pdb=" N ASNUQ 568 " --> pdb=" O PROUQ 564 " (cutoff:3.500A) Processing helix chain 'UQ' and resid 694 through 699 removed outlier: 4.841A pdb=" N ASNUQ 699 " --> pdb=" O TYRUQ 695 " (cutoff:3.500A) Processing helix chain 'UQ' and resid 705 through 712 removed outlier: 4.931A pdb=" N ARGUQ 709 " --> pdb=" O GLYUQ 705 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N THRUQ 712 " --> pdb=" O ASPUQ 708 " (cutoff:3.500A) Processing helix chain 'UQ' and resid 818 through 829 Processing helix chain 'UQ' and resid 849 through 862 removed outlier: 5.242A pdb=" N LYSUQ 862 " --> pdb=" O ILEUQ 858 " (cutoff:3.500A) Processing helix chain 'UQ' and resid 872 through 879 removed outlier: 6.138A pdb=" N PHEUQ 876 " --> pdb=" O PHEUQ 872 " (cutoff:3.500A) Processing helix chain 'UQ' and resid 883 through 896 Processing helix chain 'UQ' and resid 519 through 524 removed outlier: 4.113A pdb=" N LYSUQ 523 " --> pdb=" O LEUUQ 520 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASPUQ 524 " --> pdb=" O SERUQ 521 " (cutoff:3.500A) Processing helix chain 'UR' and resid 16 through 28 Processing helix chain 'UR' and resid 30 through 40 Processing helix chain 'UR' and resid 127 through 133 Processing helix chain 'UR' and resid 140 through 148 removed outlier: 6.319A pdb=" N THRUR 148 " --> pdb=" O LYSUR 144 " (cutoff:3.500A) Processing helix chain 'UR' and resid 156 through 173 Proline residue: UR 173 - end of helix Processing helix chain 'UR' and resid 175 through 181 Processing helix chain 'UR' and resid 206 through 216 removed outlier: 5.697A pdb=" N TYRUR 216 " --> pdb=" O LEUUR 212 " (cutoff:3.500A) Processing helix chain 'UR' and resid 495 through 503 removed outlier: 4.789A pdb=" N THRUR 501 " --> pdb=" O ASNUR 497 " (cutoff:3.500A) Processing helix chain 'UR' and resid 240 through 245 removed outlier: 5.512A pdb=" N SERUR 244 " --> pdb=" O ALAUR 241 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HISUR 245 " --> pdb=" O ASNUR 242 " (cutoff:3.500A) Processing helix chain 'US' and resid 1 through 13 Processing helix chain 'US' and resid 22 through 44 Proline residue: US 37 - end of helix Processing helix chain 'US' and resid 53 through 74 Processing helix chain 'US' and resid 86 through 107 Processing helix chain 'US' and resid 113 through 134 removed outlier: 3.659A pdb=" N THRUS 132 " --> pdb=" O GLUUS 128 " (cutoff:3.500A) Processing helix chain 'US' and resid 144 through 159 removed outlier: 5.924A pdb=" N ASNUS 159 " --> pdb=" O LEUUS 155 " (cutoff:3.500A) Processing helix chain 'US' and resid 174 through 183 Processing helix chain 'US' and resid 184 through 189 removed outlier: 5.105A pdb=" N PHEUS 188 " --> pdb=" O TYRUS 184 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALAUS 189 " --> pdb=" O TYRUS 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'US' and resid 184 through 189' Processing helix chain 'US' and resid 190 through 206 Proline residue: US 206 - end of helix Processing helix chain 'US' and resid 207 through 216 removed outlier: 5.270A pdb=" N LEUUS 211 " --> pdb=" O ALAUS 207 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASNUS 215 " --> pdb=" O LEUUS 211 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VALUS 216 " --> pdb=" O LEUUS 212 " (cutoff:3.500A) Processing helix chain 'US' and resid 217 through 225 removed outlier: 6.739A pdb=" N HISUS 225 " --> pdb=" O ALAUS 221 " (cutoff:3.500A) Processing helix chain 'US' and resid 249 through 268 removed outlier: 5.084A pdb=" N GLNUS 268 " --> pdb=" O LEUUS 264 " (cutoff:3.500A) Processing helix chain 'US' and resid 270 through 284 Processing helix chain 'US' and resid 291 through 305 removed outlier: 4.651A pdb=" N ASPUS 297 " --> pdb=" O THRUS 293 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHEUS 298 " --> pdb=" O LYSUS 294 " (cutoff:3.500A) Processing helix chain 'US' and resid 309 through 331 removed outlier: 4.071A pdb=" N VALUS 314 " --> pdb=" O LYSUS 310 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VALUS 315 " --> pdb=" O ASNUS 311 " (cutoff:3.500A) Proline residue: US 316 - end of helix removed outlier: 4.074A pdb=" N ASNUS 331 " --> pdb=" O METUS 327 " (cutoff:3.500A) Processing helix chain 'US' and resid 336 through 346 removed outlier: 6.091A pdb=" N ASNUS 346 " --> pdb=" O TYRUS 342 " (cutoff:3.500A) Processing helix chain 'US' and resid 347 through 352 Processing helix chain 'US' and resid 354 through 367 removed outlier: 5.277A pdb=" N ARGUS 360 " --> pdb=" O ALAUS 356 " (cutoff:3.500A) Processing helix chain 'US' and resid 372 through 390 Processing helix chain 'US' and resid 392 through 410 Proline residue: US 400 - end of helix Proline residue: US 410 - end of helix Processing helix chain 'US' and resid 411 through 418 removed outlier: 5.604A pdb=" N METUS 415 " --> pdb=" O ASNUS 411 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEUUS 416 " --> pdb=" O CYSUS 412 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HISUS 417 " --> pdb=" O METUS 413 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASNUS 418 " --> pdb=" O ILEUS 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'US' and resid 411 through 418' Processing helix chain 'US' and resid 428 through 442 Processing helix chain 'US' and resid 452 through 457 removed outlier: 5.962A pdb=" N HISUS 457 " --> pdb=" O PROUS 453 " (cutoff:3.500A) Processing helix chain 'US' and resid 458 through 472 removed outlier: 6.385A pdb=" N SERUS 462 " --> pdb=" O ALAUS 458 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N LEUUS 463 " --> pdb=" O LEUUS 459 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N TRPUS 464 " --> pdb=" O ASPUS 460 " (cutoff:3.500A) removed outlier: 9.711A pdb=" N GLUUS 465 " --> pdb=" O SERUS 461 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEUUS 466 " --> pdb=" O SERUS 462 " (cutoff:3.500A) Processing helix chain 'US' and resid 474 through 487 removed outlier: 4.296A pdb=" N PHEUS 484 " --> pdb=" O LEUUS 480 " (cutoff:3.500A) Proline residue: US 487 - end of helix Processing helix chain 'US' and resid 494 through 500 removed outlier: 5.141A pdb=" N ASPUS 500 " --> pdb=" O GLUUS 496 " (cutoff:3.500A) Processing helix chain 'US' and resid 502 through 512 Processing helix chain 'UU' and resid 332 through 337 removed outlier: 5.674A pdb=" N VALUU 336 " --> pdb=" O SERUU 332 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VALUU 337 " --> pdb=" O GLYUU 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'UU' and resid 332 through 337' Processing helix chain 'UU' and resid 656 through 661 Processing helix chain 'UU' and resid 668 through 673 Processing helix chain 'UU' and resid 702 through 708 Processing helix chain 'UU' and resid 729 through 737 Processing helix chain 'UU' and resid 738 through 746 Proline residue: UU 746 - end of helix Processing helix chain 'UU' and resid 759 through 764 Processing helix chain 'UU' and resid 815 through 828 Processing helix chain 'UU' and resid 830 through 840 Processing helix chain 'UU' and resid 841 through 852 Processing helix chain 'UU' and resid 858 through 875 Processing helix chain 'UU' and resid 877 through 893 Processing helix chain 'UU' and resid 894 through 900 Processing helix chain 'UU' and resid 902 through 938 removed outlier: 3.565A pdb=" N ALAUU 906 " --> pdb=" O ASNUU 902 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ARGUU 921 " --> pdb=" O LYSUU 917 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEUUU 922 " --> pdb=" O LYSUU 918 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASPUU 923 " --> pdb=" O GLUUU 919 " (cutoff:3.500A) Processing helix chain 'UV' and resid 81 through 97 Processing helix chain 'UV' and resid 98 through 115 Processing helix chain 'UV' and resid 117 through 139 Proline residue: UV 139 - end of helix Processing helix chain 'UV' and resid 145 through 157 removed outlier: 5.289A pdb=" N ILEUV 157 " --> pdb=" O PHEUV 153 " (cutoff:3.500A) Processing helix chain 'UV' and resid 168 through 173 removed outlier: 4.735A pdb=" N ASNUV 173 " --> pdb=" O PROUV 169 " (cutoff:3.500A) Processing helix chain 'UV' and resid 187 through 192 Processing helix chain 'UV' and resid 210 through 215 removed outlier: 4.888A pdb=" N GLUUV 215 " --> pdb=" O LYSUV 211 " (cutoff:3.500A) Processing helix chain 'UV' and resid 222 through 247 Processing helix chain 'UV' and resid 304 through 309 Processing helix chain 'UV' and resid 329 through 342 Processing helix chain 'UV' and resid 343 through 357 removed outlier: 5.039A pdb=" N GLUUV 357 " --> pdb=" O LYSUV 353 " (cutoff:3.500A) Processing helix chain 'UV' and resid 358 through 374 Processing helix chain 'UV' and resid 389 through 403 Processing helix chain 'UV' and resid 417 through 432 Processing helix chain 'UV' and resid 481 through 501 Processing helix chain 'UV' and resid 506 through 511 Processing helix chain 'UV' and resid 518 through 523 Processing helix chain 'UV' and resid 535 through 543 removed outlier: 4.913A pdb=" N GLUUV 540 " --> pdb=" O TYRUV 536 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N THRUV 541 " --> pdb=" O ASNUV 537 " (cutoff:3.500A) Processing helix chain 'UV' and resid 548 through 556 Processing helix chain 'UV' and resid 557 through 575 Processing helix chain 'UV' and resid 639 through 650 Processing helix chain 'UV' and resid 676 through 689 Processing helix chain 'UV' and resid 698 through 709 Proline residue: UV 709 - end of helix Processing helix chain 'UV' and resid 724 through 744 Processing helix chain 'UV' and resid 757 through 762 Processing helix chain 'UV' and resid 795 through 818 Processing helix chain 'UV' and resid 857 through 870 removed outlier: 4.447A pdb=" N ILEUV 861 " --> pdb=" O GLUUV 857 " (cutoff:3.500A) Processing helix chain 'UV' and resid 871 through 890 Proline residue: UV 876 - end of helix removed outlier: 3.961A pdb=" N LEUUV 890 " --> pdb=" O THRUV 886 " (cutoff:3.500A) Processing helix chain 'UV' and resid 891 through 907 Processing helix chain 'UV' and resid 908 through 924 removed outlier: 4.319A pdb=" N VALUV 912 " --> pdb=" O PHEUV 908 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYSUV 917 " --> pdb=" O VALUV 913 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THRUV 922 " --> pdb=" O ARGUV 918 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HISUV 923 " --> pdb=" O TRPUV 919 " (cutoff:3.500A) Processing helix chain 'UV' and resid 925 through 930 removed outlier: 4.823A pdb=" N ILEUV 929 " --> pdb=" O LEUUV 925 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N THRUV 930 " --> pdb=" O LEUUV 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'UV' and resid 925 through 930' Processing helix chain 'UV' and resid 931 through 945 Proline residue: UV 941 - end of helix Proline residue: UV 945 - end of helix Processing helix chain 'UV' and resid 953 through 968 Processing helix chain 'UV' and resid 1013 through 1031 Processing helix chain 'UV' and resid 1057 through 1078 Processing helix chain 'UV' and resid 1081 through 1090 Processing helix chain 'UV' and resid 1108 through 1113 Processing helix chain 'UV' and resid 1135 through 1144 removed outlier: 4.995A pdb=" N ASPUV1144 " --> pdb=" O SERUV1140 " (cutoff:3.500A) Processing helix chain 'UV' and resid 1145 through 1158 Processing helix chain 'UV' and resid 1168 through 1173 Processing helix chain 'UV' and resid 1187 through 1193 removed outlier: 5.275A pdb=" N ALAUV1193 " --> pdb=" O LEUUV1189 " (cutoff:3.500A) Processing helix chain 'UV' and resid 1215 through 1228 Processing helix chain 'UV' and resid 775 through 780 removed outlier: 4.695A pdb=" N PHEUV 779 " --> pdb=" O PROUV 776 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLNUV 780 " --> pdb=" O ASPUV 777 " (cutoff:3.500A) Processing helix chain 'UX' and resid 25 through 30 removed outlier: 4.586A pdb=" N GLUUX 30 " --> pdb=" O LYSUX 26 " (cutoff:3.500A) Processing helix chain 'UX' and resid 68 through 79 Processing helix chain 'UX' and resid 82 through 91 Processing helix chain 'UX' and resid 99 through 110 Processing helix chain 'UX' and resid 113 through 122 removed outlier: 4.789A pdb=" N ASPUX 122 " --> pdb=" O LYSUX 118 " (cutoff:3.500A) Processing helix chain 'UX' and resid 136 through 149 Processing helix chain 'UX' and resid 157 through 168 Proline residue: UX 168 - end of helix Processing helix chain 'UZ' and resid 11 through 27 Processing helix chain 'UZ' and resid 28 through 34 removed outlier: 3.949A pdb=" N ASNUZ 32 " --> pdb=" O PROUZ 28 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASPUZ 33 " --> pdb=" O SERUZ 29 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LYSUZ 34 " --> pdb=" O LEUUZ 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'UZ' and resid 28 through 34' Processing helix chain 'UZ' and resid 66 through 71 removed outlier: 5.586A pdb=" N ASNUZ 71 " --> pdb=" O PROUZ 67 " (cutoff:3.500A) Processing helix chain 'UZ' and resid 80 through 90 Processing helix chain 'UZ' and resid 102 through 110 Processing helix chain 'UZ' and resid 111 through 122 removed outlier: 4.202A pdb=" N LEUUZ 115 " --> pdb=" O LYSUZ 111 " (cutoff:3.500A) Processing helix chain 'UZ' and resid 128 through 140 removed outlier: 4.498A pdb=" N HISUZ 133 " --> pdb=" O TYRUZ 129 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEUUZ 134 " --> pdb=" O ARGUZ 130 " (cutoff:3.500A) Proline residue: UZ 136 - end of helix Processing helix chain 'UZ' and resid 172 through 186 Processing helix chain 'UZ' and resid 208 through 225 Processing helix chain 'CA' and resid 149 through 158 removed outlier: 4.158A pdb=" N ALACA 153 " --> pdb=" O SERCA 149 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLYCA 154 " --> pdb=" O LYSCA 150 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILECA 155 " --> pdb=" O LEUCA 151 " (cutoff:3.500A) Processing helix chain 'CA' and resid 179 through 189 removed outlier: 5.681A pdb=" N HISCA 183 " --> pdb=" O THRCA 179 " (cutoff:3.500A) Processing helix chain 'CA' and resid 200 through 215 Proline residue: CA 215 - end of helix Processing helix chain 'CA' and resid 226 through 231 Processing helix chain 'CA' and resid 248 through 260 Processing helix chain 'CA' and resid 272 through 277 Processing helix chain 'CA' and resid 281 through 297 Processing helix chain 'CB' and resid 145 through 150 removed outlier: 5.029A pdb=" N LYSCB 150 " --> pdb=" O PROCB 146 " (cutoff:3.500A) Processing helix chain 'CB' and resid 151 through 158 Processing helix chain 'CB' and resid 178 through 189 Processing helix chain 'CB' and resid 201 through 214 Processing helix chain 'CB' and resid 227 through 234 removed outlier: 5.270A pdb=" N LEUCB 233 " --> pdb=" O LYSCB 229 " (cutoff:3.500A) Processing helix chain 'CB' and resid 248 through 260 Processing helix chain 'CB' and resid 272 through 277 Processing helix chain 'CB' and resid 281 through 297 Processing helix chain 'CD' and resid 25 through 30 removed outlier: 4.433A pdb=" N SERCD 29 " --> pdb=" O ASPCD 25 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ARGCD 30 " --> pdb=" O ASPCD 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'CD' and resid 25 through 30' Processing helix chain 'CD' and resid 31 through 41 removed outlier: 5.517A pdb=" N PHECD 41 " --> pdb=" O GLNCD 37 " (cutoff:3.500A) Processing helix chain 'CD' and resid 42 through 49 removed outlier: 4.761A pdb=" N LYSCD 46 " --> pdb=" O GLYCD 42 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLUCD 49 " --> pdb=" O THRCD 45 " (cutoff:3.500A) Processing helix chain 'CD' and resid 58 through 72 Processing helix chain 'CD' and resid 75 through 86 Processing helix chain 'CD' and resid 102 through 114 Proline residue: CD 107 - end of helix Proline residue: CD 114 - end of helix Processing helix chain 'CD' and resid 121 through 135 Processing helix chain 'CD' and resid 146 through 164 Processing helix chain 'CD' and resid 166 through 199 removed outlier: 5.536A pdb=" N ASNCD 170 " --> pdb=" O SERCD 166 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASPCD 171 " --> pdb=" O VALCD 167 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASNCD 172 " --> pdb=" O GLNCD 168 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N HISCD 173 " --> pdb=" O LYSCD 169 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILECD 174 " --> pdb=" O ASNCD 170 " (cutoff:3.500A) Processing helix chain 'CD' and resid 203 through 210 Processing helix chain 'CD' and resid 212 through 224 removed outlier: 5.212A pdb=" N LYSCD 224 " --> pdb=" O VALCD 220 " (cutoff:3.500A) Processing helix chain 'CD' and resid 230 through 241 Processing helix chain 'CD' and resid 246 through 258 Processing helix chain 'CD' and resid 264 through 300 Processing helix chain 'CD' and resid 301 through 307 Processing helix chain 'CD' and resid 308 through 320 Processing helix chain 'CD' and resid 321 through 329 removed outlier: 5.695A pdb=" N ALACD 329 " --> pdb=" O LEUCD 325 " (cutoff:3.500A) Processing helix chain 'CD' and resid 370 through 393 Processing helix chain 'CD' and resid 397 through 415 Processing helix chain 'CE' and resid 21 through 32 Processing helix chain 'CE' and resid 35 through 43 Processing helix chain 'CE' and resid 53 through 67 Processing helix chain 'CE' and resid 69 through 79 removed outlier: 4.994A pdb=" N GLUCE 78 " --> pdb=" O LYSCE 74 " (cutoff:3.500A) Processing helix chain 'CE' and resid 91 through 101 Processing helix chain 'CE' and resid 113 through 128 Proline residue: CE 125 - end of helix removed outlier: 3.744A pdb=" N LEUCE 128 " --> pdb=" O LEUCE 124 " (cutoff:3.500A) Processing helix chain 'CE' and resid 135 through 153 removed outlier: 4.197A pdb=" N METCE 139 " --> pdb=" O ASPCE 135 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LYSCE 153 " --> pdb=" O ARGCE 149 " (cutoff:3.500A) Processing helix chain 'CE' and resid 159 through 192 Processing helix chain 'CE' and resid 193 through 199 Processing helix chain 'CE' and resid 201 through 212 Processing helix chain 'CE' and resid 214 through 221 Processing helix chain 'CE' and resid 228 through 242 Processing helix chain 'CE' and resid 248 through 284 Processing helix chain 'CE' and resid 285 through 291 Processing helix chain 'CE' and resid 292 through 304 Processing helix chain 'CE' and resid 305 through 313 Proline residue: CE 313 - end of helix Processing helix chain 'CE' and resid 314 through 320 Processing helix chain 'CE' and resid 322 through 333 Processing helix chain 'CE' and resid 345 through 352 removed outlier: 4.875A pdb=" N THRCE 352 " --> pdb=" O VALCE 348 " (cutoff:3.500A) Processing helix chain 'CE' and resid 353 through 375 Processing helix chain 'CE' and resid 384 through 404 Processing helix chain 'CE' and resid 428 through 434 removed outlier: 6.230A pdb=" N ALACE 434 " --> pdb=" O ASPCE 430 " (cutoff:3.500A) Processing helix chain 'CF' and resid 13 through 31 Processing helix chain 'CF' and resid 36 through 47 Processing helix chain 'CF' and resid 61 through 75 removed outlier: 5.628A pdb=" N LEUCF 67 " --> pdb=" O ILECF 63 " (cutoff:3.500A) Proline residue: CF 68 - end of helix Processing helix chain 'CF' and resid 83 through 92 Processing helix chain 'CF' and resid 110 through 126 Processing helix chain 'CG' and resid 13 through 31 Processing helix chain 'CG' and resid 36 through 47 Processing helix chain 'CG' and resid 61 through 75 removed outlier: 5.141A pdb=" N LEUCG 67 " --> pdb=" O ILECG 63 " (cutoff:3.500A) Proline residue: CG 68 - end of helix Processing helix chain 'CG' and resid 83 through 92 Processing helix chain 'CG' and resid 110 through 125 Processing helix chain 'CH' and resid 115 through 127 Processing helix chain 'CH' and resid 136 through 141 removed outlier: 3.963A pdb=" N LEUCH 140 " --> pdb=" O PHECH 136 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEUCH 141 " --> pdb=" O GLYCH 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 136 through 141' Processing helix chain 'CH' and resid 226 through 231 removed outlier: 6.976A pdb=" N ASNCH 230 " --> pdb=" O HISCH 226 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THRCH 231 " --> pdb=" O GLUCH 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 226 through 231' Processing helix chain 'CH' and resid 364 through 375 removed outlier: 3.832A pdb=" N GLUCH 375 " --> pdb=" O ARGCH 371 " (cutoff:3.500A) Processing helix chain 'CH' and resid 447 through 452 Processing helix chain 'CH' and resid 456 through 465 Processing helix chain 'CI' and resid 6 through 14 Processing helix chain 'CI' and resid 27 through 37 Processing helix chain 'CI' and resid 40 through 65 Proline residue: CI 65 - end of helix Processing helix chain 'CI' and resid 68 through 86 Processing helix chain 'CI' and resid 93 through 100 Processing helix chain 'CI' and resid 102 through 111 removed outlier: 5.619A pdb=" N LEUCI 111 " --> pdb=" O CYSCI 107 " (cutoff:3.500A) Processing helix chain 'CI' and resid 112 through 119 Processing helix chain 'CI' and resid 123 through 134 Processing helix chain 'CI' and resid 151 through 158 removed outlier: 4.731A pdb=" N TYRCI 157 " --> pdb=" O ASNCI 153 " (cutoff:3.500A) Processing helix chain 'CI' and resid 164 through 175 Processing helix chain 'CJ' and resid 2 through 26 removed outlier: 4.671A pdb=" N GLNCJ 24 " --> pdb=" O LEUCJ 20 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEUCJ 25 " --> pdb=" O GLNCJ 21 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 44 through 49 Processing helix chain 'CJ' and resid 50 through 56 Processing helix chain 'CJ' and resid 57 through 63 removed outlier: 4.847A pdb=" N LYSCJ 63 " --> pdb=" O ASPCJ 59 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 97 through 112 Proline residue: CJ 112 - end of helix Processing helix chain 'CJ' and resid 123 through 135 Processing helix chain 'CJ' and resid 172 through 177 Processing helix chain 'CJ' and resid 196 through 211 removed outlier: 5.056A pdb=" N ASNCJ 211 " --> pdb=" O LYSCJ 207 " (cutoff:3.500A) Processing helix chain 'CK' and resid 298 through 320 Processing helix chain 'CK' and resid 323 through 328 removed outlier: 4.948A pdb=" N GLYCK 328 " --> pdb=" O TRPCK 324 " (cutoff:3.500A) Processing helix chain 'CK' and resid 331 through 336 Proline residue: CK 336 - end of helix Processing helix chain 'CK' and resid 338 through 344 removed outlier: 4.874A pdb=" N GLUCK 344 " --> pdb=" O LEUCK 340 " (cutoff:3.500A) Processing helix chain 'CK' and resid 358 through 376 Processing helix chain 'CK' and resid 427 through 453 Processing helix chain 'CK' and resid 472 through 478 removed outlier: 5.014A pdb=" N ASPCK 478 " --> pdb=" O ILECK 474 " (cutoff:3.500A) Processing helix chain 'CK' and resid 491 through 496 Processing helix chain 'CK' and resid 516 through 521 removed outlier: 4.001A pdb=" N LEUCK 520 " --> pdb=" O SERCK 516 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THRCK 521 " --> pdb=" O LYSCK 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'CK' and resid 516 through 521' Processing helix chain 'CK' and resid 522 through 539 Processing helix chain 'CL' and resid 36 through 55 removed outlier: 5.482A pdb=" N HISCL 55 " --> pdb=" O GLUCL 51 " (cutoff:3.500A) Processing helix chain 'CL' and resid 81 through 94 Processing helix chain 'CL' and resid 124 through 135 Processing helix chain 'CL' and resid 149 through 163 Processing helix chain 'CL' and resid 173 through 178 removed outlier: 4.965A pdb=" N PHECL 177 " --> pdb=" O HISCL 173 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LYSCL 178 " --> pdb=" O LEUCL 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'CL' and resid 173 through 178' Processing helix chain 'CL' and resid 179 through 199 removed outlier: 4.710A pdb=" N TYRCL 199 " --> pdb=" O TRPCL 195 " (cutoff:3.500A) Processing helix chain 'CL' and resid 216 through 230 Processing helix chain 'CL' and resid 235 through 241 Processing helix chain 'CL' and resid 254 through 262 Processing helix chain 'CL' and resid 310 through 322 Processing helix chain 'CL' and resid 548 through 555 Processing helix chain 'CL' and resid 559 through 568 Processing helix chain 'CL' and resid 617 through 626 Processing helix chain 'CL' and resid 628 through 636 removed outlier: 4.767A pdb=" N ARGCL 634 " --> pdb=" O ALACL 630 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEUCL 636 " --> pdb=" O LYSCL 632 " (cutoff:3.500A) Processing helix chain 'CL' and resid 749 through 773 removed outlier: 5.337A pdb=" N METCL 772 " --> pdb=" O GLUCL 768 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THRCL 773 " --> pdb=" O TYRCL 769 " (cutoff:3.500A) Processing helix chain 'CL' and resid 774 through 779 removed outlier: 4.411A pdb=" N GLNCL 778 " --> pdb=" O PROCL 774 " (cutoff:3.500A) Processing helix chain 'CL' and resid 797 through 803 Processing helix chain 'CL' and resid 816 through 821 Processing helix chain 'CL' and resid 903 through 908 removed outlier: 4.741A pdb=" N GLYCL 908 " --> pdb=" O ASNCL 904 " (cutoff:3.500A) Processing helix chain 'CL' and resid 954 through 962 Processing helix chain 'CL' and resid 1019 through 1024 removed outlier: 5.279A pdb=" N LYSCL1024 " --> pdb=" O SERCL1020 " (cutoff:3.500A) Processing helix chain 'CL' and resid 1034 through 1043 Processing helix chain 'CL' and resid 1049 through 1054 removed outlier: 6.024A pdb=" N TYRCL1054 " --> pdb=" O PROCL1050 " (cutoff:3.500A) Processing helix chain 'CL' and resid 1070 through 1077 Processing helix chain 'CL' and resid 1093 through 1099 Processing helix chain 'CL' and resid 1104 through 1161 Processing helix chain 'CM' and resid 16 through 28 Processing helix chain 'CM' and resid 46 through 60 Processing helix chain 'CM' and resid 95 through 107 Proline residue: CM 102 - end of helix Processing helix chain 'CM' and resid 129 through 145 removed outlier: 4.339A pdb=" N METCM 138 " --> pdb=" O LYSCM 134 " (cutoff:3.500A) Proline residue: CM 139 - end of helix Processing helix chain 'CM' and resid 201 through 217 Processing helix chain 'CM' and resid 267 through 286 Processing helix chain 'CM' and resid 290 through 305 Proline residue: CM 295 - end of helix removed outlier: 5.690A pdb=" N LYSCM 305 " --> pdb=" O METCM 301 " (cutoff:3.500A) Processing helix chain 'CM' and resid 314 through 319 removed outlier: 5.062A pdb=" N ASPCM 319 " --> pdb=" O LYSCM 315 " (cutoff:3.500A) Processing helix chain 'CM' and resid 320 through 333 Processing helix chain 'CN' and resid 63 through 79 Processing helix chain 'CN' and resid 99 through 105 Processing helix chain 'CN' and resid 130 through 151 Processing helix chain 'CN' and resid 164 through 173 Processing helix chain 'CN' and resid 176 through 204 Processing helix chain 'CN' and resid 222 through 233 Processing helix chain 'CN' and resid 258 through 270 Processing helix chain 'JF' and resid 73 through 81 removed outlier: 4.539A pdb=" N LEUJF 77 " --> pdb=" O HISJF 73 " (cutoff:3.500A) Processing helix chain 'JF' and resid 88 through 102 removed outlier: 4.191A pdb=" N THRJF 92 " --> pdb=" O ARGJF 88 " (cutoff:3.500A) Processing helix chain 'JF' and resid 103 through 108 Processing helix chain 'JF' and resid 133 through 148 Processing helix chain 'JF' and resid 167 through 172 Proline residue: JF 172 - end of helix Processing helix chain 'JF' and resid 188 through 197 removed outlier: 5.222A pdb=" N ASPJF 197 " --> pdb=" O ILEJF 193 " (cutoff:3.500A) Processing helix chain 'JF' and resid 233 through 250 Processing helix chain 'JF' and resid 213 through 220 removed outlier: 4.054A pdb=" N PHEJF 216 " --> pdb=" O LYSJF 213 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALAJF 217 " --> pdb=" O ASPJF 214 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASPJF 218 " --> pdb=" O ASNJF 215 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLUJF 219 " --> pdb=" O PHEJF 216 " (cutoff:3.500A) Processing helix chain 'JG' and resid 73 through 81 removed outlier: 4.159A pdb=" N LEUJG 77 " --> pdb=" O HISJG 73 " (cutoff:3.500A) Processing helix chain 'JG' and resid 83 through 102 removed outlier: 5.336A pdb=" N ARGJG 88 " --> pdb=" O ILEJG 84 " (cutoff:3.500A) Proline residue: JG 89 - end of helix removed outlier: 5.030A pdb=" N THRJG 92 " --> pdb=" O ARGJG 88 " (cutoff:3.500A) Processing helix chain 'JG' and resid 103 through 108 Processing helix chain 'JG' and resid 133 through 147 Processing helix chain 'JG' and resid 166 through 172 Proline residue: JG 172 - end of helix Processing helix chain 'JG' and resid 188 through 197 removed outlier: 5.744A pdb=" N ASPJG 197 " --> pdb=" O ILEJG 193 " (cutoff:3.500A) Processing helix chain 'JG' and resid 233 through 250 Processing helix chain 'JH' and resid 207 through 225 removed outlier: 6.661A pdb=" N THRJH 225 " --> pdb=" O LEUJH 221 " (cutoff:3.500A) Processing helix chain 'JH' and resid 230 through 240 Proline residue: JH 237 - end of helix removed outlier: 4.831A pdb=" N ARGJH 240 " --> pdb=" O ILEJH 236 " (cutoff:3.500A) Processing helix chain 'JH' and resid 241 through 250 Processing helix chain 'JH' and resid 255 through 269 Processing helix chain 'JH' and resid 272 through 295 removed outlier: 4.937A pdb=" N GLUJH 295 " --> pdb=" O ILEJH 291 " (cutoff:3.500A) Processing helix chain 'JH' and resid 300 through 314 Proline residue: JH 314 - end of helix Processing helix chain 'JH' and resid 315 through 320 removed outlier: 4.208A pdb=" N LYSJH 319 " --> pdb=" O SERJH 315 " (cutoff:3.500A) Processing helix chain 'JH' and resid 321 through 329 Processing helix chain 'JH' and resid 331 through 345 Processing helix chain 'JH' and resid 348 through 363 Proline residue: JH 363 - end of helix Processing helix chain 'JH' and resid 365 through 379 Processing helix chain 'JH' and resid 383 through 399 removed outlier: 6.010A pdb=" N ILEJH 399 " --> pdb=" O METJH 395 " (cutoff:3.500A) Processing helix chain 'JH' and resid 406 through 411 Processing helix chain 'JH' and resid 414 through 427 Processing helix chain 'JH' and resid 428 through 433 removed outlier: 3.790A pdb=" N ILEJH 432 " --> pdb=" O TYRJH 428 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N THRJH 433 " --> pdb=" O LYSJH 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'JH' and resid 428 through 433' Processing helix chain 'JH' and resid 434 through 448 Processing helix chain 'JH' and resid 450 through 463 Proline residue: JH 454 - end of helix Processing helix chain 'JJ' and resid 104 through 113 Proline residue: JJ 108 - end of helix Processing helix chain 'JJ' and resid 114 through 122 Proline residue: JJ 118 - end of helix Processing helix chain 'JJ' and resid 150 through 165 Processing helix chain 'JJ' and resid 167 through 177 Processing helix chain 'JJ' and resid 186 through 191 Processing helix chain 'JJ' and resid 195 through 207 Processing helix chain 'JJ' and resid 210 through 220 Processing helix chain 'JJ' and resid 236 through 253 Processing helix chain 'JJ' and resid 255 through 272 Processing helix chain 'JM' and resid 50 through 62 Processing helix chain 'JM' and resid 67 through 75 removed outlier: 5.334A pdb=" N ALAJM 71 " --> pdb=" O THRJM 67 " (cutoff:3.500A) Processing helix chain 'JM' and resid 113 through 127 Processing helix chain 'JM' and resid 172 through 181 removed outlier: 5.038A pdb=" N GLUJM 181 " --> pdb=" O LEUJM 177 " (cutoff:3.500A) Processing helix chain 'JM' and resid 182 through 203 removed outlier: 4.578A pdb=" N LYSJM 203 " --> pdb=" O THRJM 199 " (cutoff:3.500A) Processing helix chain 'JM' and resid 204 through 216 removed outlier: 4.630A pdb=" N ARGJM 216 " --> pdb=" O METJM 212 " (cutoff:3.500A) Processing helix chain 'JN' and resid 101 through 107 removed outlier: 5.030A pdb=" N VALJN 107 " --> pdb=" O SERJN 103 " (cutoff:3.500A) Processing helix chain 'JN' and resid 111 through 119 Processing helix chain 'JN' and resid 152 through 170 removed outlier: 4.216A pdb=" N GLNJN 156 " --> pdb=" O ASPJN 152 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLNJN 157 " --> pdb=" O LEUJN 153 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N HISJN 163 " --> pdb=" O LEUJN 159 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEUJN 164 " --> pdb=" O ARGJN 160 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SERJN 166 " --> pdb=" O SERJN 162 " (cutoff:3.500A) Processing helix chain 'JN' and resid 204 through 223 removed outlier: 5.013A pdb=" N ASNJN 222 " --> pdb=" O LEUJN 218 " (cutoff:3.500A) Processing helix chain 'JN' and resid 224 through 230 Processing helix chain 'JN' and resid 235 through 261 Processing helix chain 'JN' and resid 275 through 282 Processing helix chain 'JN' and resid 291 through 301 removed outlier: 5.696A pdb=" N LYSJN 301 " --> pdb=" O GLUJN 297 " (cutoff:3.500A) Processing helix chain 'JN' and resid 322 through 330 Processing helix chain 'JO' and resid 47 through 57 removed outlier: 4.284A pdb=" N TYRJO 52 " --> pdb=" O TYRJO 48 " (cutoff:3.500A) Processing helix chain 'JO' and resid 58 through 68 Processing helix chain 'JO' and resid 90 through 107 Processing helix chain 'JO' and resid 109 through 119 removed outlier: 5.687A pdb=" N ASPJO 119 " --> pdb=" O LYSJO 115 " (cutoff:3.500A) Processing helix chain 'JO' and resid 134 through 147 Processing helix chain 'JO' and resid 150 through 161 Processing helix chain 'JO' and resid 176 through 193 Processing helix chain 'JO' and resid 195 through 213 Proline residue: JO 213 - end of helix Processing helix chain 'JO' and resid 220 through 225 Proline residue: JO 225 - end of helix Processing helix chain 'JP' and resid 9 through 14 Processing helix chain 'JP' and resid 29 through 34 Proline residue: JP 34 - end of helix Processing helix chain 'JP' and resid 35 through 55 Processing helix chain 'JP' and resid 387 through 405 Processing helix chain 'JP' and resid 407 through 416 Processing helix chain 'JP' and resid 420 through 448 Processing helix chain 'JP' and resid 455 through 460 removed outlier: 5.377A pdb=" N GLNJP 460 " --> pdb=" O GLUJP 456 " (cutoff:3.500A) Processing helix chain 'JQ' and resid 112 through 131 Processing helix chain 'JQ' and resid 133 through 148 removed outlier: 3.772A pdb=" N ASPJQ 137 " --> pdb=" O GLUJQ 133 " (cutoff:3.500A) Processing helix chain 'JQ' and resid 184 through 191 removed outlier: 4.942A pdb=" N THRJQ 188 " --> pdb=" O TYRJQ 184 " (cutoff:3.500A) Proline residue: JQ 189 - end of helix No H-bonds generated for 'chain 'JQ' and resid 184 through 191' Processing helix chain 'JQ' and resid 195 through 201 Processing helix chain 'DA' and resid 22 through 27 Processing helix chain 'DA' and resid 53 through 64 Processing helix chain 'DA' and resid 69 through 75 Processing helix chain 'DA' and resid 106 through 115 removed outlier: 6.183A pdb=" N ARGDA 115 " --> pdb=" O ARGDA 111 " (cutoff:3.500A) Processing helix chain 'DA' and resid 157 through 180 removed outlier: 5.049A pdb=" N THRDA 180 " --> pdb=" O VALDA 176 " (cutoff:3.500A) Processing helix chain 'DA' and resid 181 through 191 Proline residue: DA 190 - end of helix Processing helix chain 'DA' and resid 192 through 202 Processing helix chain 'DA' and resid 224 through 233 Processing helix chain 'DF' and resid 30 through 40 Processing helix chain 'DF' and resid 55 through 62 removed outlier: 4.288A pdb=" N VALDF 59 " --> pdb=" O ASPDF 55 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASPDF 60 " --> pdb=" O ALADF 56 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYRDF 61 " --> pdb=" O SERDF 57 " (cutoff:3.500A) Processing helix chain 'DF' and resid 82 through 88 Proline residue: DF 88 - end of helix Processing helix chain 'DF' and resid 89 through 100 removed outlier: 5.807A pdb=" N ASNDF 100 " --> pdb=" O SERDF 96 " (cutoff:3.500A) Processing helix chain 'DF' and resid 106 through 125 Processing helix chain 'DF' and resid 128 through 141 Processing helix chain 'DF' and resid 163 through 184 Processing helix chain 'DF' and resid 189 through 204 Processing helix chain 'DF' and resid 208 through 225 Processing helix chain 'DH' and resid 4 through 10 removed outlier: 4.634A pdb=" N SERDH 10 " --> pdb=" O ALADH 6 " (cutoff:3.500A) Processing helix chain 'DH' and resid 14 through 31 Processing helix chain 'DH' and resid 33 through 39 Processing helix chain 'DH' and resid 64 through 74 Processing helix chain 'DH' and resid 75 through 86 Processing helix chain 'DH' and resid 117 through 131 removed outlier: 4.557A pdb=" N VALDH 121 " --> pdb=" O THRDH 117 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HISDH 122 " --> pdb=" O LEUDH 118 " (cutoff:3.500A) Processing helix chain 'DH' and resid 165 through 177 Processing helix chain 'DJ' and resid 20 through 35 Processing helix chain 'DJ' and resid 38 through 63 removed outlier: 5.776A pdb=" N ASPDJ 63 " --> pdb=" O LEUDJ 59 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 66 through 84 Processing helix chain 'DJ' and resid 92 through 100 removed outlier: 5.902A pdb=" N LYSDJ 100 " --> pdb=" O VALDJ 96 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 101 through 108 Processing helix chain 'DJ' and resid 109 through 117 Processing helix chain 'DJ' and resid 121 through 132 Processing helix chain 'DJ' and resid 149 through 156 removed outlier: 5.066A pdb=" N HISDJ 155 " --> pdb=" O ASPDJ 151 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 170 through 186 Processing helix chain 'DN' and resid 29 through 44 Processing helix chain 'DN' and resid 46 through 57 Processing helix chain 'DN' and resid 62 through 68 Processing helix chain 'DN' and resid 70 through 79 Processing helix chain 'DN' and resid 85 through 106 Processing helix chain 'DN' and resid 108 through 133 Processing helix chain 'DN' and resid 142 through 151 Processing helix chain 'DO' and resid 43 through 48 Processing helix chain 'DO' and resid 56 through 75 Processing helix chain 'DO' and resid 95 through 109 Processing helix chain 'DQ' and resid 42 through 56 removed outlier: 5.807A pdb=" N PHEDQ 46 " --> pdb=" O GLUDQ 42 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYSDQ 47 " --> pdb=" O ILEDQ 43 " (cutoff:3.500A) Proline residue: DQ 51 - end of helix Processing helix chain 'DQ' and resid 57 through 64 removed outlier: 4.396A pdb=" N ILEDQ 63 " --> pdb=" O LYSDQ 59 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASPDQ 64 " --> pdb=" O PHEDQ 60 " (cutoff:3.500A) Processing helix chain 'DQ' and resid 73 through 96 Processing helix chain 'DQ' and resid 98 through 113 Processing helix chain 'DS' and resid 27 through 36 removed outlier: 5.652A pdb=" N LYSDS 36 " --> pdb=" O LEUDS 32 " (cutoff:3.500A) Processing helix chain 'DS' and resid 39 through 51 Processing helix chain 'DS' and resid 62 through 76 Proline residue: DS 76 - end of helix Processing helix chain 'DS' and resid 82 through 87 removed outlier: 4.432A pdb=" N LEUDS 86 " --> pdb=" O PRODS 82 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASNDS 87 " --> pdb=" O ALADS 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'DS' and resid 82 through 87' Processing helix chain 'DS' and resid 99 through 120 Processing helix chain 'DW' and resid 5 through 21 Processing helix chain 'DW' and resid 31 through 45 Processing helix chain 'DW' and resid 82 through 94 Processing helix chain 'DW' and resid 112 through 120 Processing helix chain 'DX' and resid 66 through 72 removed outlier: 5.772A pdb=" N VALDX 72 " --> pdb=" O ILEDX 68 " (cutoff:3.500A) Processing helix chain 'DX' and resid 89 through 97 removed outlier: 5.139A pdb=" N ASPDX 97 " --> pdb=" O LEUDX 93 " (cutoff:3.500A) Processing helix chain 'DX' and resid 131 through 138 Processing helix chain 'Db' and resid 11 through 18 Processing helix chain 'Db' and resid 19 through 24 removed outlier: 6.534A pdb=" N LEUDb 24 " --> pdb=" O LYSDb 20 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'UA' and resid 8 through 11 removed outlier: 5.288A pdb=" N ALAUA 692 " --> pdb=" O SERUA 687 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'UA' and resid 20 through 23 removed outlier: 6.340A pdb=" N GLNUA 28 " --> pdb=" O SERUA 23 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'UA' and resid 59 through 64 removed outlier: 5.948A pdb=" N LEUUA 69 " --> pdb=" O ASNUA 64 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARGUA 78 " --> pdb=" O ASPUA 74 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLYUA 77 " --> pdb=" O PHEUA 95 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'UA' and resid 101 through 105 removed outlier: 6.202A pdb=" N LEUUA 110 " --> pdb=" O SERUA 105 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARGUA 109 " --> pdb=" O THRUA 124 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'UA' and resid 151 through 155 removed outlier: 6.178A pdb=" N PHEUA 160 " --> pdb=" O SERUA 155 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ARGUA 159 " --> pdb=" O VALUA 175 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'UA' and resid 196 through 200 removed outlier: 6.039A pdb=" N LYSUA 205 " --> pdb=" O SERUA 200 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VALUA 217 " --> pdb=" O THRUA 251 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'UA' and resid 265 through 270 removed outlier: 8.255A pdb=" N GLYUA 282 " --> pdb=" O METUA 300 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'UA' and resid 307 through 311 removed outlier: 6.184A pdb=" N TRPUA 316 " --> pdb=" O ASNUA 311 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VALUA 329 " --> pdb=" O ILEUA 338 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'UA' and resid 350 through 354 removed outlier: 6.241A pdb=" N ARGUA 359 " --> pdb=" O SERUA 354 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N SERUA 358 " --> pdb=" O ILEUA 374 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'UA' and resid 392 through 396 removed outlier: 5.435A pdb=" N VALUA 401 " --> pdb=" O ALAUA 396 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLNUA 400 " --> pdb=" O LEUUA 416 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ARGUA 423 " --> pdb=" O ALAUA 413 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'UA' and resid 435 through 439 removed outlier: 5.569A pdb=" N VALUA 444 " --> pdb=" O ASPUA 439 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLUUA 443 " --> pdb=" O VALUA 460 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'UA' and resid 478 through 482 removed outlier: 5.511A pdb=" N LYSUA 495 " --> pdb=" O VALUA 514 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'UA' and resid 520 through 524 removed outlier: 5.610A pdb=" N GLUUA 529 " --> pdb=" O ARGUA 524 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLYUA 537 " --> pdb=" O CYSUA 555 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'UA' and resid 582 through 586 removed outlier: 5.235A pdb=" N ALAUA 591 " --> pdb=" O SERUA 586 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N METUA 590 " --> pdb=" O VALUA 606 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEUUA 603 " --> pdb=" O LEUUA 612 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VALUA 610 " --> pdb=" O ASPUA 605 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'UA' and resid 213 through 217 removed outlier: 6.375A pdb=" N GLYUA 213 " --> pdb=" O PHEUA 256 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'UA' and resid 325 through 329 removed outlier: 6.179A pdb=" N GLYUA 325 " --> pdb=" O GLYUA 343 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'UA' and resid 599 through 603 No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'UD' and resid 46 through 50 removed outlier: 4.598A pdb=" N ASNUD 75 " --> pdb=" O ARGUD 71 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILEUD 78 " --> pdb=" O GLUUD 88 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'UD' and resid 101 through 106 removed outlier: 5.186A pdb=" N LEUUD 114 " --> pdb=" O TRPUD 126 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'UD' and resid 145 through 150 removed outlier: 5.497A pdb=" N LYSUD 155 " --> pdb=" O ASNUD 150 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASPUD 154 " --> pdb=" O ILEUD 170 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VALUD 165 " --> pdb=" O LEUUD 183 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'UD' and resid 192 through 196 removed outlier: 6.648A pdb=" N PHEUD 200 " --> pdb=" O LYSUD 196 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'UD' and resid 208 through 213 removed outlier: 6.871A pdb=" N GLYUD 208 " --> pdb=" O VALUD 231 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'UD' and resid 243 through 248 Processing sheet with id= 24, first strand: chain 'UD' and resid 285 through 289 removed outlier: 6.197A pdb=" N TYRUD 294 " --> pdb=" O ASPUD 289 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASNUD 293 " --> pdb=" O GLNUD 309 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYSUD 303 " --> pdb=" O GLYUD 299 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLNUD 306 " --> pdb=" O SERUD 323 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'UD' and resid 335 through 341 removed outlier: 8.530A pdb=" N ASPUD 345 " --> pdb=" O LEUUD 361 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LYSUD 354 " --> pdb=" O THRUD 374 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N THRUD 374 " --> pdb=" O LYSUD 354 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'UD' and resid 382 through 386 removed outlier: 5.514A pdb=" N ARGUD 389 " --> pdb=" O METUD 404 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THRUD 398 " --> pdb=" O SERUD 395 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N SERUD 397 " --> pdb=" O THRUD 421 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THRUD 421 " --> pdb=" O SERUD 397 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VALUD 399 " --> pdb=" O LYSUD 419 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILEUD 401 " --> pdb=" O VALUD 417 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASNUD 413 " --> pdb=" O GLYUD 405 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'UD' and resid 431 through 434 removed outlier: 5.277A pdb=" N GLNUD 438 " --> pdb=" O LEUUD 453 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VALUD 450 " --> pdb=" O LEUUD 465 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'UD' and resid 477 through 481 removed outlier: 3.695A pdb=" N LEUUD 477 " --> pdb=" O CYSUD 489 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYSUD 479 " --> pdb=" O VALUD 487 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYSUD 485 " --> pdb=" O ILEUD 481 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N SERUD 484 " --> pdb=" O LEUUD 500 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'UD' and resid 532 through 536 removed outlier: 5.973A pdb=" N GLYUD 548 " --> pdb=" O ARGUD 565 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VALUD 550 " --> pdb=" O LEUUD 563 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'UD' and resid 571 through 576 removed outlier: 6.664A pdb=" N LYSUD 580 " --> pdb=" O METUD 596 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'UD' and resid 635 through 639 removed outlier: 5.355A pdb=" N ARGUD 645 " --> pdb=" O ASPUD 639 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N SERUD 644 " --> pdb=" O PHEUD 659 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'UD' and resid 74 through 78 removed outlier: 6.232A pdb=" N GLYUD 74 " --> pdb=" O GLYUD 93 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'UD' and resid 303 through 306 Processing sheet with id= 34, first strand: chain 'UE' and resid 6 through 11 removed outlier: 5.417A pdb=" N TYRUE 16 " --> pdb=" O ASPUE 11 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLNUE 15 " --> pdb=" O THRUE 34 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLNUE 27 " --> pdb=" O LEUUE 53 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'UE' and resid 62 through 67 removed outlier: 8.019A pdb=" N VALUE 74 " --> pdb=" O VALUE 90 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VALUE 90 " --> pdb=" O VALUE 74 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEUUE 87 " --> pdb=" O THRUE 96 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLUUE 94 " --> pdb=" O SERUE 89 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'UE' and resid 108 through 113 removed outlier: 8.436A pdb=" N ASNUE 115 " --> pdb=" O ASPUE 130 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASPUE 130 " --> pdb=" O ASNUE 115 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEUUE 117 " --> pdb=" O GLNUE 128 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLNUE 128 " --> pdb=" O LEUUE 117 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYSUE 119 " --> pdb=" O PHEUE 126 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHEUE 126 " --> pdb=" O CYSUE 119 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASPUE 121 " --> pdb=" O ASPUE 124 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLNUE 128 " --> pdb=" O LEUUE 137 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'UE' and resid 150 through 153 removed outlier: 6.594A pdb=" N LEUUE 163 " --> pdb=" O LEUUE 172 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEUUE 172 " --> pdb=" O LEUUE 163 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VALUE 165 " --> pdb=" O ILEUE 170 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILEUE 170 " --> pdb=" O VALUE 165 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N SERUE 167 " --> pdb=" O HISUE 168 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'UE' and resid 193 through 197 removed outlier: 6.704A pdb=" N PHEUE 201 " --> pdb=" O ILEUE 197 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N GLUUE 200 " --> pdb=" O ILEUE 217 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ARGUE 210 " --> pdb=" O ALAUE 228 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYSUE 271 " --> pdb=" O LYSUE 223 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'UE' and resid 234 through 238 removed outlier: 6.219A pdb=" N SERUE 243 " --> pdb=" O SERUE 238 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILEUE 244 " --> pdb=" O ILEUE 255 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILEUE 255 " --> pdb=" O ILEUE 244 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VALUE 246 " --> pdb=" O LEUUE 253 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEUUE 253 " --> pdb=" O VALUE 246 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THRUE 248 " --> pdb=" O GLYUE 251 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N GLYUE 251 " --> pdb=" O ILEUE 281 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILEUE 281 " --> pdb=" O GLYUE 251 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASNUE 324 " --> pdb=" O SERUE 276 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILEUE 330 " --> pdb=" O VALUE 282 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'UE' and resid 301 through 306 Processing sheet with id= 41, first strand: chain 'UE' and resid 84 through 87 Processing sheet with id= 42, first strand: chain 'UE' and resid 125 through 128 Processing sheet with id= 43, first strand: chain 'UG' and resid 105 through 108 removed outlier: 4.312A pdb=" N ILEUG 398 " --> pdb=" O LEUUG 106 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N THRUG 396 " --> pdb=" O LEUUG 108 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLYUG 397 " --> pdb=" O HISUG 394 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HISUG 394 " --> pdb=" O GLYUG 397 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASPUG 388 " --> pdb=" O VALUG 403 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEUUG 389 " --> pdb=" O VALUG 384 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'UG' and resid 115 through 119 removed outlier: 5.609A pdb=" N HISUG 124 " --> pdb=" O ALAUG 119 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'UG' and resid 156 through 160 removed outlier: 5.269A pdb=" N SERUG 156 " --> pdb=" O ALAUG 169 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N TYRUG 165 " --> pdb=" O LEUUG 160 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THRUG 174 " --> pdb=" O LEUUG 187 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'UG' and resid 194 through 200 removed outlier: 8.363A pdb=" N TYRUG 203 " --> pdb=" O VALUG 219 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TRPUG 213 " --> pdb=" O GLYUG 209 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYRUG 216 " --> pdb=" O VALUG 225 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'UG' and resid 236 through 242 removed outlier: 5.261A pdb=" N THRUG 255 " --> pdb=" O HISUG 251 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'UG' and resid 279 through 283 removed outlier: 5.269A pdb=" N TYRUG 288 " --> pdb=" O ASPUG 283 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'UG' and resid 321 through 324 Processing sheet with id= 50, first strand: chain 'UG' and resid 212 through 216 removed outlier: 5.392A pdb=" N GLYUG 212 " --> pdb=" O THRUG 230 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'UH' and resid 27 through 31 removed outlier: 5.960A pdb=" N LEUUH 342 " --> pdb=" O ASNUH 337 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'UH' and resid 56 through 61 removed outlier: 4.932A pdb=" N TYRUH 66 " --> pdb=" O GLYUH 82 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALAUH 76 " --> pdb=" O ASNUH 72 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLNUH 83 " --> pdb=" O ALAUH 85 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'UH' and resid 141 through 144 removed outlier: 3.546A pdb=" N ASNUH 144 " --> pdb=" O LYSUH 155 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYSUH 155 " --> pdb=" O ASNUH 144 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'UH' and resid 167 through 170 Processing sheet with id= 55, first strand: chain 'UH' and resid 209 through 213 removed outlier: 6.340A pdb=" N TYRUH 218 " --> pdb=" O TYRUH 213 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLYUH 226 " --> pdb=" O TYRUH 243 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYRUH 243 " --> pdb=" O GLYUH 226 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLUUH 228 " --> pdb=" O VALUH 241 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VALUH 241 " --> pdb=" O GLUUH 228 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VALUH 230 " --> pdb=" O ASPUH 239 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'UH' and resid 249 through 255 removed outlier: 4.522A pdb=" N GLUUH 268 " --> pdb=" O SERUH 264 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'UH' and resid 293 through 296 removed outlier: 6.510A pdb=" N GLNUH 301 " --> pdb=" O SERUH 296 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N CYSUH 300 " --> pdb=" O PROUH 316 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYSUH 313 " --> pdb=" O SERUH 322 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'UH' and resid 309 through 313 Processing sheet with id= 59, first strand: chain 'UK' and resid 229 through 235 removed outlier: 5.824A pdb=" N SERUK 229 " --> pdb=" O LYSUK 245 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'UL' and resid 7 through 11 removed outlier: 7.111A pdb=" N ILEUL 683 " --> pdb=" O ALAUL 11 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'UL' and resid 40 through 44 Processing sheet with id= 62, first strand: chain 'UL' and resid 83 through 89 Processing sheet with id= 63, first strand: chain 'UL' and resid 126 through 130 removed outlier: 8.740A pdb=" N THRUL 134 " --> pdb=" O LEUUL 150 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'UL' and resid 168 through 172 removed outlier: 7.477A pdb=" N ASPUL 175 " --> pdb=" O LEUUL 191 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEUUL 188 " --> pdb=" O ILEUL 197 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'UL' and resid 209 through 212 removed outlier: 5.423A pdb=" N GLNUL 225 " --> pdb=" O GLYUL 221 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N SERUL 224 " --> pdb=" O LYSUL 250 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'UL' and resid 258 through 263 removed outlier: 5.798A pdb=" N THRUL 280 " --> pdb=" O ASNUL 276 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYSUL 279 " --> pdb=" O SERUL 334 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'UL' and resid 339 through 345 removed outlier: 4.381A pdb=" N SERUL 349 " --> pdb=" O TYRUL 369 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N THRUL 361 " --> pdb=" O THRUL 357 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'UL' and resid 396 through 400 removed outlier: 8.656A pdb=" N ASNUL 403 " --> pdb=" O ILEUL 419 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'UL' and resid 434 through 440 Processing sheet with id= 70, first strand: chain 'UL' and resid 478 through 482 removed outlier: 6.252A pdb=" N ARGUL 487 " --> pdb=" O THRUL 482 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYSUL 486 " --> pdb=" O PHEUL 502 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHEUL 499 " --> pdb=" O ASPUL 525 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'UL' and resid 536 through 540 removed outlier: 5.832A pdb=" N TYRUL 545 " --> pdb=" O SERUL 540 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ARGUL 544 " --> pdb=" O LEUUL 560 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'UL' and resid 578 through 582 removed outlier: 5.850A pdb=" N METUL 587 " --> pdb=" O SERUL 582 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LYSUL 586 " --> pdb=" O LEUUL 602 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LYSUL 595 " --> pdb=" O ALAUL 613 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'UL' and resid 638 through 642 Processing sheet with id= 74, first strand: chain 'UL' and resid 184 through 188 removed outlier: 8.620A pdb=" N GLYUL 184 " --> pdb=" O ALAUL 202 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'UL' and resid 495 through 499 removed outlier: 5.679A pdb=" N LYSUL 495 " --> pdb=" O LEUUL 530 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'UM' and resid 7 through 13 removed outlier: 5.939A pdb=" N ASPUM 630 " --> pdb=" O ASPUM 646 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'UM' and resid 30 through 35 Processing sheet with id= 78, first strand: chain 'UM' and resid 66 through 70 removed outlier: 5.574A pdb=" N TYRUM 75 " --> pdb=" O THRUM 70 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N GLNUM 74 " --> pdb=" O LEUUM 90 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'UM' and resid 107 through 111 removed outlier: 6.480A pdb=" N LEUUM 116 " --> pdb=" O ASPUM 111 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'UM' and resid 149 through 154 removed outlier: 3.858A pdb=" N SERUM 149 " --> pdb=" O GLYUM 166 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLYUM 166 " --> pdb=" O SERUM 149 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYSUM 151 " --> pdb=" O ALAUM 164 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N TRPUM 161 " --> pdb=" O LEUUM 177 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N METUM 171 " --> pdb=" O ASPUM 167 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VALUM 174 " --> pdb=" O LEUUM 183 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'UM' and resid 209 through 215 Processing sheet with id= 82, first strand: chain 'UM' and resid 245 through 250 removed outlier: 7.755A pdb=" N ARGUM 256 " --> pdb=" O SERUM 272 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SERUM 272 " --> pdb=" O ARGUM 256 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEUUM 269 " --> pdb=" O LEUUM 278 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'UM' and resid 292 through 296 removed outlier: 6.018A pdb=" N GLNUM 301 " --> pdb=" O ILEUM 296 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SERUM 300 " --> pdb=" O VALUM 316 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLNUM 309 " --> pdb=" O GLYUM 335 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'UM' and resid 342 through 347 removed outlier: 7.436A pdb=" N ASNUM 351 " --> pdb=" O VALUM 367 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'UM' and resid 393 through 397 removed outlier: 6.225A pdb=" N TRPUM 402 " --> pdb=" O THRUM 397 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEUUM 401 " --> pdb=" O TYRUM 417 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'UM' and resid 439 through 442 Processing sheet with id= 87, first strand: chain 'UM' and resid 505 through 509 removed outlier: 6.202A pdb=" N LYSUM 513 " --> pdb=" O ASNUM 531 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'UM' and resid 538 through 542 Processing sheet with id= 89, first strand: chain 'UM' and resid 580 through 584 removed outlier: 5.178A pdb=" N ARGUM 580 " --> pdb=" O CYSUM 593 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLNUM 589 " --> pdb=" O ILEUM 584 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'UM' and resid 411 through 414 Processing sheet with id= 91, first strand: chain 'UN' and resid 310 through 313 Processing sheet with id= 92, first strand: chain 'UO' and resid 33 through 38 removed outlier: 5.638A pdb=" N GLYUO 325 " --> pdb=" O GLUUO 38 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N HISUO 317 " --> pdb=" O SERUO 308 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'UO' and resid 44 through 48 removed outlier: 4.502A pdb=" N HISUO 44 " --> pdb=" O THRUO 58 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASPUO 54 " --> pdb=" O ASNUO 48 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N HISUO 53 " --> pdb=" O SERUO 68 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'UO' and resid 86 through 90 removed outlier: 5.919A pdb=" N LEUUO 95 " --> pdb=" O ARGUO 90 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEUUO 104 " --> pdb=" O ASPUO 100 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'UO' and resid 129 through 133 removed outlier: 7.013A pdb=" N ILEUO 139 " --> pdb=" O HISUO 133 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'UO' and resid 173 through 176 removed outlier: 8.299A pdb=" N HISUO 182 " --> pdb=" O THRUO 198 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'UO' and resid 217 through 221 removed outlier: 6.625A pdb=" N GLNUO 225 " --> pdb=" O VALUO 221 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N THRUO 224 " --> pdb=" O LEUUO 239 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VALUO 236 " --> pdb=" O LEUUO 245 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'UO' and resid 257 through 262 removed outlier: 5.103A pdb=" N HISUO 280 " --> pdb=" O SERUO 276 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'UO' and resid 233 through 236 Processing sheet with id=100, first strand: chain 'UQ' and resid 10 through 15 removed outlier: 6.382A pdb=" N LEUUQ 783 " --> pdb=" O VALUQ 15 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRPUQ 765 " --> pdb=" O LEUUQ 777 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'UQ' and resid 35 through 38 removed outlier: 6.279A pdb=" N ASNUQ 43 " --> pdb=" O SERUQ 38 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ARGUQ 42 " --> pdb=" O VALUQ 57 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VALUQ 54 " --> pdb=" O VALUQ 63 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'UQ' and resid 90 through 93 removed outlier: 5.251A pdb=" N GLYUQ 114 " --> pdb=" O ILEUQ 134 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'UQ' and resid 143 through 146 removed outlier: 6.738A pdb=" N LEUUQ 173 " --> pdb=" O GLNUQ 190 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLUUQ 186 " --> pdb=" O THRUQ 177 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'UQ' and resid 198 through 202 removed outlier: 5.328A pdb=" N LEUUQ 198 " --> pdb=" O METUQ 211 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEUUQ 207 " --> pdb=" O SERUQ 202 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N LYSUQ 206 " --> pdb=" O LEUUQ 230 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VALUQ 235 " --> pdb=" O SERUQ 229 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'UQ' and resid 261 through 265 removed outlier: 5.783A pdb=" N GLNUQ 270 " --> pdb=" O ASPUQ 265 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLNUQ 269 " --> pdb=" O LEUUQ 285 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'UQ' and resid 302 through 306 removed outlier: 5.718A pdb=" N TYRUQ 311 " --> pdb=" O SERUQ 306 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'UQ' and resid 339 through 342 removed outlier: 6.404A pdb=" N ILEUQ 340 " --> pdb=" O GLNUQ 359 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILEUQ 357 " --> pdb=" O ILEUQ 342 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYRUQ 353 " --> pdb=" O LEUUQ 347 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'UQ' and resid 379 through 382 removed outlier: 6.708A pdb=" N LEUUQ 373 " --> pdb=" O LYSUQ 382 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'UQ' and resid 448 through 453 removed outlier: 7.400A pdb=" N SERUQ 455 " --> pdb=" O LEUUQ 473 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEUUQ 473 " --> pdb=" O SERUQ 455 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'UQ' and resid 497 through 501 removed outlier: 5.488A pdb=" N TRPUQ 506 " --> pdb=" O THRUQ 501 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHEUQ 531 " --> pdb=" O LYSUQ 544 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'UQ' and resid 559 through 563 removed outlier: 5.534A pdb=" N GLYUQ 572 " --> pdb=" O SERUQ 563 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLNUQ 571 " --> pdb=" O PHEUQ 587 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASPUQ 577 " --> pdb=" O GLYUQ 581 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLYUQ 581 " --> pdb=" O ASPUQ 577 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'UQ' and resid 611 through 616 removed outlier: 5.667A pdb=" N LEUUQ 621 " --> pdb=" O SERUQ 616 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SERUQ 620 " --> pdb=" O PHEUQ 635 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHEUQ 626 " --> pdb=" O LYSUQ 629 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYSUQ 629 " --> pdb=" O PHEUQ 626 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASPUQ 628 " --> pdb=" O LEUUQ 655 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N SERUQ 651 " --> pdb=" O ILEUQ 632 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'UQ' and resid 661 through 665 removed outlier: 6.733A pdb=" N ASNUQ 669 " --> pdb=" O ILEUQ 665 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THRUQ 668 " --> pdb=" O LEUUQ 683 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THRUQ 677 " --> pdb=" O THRUQ 674 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'UQ' and resid 718 through 727 Processing sheet with id=115, first strand: chain 'UQ' and resid 170 through 173 Processing sheet with id=116, first strand: chain 'UQ' and resid 352 through 360 removed outlier: 7.737A pdb=" N ASNUQ 352 " --> pdb=" O ALAUQ 376 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N METUQ 360 " --> pdb=" O ASPUQ 368 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASPUQ 368 " --> pdb=" O METUQ 360 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'UQ' and resid 528 through 531 Processing sheet with id=118, first strand: chain 'UQ' and resid 581 through 585 Processing sheet with id=119, first strand: chain 'UR' and resid 234 through 238 removed outlier: 7.427A pdb=" N ASPUR 234 " --> pdb=" O ASNUR 592 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLYUR 575 " --> pdb=" O LEUUR 591 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEUUR 576 " --> pdb=" O SERUR 571 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SERUR 567 " --> pdb=" O GLYUR 580 " (cutoff:3.500A) Processing sheet with id=120, first strand: chain 'UR' and resid 252 through 257 removed outlier: 5.481A pdb=" N LEUUR 262 " --> pdb=" O HISUR 257 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILEUR 274 " --> pdb=" O VALUR 285 " (cutoff:3.500A) Processing sheet with id=121, first strand: chain 'UR' and resid 297 through 303 removed outlier: 6.142A pdb=" N GLNUR 309 " --> pdb=" O SERUR 303 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N GLNUR 310 " --> pdb=" O LEUUR 326 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LYSUR 338 " --> pdb=" O ASPUR 325 " (cutoff:3.500A) Processing sheet with id=122, first strand: chain 'UR' and resid 357 through 364 removed outlier: 5.976A pdb=" N ASNUR 357 " --> pdb=" O GLNUR 378 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLYUR 373 " --> pdb=" O SERUR 389 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILEUR 386 " --> pdb=" O LEUUR 395 " (cutoff:3.500A) Processing sheet with id=123, first strand: chain 'UR' and resid 406 through 413 removed outlier: 6.149A pdb=" N THRUR 421 " --> pdb=" O LEUUR 437 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLYUR 430 " --> pdb=" O ASPUR 449 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain 'UR' and resid 457 through 461 removed outlier: 5.220A pdb=" N PHEUR 490 " --> pdb=" O SERUR 486 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain 'UR' and resid 520 through 524 removed outlier: 6.442A pdb=" N ILEUR 529 " --> pdb=" O SERUR 524 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLNUR 528 " --> pdb=" O LEUUR 546 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALAUR 540 " --> pdb=" O SERUR 534 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEUUR 543 " --> pdb=" O PHEUR 552 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain 'UR' and resid 270 through 274 removed outlier: 6.144A pdb=" N LYSUR 270 " --> pdb=" O LEUUR 290 " (cutoff:3.500A) Processing sheet with id=127, first strand: chain 'UR' and resid 382 through 386 Processing sheet with id=128, first strand: chain 'UU' and resid 27 through 30 removed outlier: 3.914A pdb=" N ARGUU 28 " --> pdb=" O ILEUU 653 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILEUU 651 " --> pdb=" O ILEUU 30 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEUUU 640 " --> pdb=" O SERUU 635 " (cutoff:3.500A) Processing sheet with id=129, first strand: chain 'UU' and resid 39 through 43 removed outlier: 6.127A pdb=" N PHEUU 58 " --> pdb=" O SERUU 72 " (cutoff:3.500A) Processing sheet with id=130, first strand: chain 'UU' and resid 82 through 85 Processing sheet with id=131, first strand: chain 'UU' and resid 120 through 124 removed outlier: 4.901A pdb=" N SERUU 136 " --> pdb=" O THRUU 132 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASNUU 135 " --> pdb=" O VALUU 159 " (cutoff:3.500A) Processing sheet with id=132, first strand: chain 'UU' and resid 169 through 172 removed outlier: 5.414A pdb=" N VALUU 188 " --> pdb=" O SERUU 202 " (cutoff:3.500A) Processing sheet with id=133, first strand: chain 'UU' and resid 211 through 215 removed outlier: 6.487A pdb=" N ILEUU 220 " --> pdb=" O ALAUU 215 " (cutoff:3.500A) Processing sheet with id=134, first strand: chain 'UU' and resid 253 through 257 removed outlier: 5.007A pdb=" N HISUU 263 " --> pdb=" O ARGUU 257 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N SERUU 262 " --> pdb=" O LEUUU 278 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHEUU 275 " --> pdb=" O ILEUU 284 " (cutoff:3.500A) Processing sheet with id=135, first strand: chain 'UU' and resid 299 through 304 removed outlier: 5.402A pdb=" N ILEUU 309 " --> pdb=" O LEUUU 304 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SERUU 318 " --> pdb=" O GLYUU 314 " (cutoff:3.500A) Processing sheet with id=136, first strand: chain 'UU' and resid 355 through 359 removed outlier: 6.783A pdb=" N PHEUU 365 " --> pdb=" O ALAUU 359 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N HISUU 364 " --> pdb=" O LEUUU 380 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SERUU 374 " --> pdb=" O SERUU 370 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLNUU 387 " --> pdb=" O SERUU 377 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N SERUU 379 " --> pdb=" O GLNUU 385 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLNUU 385 " --> pdb=" O SERUU 379 " (cutoff:3.500A) Processing sheet with id=137, first strand: chain 'UU' and resid 416 through 420 removed outlier: 5.518A pdb=" N ASNUU 429 " --> pdb=" O GLUUU 420 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALAUU 440 " --> pdb=" O TRPUU 453 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRPUU 453 " --> pdb=" O ALAUU 440 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N THRUU 442 " --> pdb=" O GLYUU 451 " (cutoff:3.500A) Processing sheet with id=138, first strand: chain 'UU' and resid 464 through 469 removed outlier: 5.667A pdb=" N PHEUU 474 " --> pdb=" O SERUU 469 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASNUU 473 " --> pdb=" O METUU 489 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SERUU 479 " --> pdb=" O SERUU 483 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SERUU 483 " --> pdb=" O SERUU 479 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N GLYUU 482 " --> pdb=" O LYSUU 499 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LYSUU 499 " --> pdb=" O GLYUU 482 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILEUU 484 " --> pdb=" O LYSUU 497 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYSUU 497 " --> pdb=" O ILEUU 484 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILEUU 486 " --> pdb=" O ARGUU 495 " (cutoff:3.500A) Processing sheet with id=139, first strand: chain 'UU' and resid 507 through 511 removed outlier: 5.847A pdb=" N LYSUU 516 " --> pdb=" O ASPUU 511 " (cutoff:3.500A) Processing sheet with id=140, first strand: chain 'UU' and resid 548 through 553 removed outlier: 8.847A pdb=" N ASPUU 556 " --> pdb=" O ALAUU 572 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALAUU 572 " --> pdb=" O ASPUU 556 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N SERUU 566 " --> pdb=" O LEUUU 562 " (cutoff:3.500A) Processing sheet with id=141, first strand: chain 'UU' and resid 590 through 594 removed outlier: 5.016A pdb=" N TRPUU 599 " --> pdb=" O SERUU 594 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ARGUU 598 " --> pdb=" O LEUUU 614 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THRUU 611 " --> pdb=" O ILEUU 620 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLYUU 618 " --> pdb=" O ASPUU 613 " (cutoff:3.500A) Processing sheet with id=142, first strand: chain 'UU' and resid 272 through 275 Processing sheet with id=143, first strand: chain 'UU' and resid 607 through 611 removed outlier: 5.666A pdb=" N SERUU 607 " --> pdb=" O VALUU 625 " (cutoff:3.500A) Processing sheet with id=144, first strand: chain 'UV' and resid 140 through 144 removed outlier: 5.946A pdb=" N PHEUV 176 " --> pdb=" O GLUUV 143 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHEUV 290 " --> pdb=" O CYSUV 272 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N CYSUV 272 " --> pdb=" O PHEUV 290 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHEUV 251 " --> pdb=" O SERUV 273 " (cutoff:3.500A) Processing sheet with id=145, first strand: chain 'UV' and resid 455 through 460 removed outlier: 3.513A pdb=" N GLUUV 460 " --> pdb=" O ASPUV 437 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASPUV 437 " --> pdb=" O GLUUV 460 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N THRUV 466 " --> pdb=" O GLYUV 438 " (cutoff:3.500A) Processing sheet with id=146, first strand: chain 'UV' and resid 579 through 586 Processing sheet with id=147, first strand: chain 'UV' and resid 751 through 756 removed outlier: 5.624A pdb=" N ASPUV 781 " --> pdb=" O VALUV 756 " (cutoff:3.500A) Processing sheet with id=148, first strand: chain 'UV' and resid 974 through 977 Processing sheet with id=149, first strand: chain 'UV' and resid 1097 through 1101 removed outlier: 8.637A pdb=" N ASPUV1097 " --> pdb=" O ASPUV1237 " (cutoff:3.500A) Processing sheet with id=150, first strand: chain 'UV' and resid 1204 through 1207 No H-bonds generated for sheet with id=150 Processing sheet with id=151, first strand: chain 'UX' and resid 93 through 98 removed outlier: 4.873A pdb=" N VALUX 175 " --> pdb=" O THRUX 155 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEUUX 172 " --> pdb=" O GLUUX 183 " (cutoff:3.500A) Processing sheet with id=152, first strand: chain 'UZ' and resid 54 through 57 Processing sheet with id=153, first strand: chain 'UZ' and resid 98 through 101 Processing sheet with id=154, first strand: chain 'UZ' and resid 195 through 201 removed outlier: 6.415A pdb=" N ASNUZ 195 " --> pdb=" O THRUZ 42 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THRUZ 42 " --> pdb=" O ASNUZ 195 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILEUZ 36 " --> pdb=" O VALUZ 201 " (cutoff:3.500A) Processing sheet with id=155, first strand: chain 'CA' and resid 87 through 90 removed outlier: 5.439A pdb=" N LEUCA 106 " --> pdb=" O TRPCA 144 " (cutoff:3.500A) Processing sheet with id=156, first strand: chain 'CA' and resid 170 through 173 removed outlier: 6.889A pdb=" N VALCA 317 " --> pdb=" O LEUCA 301 " (cutoff:3.500A) Processing sheet with id=157, first strand: chain 'CA' and resid 193 through 199 Processing sheet with id=158, first strand: chain 'CA' and resid 302 through 305 Processing sheet with id=159, first strand: chain 'CB' and resid 87 through 91 removed outlier: 6.240A pdb=" N VALCB 96 " --> pdb=" O HISCB 91 " (cutoff:3.500A) Processing sheet with id=160, first strand: chain 'CB' and resid 122 through 125 Processing sheet with id=161, first strand: chain 'CB' and resid 170 through 173 removed outlier: 6.846A pdb=" N VALCB 317 " --> pdb=" O LEUCB 301 " (cutoff:3.500A) Processing sheet with id=162, first strand: chain 'CB' and resid 193 through 199 Processing sheet with id=163, first strand: chain 'CB' and resid 302 through 306 removed outlier: 5.027A pdb=" N HISCB 313 " --> pdb=" O LEUCB 306 " (cutoff:3.500A) Processing sheet with id=164, first strand: chain 'CD' and resid 5 through 10 removed outlier: 6.309A pdb=" N GLUCD 5 " --> pdb=" O VALCD 20 " (cutoff:3.500A) Processing sheet with id=165, first strand: chain 'CE' and resid 45 through 49 Processing sheet with id=166, first strand: chain 'CF' and resid 32 through 35 removed outlier: 6.939A pdb=" N GLNCF 32 " --> pdb=" O THRCF 103 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILECF 98 " --> pdb=" O ALACF 55 " (cutoff:3.500A) Processing sheet with id=167, first strand: chain 'CG' and resid 32 through 35 removed outlier: 7.193A pdb=" N GLNCG 32 " --> pdb=" O THRCG 103 " (cutoff:3.500A) Processing sheet with id=168, first strand: chain 'CH' and resid 145 through 152 removed outlier: 5.128A pdb=" N ASNCH 561 " --> pdb=" O VALCH 152 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLUCH 535 " --> pdb=" O GLNCH 570 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SERCH 542 " --> pdb=" O THRCH 522 " (cutoff:3.500A) Processing sheet with id=169, first strand: chain 'CH' and resid 159 through 164 removed outlier: 5.648A pdb=" N LEUCH 185 " --> pdb=" O ILECH 201 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYSCH 198 " --> pdb=" O LEUCH 211 " (cutoff:3.500A) Processing sheet with id=170, first strand: chain 'CH' and resid 241 through 245 removed outlier: 5.677A pdb=" N TYRCH 250 " --> pdb=" O SERCH 245 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ARGCH 258 " --> pdb=" O THRCH 276 " (cutoff:3.500A) Processing sheet with id=171, first strand: chain 'CH' and resid 284 through 288 removed outlier: 6.478A pdb=" N THRCH 306 " --> pdb=" O LEUCH 315 " (cutoff:3.500A) Processing sheet with id=172, first strand: chain 'CH' and resid 354 through 360 removed outlier: 8.489A pdb=" N GLUCH 334 " --> pdb=" O ILECH 351 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N PHECH 411 " --> pdb=" O LEUCH 427 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASNCH 421 " --> pdb=" O SERCH 417 " (cutoff:3.500A) Processing sheet with id=173, first strand: chain 'CH' and resid 477 through 480 removed outlier: 6.477A pdb=" N ASNCH 485 " --> pdb=" O ILECH 501 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEUCH 496 " --> pdb=" O GLUCH 513 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLUCH 513 " --> pdb=" O LEUCH 496 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VALCH 498 " --> pdb=" O LEUCH 511 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SERCH 507 " --> pdb=" O SERCH 502 " (cutoff:3.500A) Processing sheet with id=174, first strand: chain 'CH' and resid 194 through 198 removed outlier: 4.813A pdb=" N LEUCH 194 " --> pdb=" O GLYCH 216 " (cutoff:3.500A) Processing sheet with id=175, first strand: chain 'CH' and resid 303 through 306 Processing sheet with id=176, first strand: chain 'CH' and resid 523 through 530 Processing sheet with id=177, first strand: chain 'CJ' and resid 113 through 118 removed outlier: 8.173A pdb=" N THRCJ 137 " --> pdb=" O PHECJ 157 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLNCJ 164 " --> pdb=" O PHECJ 259 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLUCJ 255 " --> pdb=" O HISCJ 168 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLNCJ 235 " --> pdb=" O VALCJ 250 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VALCJ 233 " --> pdb=" O PROCJ 252 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHECJ 254 " --> pdb=" O ILECJ 231 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILECJ 231 " --> pdb=" O PHECJ 254 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARGCJ 227 " --> pdb=" O PHECJ 230 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARGCJ 234 " --> pdb=" O THRCJ 223 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYRCJ 238 " --> pdb=" O GLUCJ 219 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLUCJ 219 " --> pdb=" O TYRCJ 238 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASNCJ 226 " --> pdb=" O ASPCJ 192 " (cutoff:3.500A) Processing sheet with id=178, first strand: chain 'CJ' and resid 161 through 164 Processing sheet with id=179, first strand: chain 'CL' and resid 104 through 109 removed outlier: 4.463A pdb=" N ARGCL 113 " --> pdb=" O SERCL 109 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLYCL 76 " --> pdb=" O CYSCL 120 " (cutoff:3.500A) Processing sheet with id=180, first strand: chain 'CL' and resid 242 through 246 removed outlier: 4.915A pdb=" N ILECL 810 " --> pdb=" O ALACL 246 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARGCL 287 " --> pdb=" O LEUCL 815 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THRCL 286 " --> pdb=" O VALCL 298 " (cutoff:3.500A) Processing sheet with id=181, first strand: chain 'CL' and resid 248 through 252 removed outlier: 3.571A pdb=" N THRCL 250 " --> pdb=" O ALACL 270 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYSCL 268 " --> pdb=" O LEUCL 252 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VALCL 269 " --> pdb=" O PHECL 793 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYRCL 788 " --> pdb=" O LEUCL 304 " (cutoff:3.500A) Processing sheet with id=182, first strand: chain 'CL' and resid 363 through 366 removed outlier: 7.745A pdb=" N GLYCL 363 " --> pdb=" O ASPCL 374 " (cutoff:3.500A) Processing sheet with id=183, first strand: chain 'CL' and resid 854 through 857 removed outlier: 6.835A pdb=" N LYSCL 826 " --> pdb=" O GLUCL 920 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHECL 885 " --> pdb=" O VALCL 825 " (cutoff:3.500A) Processing sheet with id=184, first strand: chain 'CL' and resid 928 through 934 removed outlier: 4.350A pdb=" N ILECL 928 " --> pdb=" O VALCL1009 " (cutoff:3.500A) Processing sheet with id=185, first strand: chain 'CL' and resid 944 through 949 removed outlier: 6.136A pdb=" N ASNCL 944 " --> pdb=" O PHECL 991 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHECL 991 " --> pdb=" O ASNCL 944 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARGCL 988 " --> pdb=" O LYSCL 977 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ARGCL 973 " --> pdb=" O GLUCL 992 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILECL 972 " --> pdb=" O THRCL 968 " (cutoff:3.500A) Processing sheet with id=186, first strand: chain 'CL' and resid 823 through 826 Processing sheet with id=187, first strand: chain 'CM' and resid 8 through 12 removed outlier: 6.118A pdb=" N THRCM 73 " --> pdb=" O SERCM 68 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLUCM 66 " --> pdb=" O ILECM 75 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARGCM 77 " --> pdb=" O VALCM 64 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLYCM 79 " --> pdb=" O GLYCM 62 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLYCM 62 " --> pdb=" O GLYCM 79 " (cutoff:3.500A) Processing sheet with id=188, first strand: chain 'CM' and resid 86 through 89 removed outlier: 6.419A pdb=" N PHECM 114 " --> pdb=" O VALCM 169 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VALCM 169 " --> pdb=" O PHECM 114 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILECM 116 " --> pdb=" O HISCM 167 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N HISCM 167 " --> pdb=" O ILECM 116 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHECM 118 " --> pdb=" O GLUCM 165 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLUCM 165 " --> pdb=" O PHECM 118 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLYCM 120 " --> pdb=" O GLYCM 163 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLUCM 165 " --> pdb=" O LEUCM 154 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLUCM 148 " --> pdb=" O ASPCM 171 " (cutoff:3.500A) Processing sheet with id=189, first strand: chain 'CM' and resid 180 through 183 removed outlier: 5.523A pdb=" N METCM 180 " --> pdb=" O ILECM 308 " (cutoff:3.500A) Processing sheet with id=190, first strand: chain 'CM' and resid 222 through 230 Processing sheet with id=191, first strand: chain 'CN' and resid 13 through 20 removed outlier: 4.326A pdb=" N CYSCN 52 " --> pdb=" O HISCN 42 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASPCN 51 " --> pdb=" O PHECN 128 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEUCN 125 " --> pdb=" O LEUCN 87 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYSCN 127 " --> pdb=" O GLUCN 85 " (cutoff:3.500A) Processing sheet with id=192, first strand: chain 'JF' and resid 52 through 55 Processing sheet with id=193, first strand: chain 'JF' and resid 160 through 163 removed outlier: 7.152A pdb=" N LYSJF 109 " --> pdb=" O LYSJF 39 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLUJF 200 " --> pdb=" O THRJF 38 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ARGJF 40 " --> pdb=" O GLUJF 200 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LYSJF 174 " --> pdb=" O ASPJF 199 " (cutoff:3.500A) Processing sheet with id=194, first strand: chain 'JG' and resid 40 through 46 Processing sheet with id=195, first strand: chain 'JG' and resid 51 through 56 removed outlier: 5.259A pdb=" N GLUJG 51 " --> pdb=" O LEUJG 68 " (cutoff:3.500A) Processing sheet with id=196, first strand: chain 'JG' and resid 174 through 180 Processing sheet with id=197, first strand: chain 'JJ' and resid 93 through 101 removed outlier: 8.200A pdb=" N LYSJJ 93 " --> pdb=" O PROJJ 143 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LYSJJ 135 " --> pdb=" O VALJJ 101 " (cutoff:3.500A) Processing sheet with id=198, first strand: chain 'JJ' and resid 181 through 185 removed outlier: 3.837A pdb=" N PHEJJ 185 " --> pdb=" O ILEJJ 231 " (cutoff:3.500A) Processing sheet with id=199, first strand: chain 'JN' and resid 312 through 315 Processing sheet with id=200, first strand: chain 'JO' and resid 39 through 45 removed outlier: 5.637A pdb=" N SERJO 39 " --> pdb=" O THRJO 84 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLYJO 78 " --> pdb=" O PHEJO 45 " (cutoff:3.500A) Processing sheet with id=201, first strand: chain 'JO' and resid 122 through 127 Processing sheet with id=202, first strand: chain 'JP' and resid 72 through 76 removed outlier: 5.816A pdb=" N LYSJP 82 " --> pdb=" O ASNJP 76 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VALJP 91 " --> pdb=" O SERJP 87 " (cutoff:3.500A) Processing sheet with id=203, first strand: chain 'JP' and resid 115 through 119 removed outlier: 5.250A pdb=" N SERJP 132 " --> pdb=" O VALJP 152 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N THRJP 144 " --> pdb=" O SERJP 140 " (cutoff:3.500A) Processing sheet with id=204, first strand: chain 'JP' and resid 184 through 188 removed outlier: 3.899A pdb=" N GLYJP 198 " --> pdb=" O LYSJP 200 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYSJP 200 " --> pdb=" O GLYJP 198 " (cutoff:3.500A) Processing sheet with id=205, first strand: chain 'JP' and resid 224 through 227 removed outlier: 4.905A pdb=" N SERJP 224 " --> pdb=" O THRJP 238 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ASPJP 233 " --> pdb=" O LEUJP 249 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASNJP 242 " --> pdb=" O GLNJP 260 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYSJP 257 " --> pdb=" O VALJP 465 " (cutoff:3.500A) Processing sheet with id=206, first strand: chain 'JP' and resid 266 through 269 removed outlier: 8.670A pdb=" N PHEJP 275 " --> pdb=" O METJP 291 " (cutoff:3.500A) Processing sheet with id=207, first strand: chain 'JP' and resid 310 through 314 removed outlier: 5.798A pdb=" N GLUJP 319 " --> pdb=" O SERJP 314 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N SERJP 328 " --> pdb=" O SERJP 324 " (cutoff:3.500A) Processing sheet with id=208, first strand: chain 'JP' and resid 353 through 357 removed outlier: 5.390A pdb=" N TYRJP 362 " --> pdb=" O SERJP 357 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LYSJP 361 " --> pdb=" O SERJP 377 " (cutoff:3.500A) Processing sheet with id=209, first strand: chain 'DA' and resid 45 through 48 Processing sheet with id=210, first strand: chain 'DA' and resid 119 through 128 removed outlier: 5.344A pdb=" N THRDA 119 " --> pdb=" O THRDA 143 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHEDA 138 " --> pdb=" O ARGDA 213 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASNDA 209 " --> pdb=" O PHEDA 142 " (cutoff:3.500A) Processing sheet with id=211, first strand: chain 'DA' and resid 134 through 138 removed outlier: 6.755A pdb=" N VALDA 134 " --> pdb=" O LEUDA 218 " (cutoff:3.500A) Processing sheet with id=212, first strand: chain 'DF' and resid 144 through 151 No H-bonds generated for sheet with id=212 Processing sheet with id=213, first strand: chain 'DH' and resid 44 through 51 Processing sheet with id=214, first strand: chain 'DH' and resid 135 through 144 removed outlier: 6.818A pdb=" N ILEDH 135 " --> pdb=" O LEUDH 154 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEUDH 154 " --> pdb=" O ILEDH 135 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLYDH 137 " --> pdb=" O VALDH 152 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VALDH 152 " --> pdb=" O GLYDH 137 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARGDH 139 " --> pdb=" O GLNDH 150 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLNDH 150 " --> pdb=" O ARGDH 139 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARGDH 141 " --> pdb=" O LYSDH 148 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYSDH 148 " --> pdb=" O ARGDH 141 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEUDH 143 " --> pdb=" O GLYDH 146 " (cutoff:3.500A) Processing sheet with id=215, first strand: chain 'DO' and resid 26 through 32 Processing sheet with id=216, first strand: chain 'DQ' and resid 6 through 12 Processing sheet with id=217, first strand: chain 'DS' and resid 13 through 16 removed outlier: 5.508A pdb=" N HISDS 13 " --> pdb=" O GLYDS 24 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLYDS 24 " --> pdb=" O HISDS 13 " (cutoff:3.500A) Processing sheet with id=218, first strand: chain 'DW' and resid 23 through 28 removed outlier: 5.261A pdb=" N ARGDW 23 " --> pdb=" O LEUDW 65 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VALDW 25 " --> pdb=" O VALDW 63 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VALDW 63 " --> pdb=" O VALDW 25 " (cutoff:3.500A) Processing sheet with id=219, first strand: chain 'DW' and resid 102 through 106 removed outlier: 6.906A pdb=" N ILEDW 103 " --> pdb=" O LEUDW 126 " (cutoff:3.500A) Processing sheet with id=220, first strand: chain 'DX' and resid 48 through 52 Processing sheet with id=221, first strand: chain 'DX' and resid 73 through 77 Processing sheet with id=222, first strand: chain 'Db' and resid 41 through 48 removed outlier: 6.636A pdb=" N TYRDb 31 " --> pdb=" O SERDb 48 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHEDb 32 " --> pdb=" O LYSDb 82 " (cutoff:3.500A) Processing sheet with id=223, first strand: chain 'Dc' and resid 38 through 44 removed outlier: 5.775A pdb=" N ARGDc 38 " --> pdb=" O PHEDc 32 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARGDc 29 " --> pdb=" O ILEDc 13 " (cutoff:3.500A) 7787 hydrogen bonds defined for protein. 22734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1200 hydrogen bonds 1958 hydrogen bond angles 0 basepair planarities 491 basepair parallelities 734 stacking parallelities Total time for adding SS restraints: 106.58 Time building geometry restraints manager: 50.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.27: 20530 1.27 - 1.36: 25388 1.36 - 1.46: 26935 1.46 - 1.55: 53746 1.55 - 1.65: 2974 Bond restraints: 129573 Sorted by residual: bond pdb=" CA PHEUG 84 " pdb=" C PHEUG 84 " ideal model delta sigma weight residual 1.522 1.439 0.083 1.39e-02 5.18e+03 3.59e+01 bond pdb=" C GLNUH 83 " pdb=" O GLNUH 83 " ideal model delta sigma weight residual 1.235 1.303 -0.068 1.26e-02 6.30e+03 2.89e+01 bond pdb=" C ALAUA 134 " pdb=" N PROUA 135 " ideal model delta sigma weight residual 1.334 1.290 0.043 8.40e-03 1.42e+04 2.67e+01 bond pdb=" C GLYUG 335 " pdb=" N PROUG 336 " ideal model delta sigma weight residual 1.333 1.293 0.040 7.80e-03 1.64e+04 2.65e+01 bond pdb=" CA METUQ 869 " pdb=" C METUQ 869 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.37e-02 5.33e+03 2.60e+01 ... (remaining 129568 not shown) Histogram of bond angle deviations from ideal: 84.05 - 97.17: 3 97.17 - 110.30: 43389 110.30 - 123.42: 131989 123.42 - 136.54: 10759 136.54 - 149.66: 4 Bond angle restraints: 186144 Sorted by residual: angle pdb=" N PROUB 400 " pdb=" CA PROUB 400 " pdb=" CB PROUB 400 " ideal model delta sigma weight residual 103.46 113.01 -9.55 9.30e-01 1.16e+00 1.05e+02 angle pdb=" N PROJN 108 " pdb=" CA PROJN 108 " pdb=" CB PROJN 108 " ideal model delta sigma weight residual 103.08 111.42 -8.34 9.70e-01 1.06e+00 7.38e+01 angle pdb=" C LEUUE 472 " pdb=" N LYSUE 473 " pdb=" CA LYSUE 473 " ideal model delta sigma weight residual 121.27 149.66 -28.39 3.40e+00 8.65e-02 6.97e+01 angle pdb=" O3' UD2 524 " pdb=" P UD2 525 " pdb=" OP1 UD2 525 " ideal model delta sigma weight residual 108.00 84.05 23.95 3.00e+00 1.11e-01 6.37e+01 angle pdb=" C PROCL 77 " pdb=" N PROCL 78 " pdb=" CA PROCL 78 " ideal model delta sigma weight residual 119.84 129.64 -9.80 1.25e+00 6.40e-01 6.14e+01 ... (remaining 186139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 71351 35.93 - 71.87: 1324 71.87 - 107.80: 119 107.80 - 143.74: 15 143.74 - 179.67: 20 Dihedral angle restraints: 72829 sinusoidal: 17753 harmonic: 55076 Sorted by residual: dihedral pdb=" CA LEUUA 289 " pdb=" C LEUUA 289 " pdb=" N PROUA 290 " pdb=" CA PROUA 290 " ideal model delta harmonic sigma weight residual 180.00 127.65 52.35 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" C5' GD3 586 " pdb=" C4' GD3 586 " pdb=" C3' GD3 586 " pdb=" O3' GD3 586 " ideal model delta sinusoidal sigma weight residual 147.00 79.54 67.46 1 8.00e+00 1.56e-02 9.25e+01 dihedral pdb=" C4' GD3 586 " pdb=" C3' GD3 586 " pdb=" C2' GD3 586 " pdb=" C1' GD3 586 " ideal model delta sinusoidal sigma weight residual -35.00 31.81 -66.81 1 8.00e+00 1.56e-02 9.09e+01 ... (remaining 72826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.429: 25517 0.429 - 0.858: 0 0.858 - 1.287: 0 1.287 - 1.716: 0 1.716 - 2.145: 1 Chirality restraints: 25518 Sorted by residual: chirality pdb=" P UD2 525 " pdb=" OP1 UD2 525 " pdb=" OP2 UD2 525 " pdb=" O5' UD2 525 " both_signs ideal model delta sigma weight residual True 2.41 0.27 2.14 2.00e-01 2.50e+01 1.15e+02 chirality pdb=" C1' AD4 103 " pdb=" O4' AD4 103 " pdb=" C2' AD4 103 " pdb=" N9 AD4 103 " both_signs ideal model delta sigma weight residual False 2.46 2.06 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" C3' GD3 586 " pdb=" C4' GD3 586 " pdb=" O3' GD3 586 " pdb=" C2' GD3 586 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 25515 not shown) Planarity restraints: 20382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' AD4 103 " 0.074 2.00e-02 2.50e+03 3.36e-02 3.10e+01 pdb=" N9 AD4 103 " -0.077 2.00e-02 2.50e+03 pdb=" C8 AD4 103 " -0.005 2.00e-02 2.50e+03 pdb=" N7 AD4 103 " 0.003 2.00e-02 2.50e+03 pdb=" C5 AD4 103 " 0.004 2.00e-02 2.50e+03 pdb=" C6 AD4 103 " 0.008 2.00e-02 2.50e+03 pdb=" N6 AD4 103 " 0.023 2.00e-02 2.50e+03 pdb=" N1 AD4 103 " -0.003 2.00e-02 2.50e+03 pdb=" C2 AD4 103 " -0.006 2.00e-02 2.50e+03 pdb=" N3 AD4 103 " -0.011 2.00e-02 2.50e+03 pdb=" C4 AD4 103 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GD31164 " 0.024 2.00e-02 2.50e+03 3.15e-02 2.97e+01 pdb=" N9 GD31164 " -0.018 2.00e-02 2.50e+03 pdb=" C8 GD31164 " 0.004 2.00e-02 2.50e+03 pdb=" N7 GD31164 " 0.002 2.00e-02 2.50e+03 pdb=" C5 GD31164 " -0.017 2.00e-02 2.50e+03 pdb=" C6 GD31164 " -0.076 2.00e-02 2.50e+03 pdb=" O6 GD31164 " 0.068 2.00e-02 2.50e+03 pdb=" N1 GD31164 " -0.004 2.00e-02 2.50e+03 pdb=" C2 GD31164 " 0.013 2.00e-02 2.50e+03 pdb=" N2 GD31164 " -0.004 2.00e-02 2.50e+03 pdb=" N3 GD31164 " 0.003 2.00e-02 2.50e+03 pdb=" C4 GD31164 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GD31748 " 0.041 2.00e-02 2.50e+03 3.08e-02 2.85e+01 pdb=" N9 GD31748 " -0.023 2.00e-02 2.50e+03 pdb=" C8 GD31748 " -0.010 2.00e-02 2.50e+03 pdb=" N7 GD31748 " 0.001 2.00e-02 2.50e+03 pdb=" C5 GD31748 " -0.003 2.00e-02 2.50e+03 pdb=" C6 GD31748 " -0.027 2.00e-02 2.50e+03 pdb=" O6 GD31748 " 0.039 2.00e-02 2.50e+03 pdb=" N1 GD31748 " 0.017 2.00e-02 2.50e+03 pdb=" C2 GD31748 " -0.073 2.00e-02 2.50e+03 pdb=" N2 GD31748 " 0.036 2.00e-02 2.50e+03 pdb=" N3 GD31748 " 0.003 2.00e-02 2.50e+03 pdb=" C4 GD31748 " -0.000 2.00e-02 2.50e+03 ... (remaining 20379 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 667 2.57 - 3.15: 98344 3.15 - 3.73: 203566 3.73 - 4.32: 221357 4.32 - 4.90: 338314 Nonbonded interactions: 862248 Sorted by model distance: nonbonded pdb=" N2 GD31541 " pdb=" C6 AD31569 " model vdw 1.986 2.672 nonbonded pdb=" O TYRUL 364 " pdb=" O THRUL 382 " model vdw 2.087 2.432 nonbonded pdb=" C2 GD31541 " pdb=" N6 AD31570 " model vdw 2.104 3.340 nonbonded pdb=" O6 GD31273 " pdb=" O2 UD31437 " model vdw 2.106 2.432 nonbonded pdb=" N2 GD31654 " pdb=" N6 AD31746 " model vdw 2.132 2.560 ... (remaining 862243 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'CA' and (resid 85 through 125 or resid 138 through 324)) selection = chain 'CB' } ncs_group { reference = (chain 'CF' and resid 4 through 125) selection = (chain 'CG' and resid 4 through 125) } ncs_group { reference = chain 'JF' selection = (chain 'JG' and (resid 29 through 55 or resid 63 through 251)) } 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: 6.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 26.160 Check model and map are aligned: 1.410 Set scattering table: 0.890 Process input model: 411.270 Find NCS groups from input model: 7.760 Set up NCS constraints: 0.510 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: 0.020 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 456.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 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 0.140 129573 Z= 0.429 Angle : 1.110 28.390 186144 Z= 0.667 Chirality : 0.057 2.145 25518 Planarity : 0.005 0.050 20382 Dihedral : 14.622 179.674 36649 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.26 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.01 % Twisted Proline : 0.15 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.05), residues: 18746 helix: -1.45 (0.05), residues: 7074 sheet: -1.47 (0.08), residues: 3753 loop : -3.17 (0.06), residues: 7919 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.797 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.8593 time to fit residues: 522.4175 Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.678 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.4483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 2031 random chunks: chunk 1715 optimal weight: 30.0000 chunk 1539 optimal weight: 40.0000 chunk 854 optimal weight: 20.0000 chunk 525 optimal weight: 10.0000 chunk 1038 optimal weight: 50.0000 chunk 822 optimal weight: 9.9990 chunk 1591 optimal weight: 30.0000 chunk 616 optimal weight: 40.0000 chunk 967 optimal weight: 9.9990 chunk 1184 optimal weight: 20.0000 chunk 1844 optimal weight: 30.0000 overall best weight: 13.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.196 129573 Z= 0.552 Angle : 1.127 26.044 186144 Z= 0.632 Chirality : 0.057 2.013 25518 Planarity : 0.006 0.051 20382 Dihedral : 15.621 179.458 36649 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.05 % Favored : 88.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.01 % Twisted Proline : 0.73 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.05), residues: 18746 helix: -0.91 (0.06), residues: 7053 sheet: -1.48 (0.08), residues: 3730 loop : -3.27 (0.06), residues: 7963 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.923 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 1.0301 time to fit residues: 622.0721 Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.925 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.7334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 2031 random chunks: chunk 1025 optimal weight: 10.0000 chunk 572 optimal weight: 20.0000 chunk 1535 optimal weight: 20.0000 chunk 1255 optimal weight: 9.9990 chunk 508 optimal weight: 20.0000 chunk 1847 optimal weight: 30.0000 chunk 1996 optimal weight: 0.9980 chunk 1645 optimal weight: 10.0000 chunk 1832 optimal weight: 20.0000 chunk 629 optimal weight: 9.9990 chunk 1482 optimal weight: 20.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 129573 Z= 0.333 Angle : 0.793 25.017 186144 Z= 0.440 Chirality : 0.049 2.025 25518 Planarity : 0.004 0.049 20382 Dihedral : 14.783 177.719 36649 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.21 % Favored : 89.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.01 % Twisted Proline : 0.44 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.06), residues: 18746 helix: 0.16 (0.06), residues: 7098 sheet: -1.46 (0.08), residues: 3755 loop : -3.14 (0.06), residues: 7893 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.801 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.9930 time to fit residues: 599.9893 Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.805 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.6130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 2031 random chunks: chunk 1825 optimal weight: 20.0000 chunk 1389 optimal weight: 20.0000 chunk 958 optimal weight: 30.0000 chunk 204 optimal weight: 30.0000 chunk 881 optimal weight: 10.0000 chunk 1240 optimal weight: 30.0000 chunk 1854 optimal weight: 30.0000 chunk 1963 optimal weight: 10.0000 chunk 968 optimal weight: 30.0000 chunk 1757 optimal weight: 20.0000 chunk 529 optimal weight: 40.0000 overall best weight: 16.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.198 129573 Z= 0.614 Angle : 1.225 26.063 186144 Z= 0.679 Chirality : 0.061 2.012 25518 Planarity : 0.007 0.050 20382 Dihedral : 16.559 179.376 36649 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.36 % Allowed : 16.26 % Favored : 83.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.01 % Twisted Proline : 1.17 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.05), residues: 18746 helix: -1.23 (0.06), residues: 6980 sheet: -1.72 (0.08), residues: 3596 loop : -3.64 (0.06), residues: 8170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.894 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 1.0098 time to fit residues: 612.0624 Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.836 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.6578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 2031 random chunks: chunk 1635 optimal weight: 20.0000 chunk 1114 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 1461 optimal weight: 5.9990 chunk 810 optimal weight: 10.0000 chunk 1675 optimal weight: 9.9990 chunk 1357 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 1002 optimal weight: 40.0000 chunk 1762 optimal weight: 10.0000 chunk 495 optimal weight: 40.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.145 129573 Z= 0.325 Angle : 0.828 25.241 186144 Z= 0.457 Chirality : 0.049 2.006 25518 Planarity : 0.004 0.050 20382 Dihedral : 15.389 178.675 36649 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.51 % Favored : 87.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.01 % Twisted Proline : 0.73 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.06), residues: 18746 helix: -0.24 (0.06), residues: 7058 sheet: -1.66 (0.08), residues: 3603 loop : -3.45 (0.06), residues: 8085 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.902 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 1.0040 time to fit residues: 607.8692 Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.894 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.6759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 2031 random chunks: chunk 660 optimal weight: 20.0000 chunk 1767 optimal weight: 50.0000 chunk 388 optimal weight: 0.5980 chunk 1152 optimal weight: 20.0000 chunk 484 optimal weight: 20.0000 chunk 1965 optimal weight: 20.0000 chunk 1631 optimal weight: 20.0000 chunk 909 optimal weight: 20.0000 chunk 163 optimal weight: 30.0000 chunk 650 optimal weight: 7.9990 chunk 1031 optimal weight: 50.0000 overall best weight: 13.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.195 129573 Z= 0.525 Angle : 1.076 25.864 186144 Z= 0.596 Chirality : 0.056 2.021 25518 Planarity : 0.005 0.051 20382 Dihedral : 16.306 177.287 36649 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 17.86 % Favored : 82.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.01 % Twisted Proline : 1.32 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.06), residues: 18746 helix: -0.92 (0.06), residues: 6998 sheet: -1.80 (0.08), residues: 3469 loop : -3.68 (0.06), residues: 8279 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.826 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.8859 time to fit residues: 538.1035 Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.832 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.5876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 2031 random chunks: chunk 1894 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 1119 optimal weight: 3.9990 chunk 1435 optimal weight: 6.9990 chunk 1111 optimal weight: 50.0000 chunk 1654 optimal weight: 20.0000 chunk 1097 optimal weight: 3.9990 chunk 1957 optimal weight: 10.0000 chunk 1225 optimal weight: 30.0000 chunk 1193 optimal weight: 10.0000 chunk 903 optimal weight: 0.0570 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 129573 Z= 0.199 Angle : 0.670 25.395 186144 Z= 0.367 Chirality : 0.046 1.992 25518 Planarity : 0.003 0.051 20382 Dihedral : 14.874 179.356 36649 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.19 % Favored : 90.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.01 % Twisted Proline : 0.15 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.06), residues: 18746 helix: 0.68 (0.06), residues: 7061 sheet: -1.70 (0.08), residues: 3612 loop : -3.31 (0.06), residues: 8073 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.907 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 1.0593 time to fit residues: 637.8433 Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.941 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.6711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 2031 random chunks: chunk 1211 optimal weight: 30.0000 chunk 781 optimal weight: 10.0000 chunk 1169 optimal weight: 20.0000 chunk 589 optimal weight: 40.0000 chunk 384 optimal weight: 30.0000 chunk 379 optimal weight: 9.9990 chunk 1244 optimal weight: 20.0000 chunk 1333 optimal weight: 9.9990 chunk 967 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 chunk 1538 optimal weight: 20.0000 overall best weight: 11.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.169 129573 Z= 0.439 Angle : 0.935 25.701 186144 Z= 0.519 Chirality : 0.053 2.019 25518 Planarity : 0.005 0.051 20382 Dihedral : 15.637 177.917 36649 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 16.72 % Favored : 83.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.01 % Twisted Proline : 0.44 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.06), residues: 18746 helix: -0.17 (0.06), residues: 7035 sheet: -1.79 (0.08), residues: 3524 loop : -3.53 (0.06), residues: 8187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.943 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.9055 time to fit residues: 549.9232 Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.805 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.5985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 2031 random chunks: chunk 1780 optimal weight: 30.0000 chunk 1875 optimal weight: 50.0000 chunk 1711 optimal weight: 20.0000 chunk 1824 optimal weight: 20.0000 chunk 1874 optimal weight: 40.0000 chunk 1097 optimal weight: 10.0000 chunk 794 optimal weight: 30.0000 chunk 1432 optimal weight: 40.0000 chunk 559 optimal weight: 7.9990 chunk 1648 optimal weight: 20.0000 chunk 1725 optimal weight: 9.9990 overall best weight: 13.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.203 129573 Z= 0.514 Angle : 1.068 25.941 186144 Z= 0.593 Chirality : 0.056 2.019 25518 Planarity : 0.005 0.052 20382 Dihedral : 16.465 176.676 36649 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 17.43 % Favored : 82.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.01 % Twisted Proline : 1.32 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.06), residues: 18746 helix: -0.91 (0.06), residues: 7012 sheet: -1.86 (0.09), residues: 3437 loop : -3.76 (0.06), residues: 8297 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.975 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 1.0284 time to fit residues: 623.0010 Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.813 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.7199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 2031 random chunks: chunk 1817 optimal weight: 20.0000 chunk 1197 optimal weight: 3.9990 chunk 1928 optimal weight: 10.0000 chunk 1177 optimal weight: 9.9990 chunk 915 optimal weight: 20.0000 chunk 1340 optimal weight: 10.0000 chunk 2023 optimal weight: 10.0000 chunk 1862 optimal weight: 10.0000 chunk 1611 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 1244 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.6231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.160 129573 Z= 0.344 Angle : 0.836 25.469 186144 Z= 0.461 Chirality : 0.050 2.009 25518 Planarity : 0.004 0.052 20382 Dihedral : 15.754 178.452 36649 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 16.00 % Favored : 83.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.01 % Twisted Proline : 0.44 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.06), residues: 18746 helix: -0.27 (0.06), residues: 7056 sheet: -1.91 (0.08), residues: 3572 loop : -3.67 (0.06), residues: 8118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37492 Ramachandran restraints generated. 18746 Oldfield, 0 Emsley, 18746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.817 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 1.0368 time to fit residues: 628.2037 Evaluate side-chains 315 residues out of total 16965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 8.926 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.8619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 2031 random chunks: chunk 987 optimal weight: 6.9990 chunk 1279 optimal weight: 20.0000 chunk 1716 optimal weight: 9.9990 chunk 493 optimal weight: 20.0000 chunk 1485 optimal weight: 20.0000 chunk 237 optimal weight: 30.0000 chunk 447 optimal weight: 30.0000 chunk 1613 optimal weight: 30.0000 chunk 675 optimal weight: 20.0000 chunk 1657 optimal weight: 30.0000 chunk 204 optimal weight: 30.0000 overall best weight: 15.3996 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.113382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.101509 restraints weight = 568226.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.100806 restraints weight = 1480829.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.100801 restraints weight = 1612404.069| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.219 129573 Z= 0.579 Angle : 1.128 26.319 186144 Z= 0.625 Chirality : 0.058 2.023 25518 Planarity : 0.006 0.053 20382 Dihedral : 16.689 177.762 36649 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 19.95 % Favored : 79.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.01 % Twisted Proline : 1.46 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.06), residues: 18746 helix: -1.06 (0.06), residues: 6960 sheet: -1.99 (0.09), residues: 3362 loop : -3.91 (0.06), residues: 8424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14526.11 seconds wall clock time: 257 minutes 5.76 seconds (15425.76 seconds total)