Starting phenix.real_space_refine on Mon Mar 25 13:49:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g4s_4348/03_2024/6g4s_4348.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g4s_4348/03_2024/6g4s_4348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g4s_4348/03_2024/6g4s_4348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g4s_4348/03_2024/6g4s_4348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g4s_4348/03_2024/6g4s_4348.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g4s_4348/03_2024/6g4s_4348.pdb" } resolution = 4.0 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians P 1612 5.49 5 C 25695 2.51 5 N 5992 2.21 5 O 15668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 48967 Number of models: 1 Model: "" Number of chains: 33 Chain: "2" Number of atoms: 19353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1613, 19353 Inner-chain residues flagged as termini: ['pdbres=" C 21698 "'] Classifications: {'RNA': 1613} Modifications used: {'5*END': 1, 'rna3p_pur': 856, 'rna3p_pyr': 757} Link IDs: {'rna3p': 1612} Chain breaks: 23 Unresolved non-hydrogen bonds: 17559 Unresolved non-hydrogen angles: 27810 Unresolved non-hydrogen dihedrals: 17276 Unresolved non-hydrogen chiralities: 1613 Planarities with less than four sites: {' G%rna3p_pur:plan2': 474, ' C%rna3p_pyr:plan': 389, ' A%rna3p_pur:plan2': 382, ' C%rna3p_pyr%5*END:plan2': 1, ' U%rna3p_pyr:plan': 367, ' C%rna3p_pyr%5*END:plan': 1, ' C%rna3p_pyr:plan2': 389, ' G%rna3p_pur:plan': 474, ' A%rna3p_pur:plan': 382} Unresolved non-hydrogen planarities: 17582 Chain: "R" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 595 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 207 Chain: "A" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1068 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 12, 'TRANS': 203} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 675 Unresolved non-hydrogen angles: 870 Unresolved non-hydrogen dihedrals: 563 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 15, 'TYR:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 15, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 374 Chain: "b" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 405 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 5, 'TRANS': 76} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 113 Chain: "B" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1054 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PTRANS': 5, 'TRANS': 207} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 703 Unresolved non-hydrogen angles: 879 Unresolved non-hydrogen dihedrals: 588 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 10, 'GLU:plan': 10, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 347 Chain: "C" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1072 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 184} Link IDs: {'PTRANS': 12, 'TRANS': 205} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 555 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 9, 'PHE:plan': 9, 'GLU:plan': 9, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 288 Chain: "c" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 300 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 95 Chain: "E" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1287 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 224} Link IDs: {'PTRANS': 14, 'TRANS': 247} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 831 Unresolved non-hydrogen angles: 1050 Unresolved non-hydrogen dihedrals: 695 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 8, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 12, 'GLU:plan': 9, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 401 Chain: "e" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 270 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 3, 'TRANS': 51} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 82 Chain: "F" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 935 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PTRANS': 5, 'TRANS': 183} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 581 Unresolved non-hydrogen angles: 732 Unresolved non-hydrogen dihedrals: 480 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 17, 'TYR:plan': 5, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 10, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 309 Chain: "H" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 920 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 9, 'TRANS': 176} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 605 Unresolved non-hydrogen angles: 754 Unresolved non-hydrogen dihedrals: 496 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 7, 'PHE:plan': 10, 'GLU:plan': 16, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 303 Chain: "G" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1135 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 751 Unresolved non-hydrogen angles: 923 Unresolved non-hydrogen dihedrals: 625 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 371 Chain: "Z" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 358 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 281 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 98 Chain: "Y" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 610 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 4, 'TRANS': 119} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 422 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 359 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 208 Chain: "y" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 1566 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 278} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 991 Unresolved non-hydrogen angles: 1259 Unresolved non-hydrogen dihedrals: 822 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 13, 'TYR:plan': 9, 'ASN:plan1': 12, 'TRP:plan': 1, 'HIS:plan': 11, 'PHE:plan': 13, 'GLU:plan': 13, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 513 Chain: "x" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 865 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PTRANS': 7, 'TRANS': 167} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 685 Unresolved non-hydrogen dihedrals: 441 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 9, 'GLU:plan': 10, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 260 Chain: "X" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 690 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 5, 'TRANS': 135} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 427 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 214 Chain: "w" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1232 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'PTRANS': 13, 'TRANS': 234} Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 835 Unresolved non-hydrogen angles: 1065 Unresolved non-hydrogen dihedrals: 709 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 5, 'TYR:plan': 11, 'ASN:plan1': 5, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 10, 'GLU:plan': 17, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 435 Chain: "W" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 634 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 8, 'GLU:plan': 6, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 218 Chain: "V" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 403 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 229 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 127 Chain: "u" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 3106 Classifications: {'peptide': 628} Incomplete info: {'truncation_to_alanine': 556} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 585} Chain breaks: 4 Unresolved chain link angles: 42 Unresolved non-hydrogen bonds: 2104 Unresolved non-hydrogen angles: 2677 Unresolved non-hydrogen dihedrals: 1791 Unresolved non-hydrogen chiralities: 168 Planarities with less than four sites: {'GLN:plan1': 34, 'ASP:plan': 34, 'TYR:plan': 15, 'ASN:plan1': 17, 'TRP:plan': 9, 'HIS:plan': 21, 'PHE:plan': 34, 'GLU:plan': 37, 'ARG:plan': 41} Unresolved non-hydrogen planarities: 1137 Chain: "t" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 355 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 141 Chain: "T" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 705 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 4, 'TRANS': 139} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 438 Unresolved non-hydrogen angles: 551 Unresolved non-hydrogen dihedrals: 372 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 239 Chain: "S" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 704 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 3, 'TRANS': 139} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 631 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 9, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 285 Chain: "Q" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 683 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 5, 'TRANS': 133} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 555 Unresolved non-hydrogen dihedrals: 370 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 235 Chain: "P" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 590 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 7, 'TRANS': 112} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 414 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 350 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 217 Chain: "O" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 659 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 295 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 14, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 6, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 186 Chain: "N" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 737 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 8, 'TRANS': 140} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 490 Unresolved non-hydrogen angles: 617 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 233 Chain: "L" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 744 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 6, 'TRANS': 144} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 507 Unresolved non-hydrogen angles: 635 Unresolved non-hydrogen dihedrals: 424 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 255 Chain: "J" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 888 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 6, 'TRANS': 173} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 637 Unresolved non-hydrogen angles: 796 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 7, 'GLU:plan': 10, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 343 Chain: "I" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1009 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 7, 'TRANS': 197} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 703 Unresolved non-hydrogen angles: 875 Unresolved non-hydrogen dihedrals: 603 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 10, 'ASN:plan1': 10, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 378 Chain: "s" Number of atoms: 3840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 3840 Classifications: {'peptide': 768} Incomplete info: {'truncation_to_alanine': 768} Link IDs: {'TRANS': 767} Chain breaks: 39 Unresolved non-hydrogen bonds: 1536 Unresolved non-hydrogen angles: 2304 Unresolved non-hydrogen dihedrals: 768 Planarities with less than four sites: {'UNK:plan-1': 768} Unresolved non-hydrogen planarities: 768 Chain: "k" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 195 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain breaks: 1 Time building chain proxies: 29.83, per 1000 atoms: 0.61 Number of scatterers: 48967 At special positions: 0 Unit cell: (227.64, 247.152, 199.456, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 1612 15.00 O 15668 8.00 N 5992 7.00 C 25695 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: 23.11 Conformation dependent library (CDL) restraints added in 7.3 seconds 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11292 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 51 sheets defined 52.2% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.67 Creating SS restraints... Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 27 through 36 Processing helix chain 'R' and resid 43 through 61 Processing helix chain 'R' and resid 73 through 83 removed outlier: 3.676A pdb=" N ASN R 83 " --> pdb=" O GLU R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 109 Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.969A pdb=" N VAL A 15 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 36 Processing helix chain 'A' and resid 50 through 66 Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.862A pdb=" N ARG A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 168 through 186 Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.748A pdb=" N GLN A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 18 Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 57 through 64 removed outlier: 4.406A pdb=" N GLY B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 157 through 175 Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 225 through 233 Processing helix chain 'C' and resid 64 through 72 removed outlier: 3.528A pdb=" N ARG C 68 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 removed outlier: 3.834A pdb=" N TYR C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 4.322A pdb=" N ILE C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 160 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 232 through 246 removed outlier: 3.563A pdb=" N PHE C 236 " --> pdb=" O THR C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.879A pdb=" N TRP C 256 " --> pdb=" O PRO C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.529A pdb=" N PHE C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.908A pdb=" N TRP E 18 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 50 Processing helix chain 'E' and resid 57 through 66 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 247 through 262 Processing helix chain 'e' and resid 31 through 43 removed outlier: 3.986A pdb=" N ARG e 41 " --> pdb=" O GLN e 37 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL e 43 " --> pdb=" O ASN e 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 67 through 75 Processing helix chain 'F' and resid 85 through 104 removed outlier: 3.664A pdb=" N THR F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 118 removed outlier: 3.740A pdb=" N VAL F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 161 Processing helix chain 'F' and resid 168 through 182 Processing helix chain 'F' and resid 187 through 204 Processing helix chain 'H' and resid 17 through 31 Processing helix chain 'H' and resid 38 through 43 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 68 through 74 Processing helix chain 'H' and resid 75 through 87 removed outlier: 3.532A pdb=" N PHE H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 120 removed outlier: 3.737A pdb=" N ARG H 120 " --> pdb=" O PRO H 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 117 through 120' Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.615A pdb=" N HIS H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 163 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 181 through 229 Processing helix chain 'Z' and resid 51 through 59 Processing helix chain 'Z' and resid 61 through 65 removed outlier: 3.646A pdb=" N TYR Z 65 " --> pdb=" O VAL Z 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 69 through 77 removed outlier: 3.712A pdb=" N LEU Z 77 " --> pdb=" O VAL Z 73 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 95 Processing helix chain 'Y' and resid 36 through 49 removed outlier: 3.612A pdb=" N ILE Y 40 " --> pdb=" O PRO Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 84 Processing helix chain 'Y' and resid 103 through 116 removed outlier: 3.912A pdb=" N ARG Y 107 " --> pdb=" O SER Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 120 through 124 removed outlier: 3.933A pdb=" N ALA Y 123 " --> pdb=" O THR Y 120 " (cutoff:3.500A) Processing helix chain 'y' and resid 10 through 16 removed outlier: 3.506A pdb=" N PHE y 14 " --> pdb=" O ASP y 10 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG y 16 " --> pdb=" O GLY y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 31 through 36 Processing helix chain 'y' and resid 39 through 49 Processing helix chain 'y' and resid 50 through 53 Processing helix chain 'y' and resid 59 through 70 removed outlier: 3.617A pdb=" N VAL y 63 " --> pdb=" O LEU y 59 " (cutoff:3.500A) Processing helix chain 'y' and resid 75 through 79 Processing helix chain 'y' and resid 80 through 97 Processing helix chain 'y' and resid 99 through 103 Processing helix chain 'y' and resid 209 through 213 removed outlier: 4.421A pdb=" N SER y 212 " --> pdb=" O ILE y 209 " (cutoff:3.500A) Processing helix chain 'y' and resid 238 through 249 Processing helix chain 'y' and resid 380 through 385 removed outlier: 3.965A pdb=" N THR y 384 " --> pdb=" O SER y 380 " (cutoff:3.500A) Processing helix chain 'y' and resid 394 through 399 removed outlier: 4.034A pdb=" N ARG y 398 " --> pdb=" O ALA y 394 " (cutoff:3.500A) Processing helix chain 'x' and resid 84 through 91 Processing helix chain 'x' and resid 91 through 101 Proline residue: x 98 - end of helix Processing helix chain 'x' and resid 127 through 142 removed outlier: 4.087A pdb=" N THR x 131 " --> pdb=" O VAL x 127 " (cutoff:3.500A) Processing helix chain 'x' and resid 145 through 155 removed outlier: 3.719A pdb=" N ALA x 149 " --> pdb=" O GLN x 145 " (cutoff:3.500A) Processing helix chain 'x' and resid 166 through 168 No H-bonds generated for 'chain 'x' and resid 166 through 168' Processing helix chain 'x' and resid 174 through 185 Processing helix chain 'x' and resid 188 through 198 Processing helix chain 'x' and resid 214 through 231 removed outlier: 3.701A pdb=" N GLY x 231 " --> pdb=" O ASN x 227 " (cutoff:3.500A) Processing helix chain 'x' and resid 233 through 245 removed outlier: 3.552A pdb=" N VAL x 237 " --> pdb=" O PRO x 233 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 23 removed outlier: 3.629A pdb=" N LEU X 13 " --> pdb=" O THR X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 32 removed outlier: 3.587A pdb=" N LEU X 32 " --> pdb=" O LYS X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 38 Processing helix chain 'X' and resid 89 through 94 Processing helix chain 'X' and resid 130 through 134 Processing helix chain 'w' and resid 181 through 193 Processing helix chain 'w' and resid 212 through 220 removed outlier: 3.542A pdb=" N TYR w 218 " --> pdb=" O GLU w 214 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL w 219 " --> pdb=" O GLN w 215 " (cutoff:3.500A) Processing helix chain 'w' and resid 221 through 225 removed outlier: 3.658A pdb=" N TRP w 225 " --> pdb=" O PRO w 222 " (cutoff:3.500A) Processing helix chain 'w' and resid 226 through 241 removed outlier: 3.553A pdb=" N LEU w 241 " --> pdb=" O PHE w 237 " (cutoff:3.500A) Processing helix chain 'w' and resid 243 through 253 Processing helix chain 'w' and resid 253 through 266 removed outlier: 3.632A pdb=" N ARG w 257 " --> pdb=" O VAL w 253 " (cutoff:3.500A) Processing helix chain 'w' and resid 269 through 280 Processing helix chain 'w' and resid 282 through 290 Processing helix chain 'w' and resid 290 through 297 Processing helix chain 'w' and resid 302 through 315 Processing helix chain 'w' and resid 318 through 331 removed outlier: 3.604A pdb=" N GLU w 331 " --> pdb=" O LEU w 327 " (cutoff:3.500A) Processing helix chain 'w' and resid 337 through 347 removed outlier: 4.246A pdb=" N PHE w 341 " --> pdb=" O ALA w 337 " (cutoff:3.500A) Processing helix chain 'w' and resid 353 through 367 removed outlier: 3.961A pdb=" N LEU w 357 " --> pdb=" O PRO w 353 " (cutoff:3.500A) Processing helix chain 'w' and resid 375 through 389 Processing helix chain 'w' and resid 390 through 393 removed outlier: 4.183A pdb=" N LEU w 393 " --> pdb=" O LYS w 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 390 through 393' Processing helix chain 'w' and resid 394 through 408 Processing helix chain 'w' and resid 412 through 422 removed outlier: 3.951A pdb=" N GLU w 416 " --> pdb=" O GLN w 412 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 19 removed outlier: 3.627A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 32 through 44 Processing helix chain 'W' and resid 85 through 93 removed outlier: 3.908A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'V' and resid 56 through 62 removed outlier: 3.636A pdb=" N ARG V 60 " --> pdb=" O CYS V 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 76 removed outlier: 3.679A pdb=" N ASP V 76 " --> pdb=" O LEU V 72 " (cutoff:3.500A) Processing helix chain 'u' and resid 49 through 74 removed outlier: 3.618A pdb=" N GLN u 53 " --> pdb=" O SER u 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG u 54 " --> pdb=" O ARG u 50 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG u 73 " --> pdb=" O LEU u 69 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN u 74 " --> pdb=" O ALA u 70 " (cutoff:3.500A) Processing helix chain 'u' and resid 95 through 104 Processing helix chain 'u' and resid 142 through 150 Processing helix chain 'u' and resid 167 through 181 Processing helix chain 'u' and resid 191 through 195 removed outlier: 3.634A pdb=" N LEU u 195 " --> pdb=" O ILE u 192 " (cutoff:3.500A) Processing helix chain 'u' and resid 196 through 212 Processing helix chain 'u' and resid 225 through 238 removed outlier: 3.669A pdb=" N ASN u 238 " --> pdb=" O ARG u 234 " (cutoff:3.500A) Processing helix chain 'u' and resid 246 through 250 removed outlier: 3.545A pdb=" N ARG u 249 " --> pdb=" O PHE u 246 " (cutoff:3.500A) Processing helix chain 'u' and resid 398 through 404 Processing helix chain 'u' and resid 465 through 481 Processing helix chain 'u' and resid 532 through 546 removed outlier: 3.592A pdb=" N THR u 536 " --> pdb=" O ASN u 532 " (cutoff:3.500A) Processing helix chain 'u' and resid 566 through 576 removed outlier: 4.243A pdb=" N VAL u 570 " --> pdb=" O PRO u 566 " (cutoff:3.500A) Processing helix chain 'u' and resid 720 through 726 removed outlier: 3.737A pdb=" N LEU u 724 " --> pdb=" O ARG u 720 " (cutoff:3.500A) Processing helix chain 't' and resid 425 through 469 removed outlier: 3.861A pdb=" N ARG t 430 " --> pdb=" O ASP t 426 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 10 through 26 removed outlier: 3.600A pdb=" N GLY T 26 " --> pdb=" O LEU T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 36 removed outlier: 4.385A pdb=" N ASP T 35 " --> pdb=" O GLU T 32 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR T 36 " --> pdb=" O TRP T 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 32 through 36' Processing helix chain 'T' and resid 51 through 67 Processing helix chain 'T' and resid 71 through 79 removed outlier: 3.510A pdb=" N TYR T 79 " --> pdb=" O MET T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 110 removed outlier: 3.566A pdb=" N LEU T 110 " --> pdb=" O ALA T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 144 removed outlier: 3.542A pdb=" N LYS T 144 " --> pdb=" O ALA T 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 30 removed outlier: 3.711A pdb=" N ILE S 30 " --> pdb=" O ILE S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 49 removed outlier: 3.824A pdb=" N ALA S 41 " --> pdb=" O GLY S 37 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS S 47 " --> pdb=" O VAL S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 73 Processing helix chain 'S' and resid 99 through 118 Processing helix chain 'S' and resid 119 through 128 removed outlier: 3.663A pdb=" N LEU S 123 " --> pdb=" O ALA S 119 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG S 124 " --> pdb=" O HIS S 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 52 Processing helix chain 'Q' and resid 52 through 59 removed outlier: 3.782A pdb=" N LEU Q 58 " --> pdb=" O PRO Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 63 Processing helix chain 'Q' and resid 76 through 100 Processing helix chain 'Q' and resid 102 through 116 removed outlier: 3.512A pdb=" N GLN Q 114 " --> pdb=" O ASP Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 Processing helix chain 'P' and resid 22 through 27 Processing helix chain 'P' and resid 29 through 34 removed outlier: 4.156A pdb=" N MET P 34 " --> pdb=" O TYR P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 48 Processing helix chain 'P' and resid 50 through 66 Processing helix chain 'P' and resid 86 through 90 Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.986A pdb=" N ILE P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 119 removed outlier: 3.815A pdb=" N GLU P 118 " --> pdb=" O TYR P 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 88 Processing helix chain 'O' and resid 109 through 122 removed outlier: 4.129A pdb=" N GLN O 113 " --> pdb=" O GLY O 109 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER O 122 " --> pdb=" O ALA O 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 43 Processing helix chain 'N' and resid 46 through 57 Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 103 Processing helix chain 'N' and resid 108 through 132 Processing helix chain 'L' and resid 23 through 30 removed outlier: 3.968A pdb=" N LYS L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 53 removed outlier: 3.891A pdb=" N ILE L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 39 through 60 removed outlier: 4.347A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 83 Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.751A pdb=" N MET J 92 " --> pdb=" O GLU J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 100 removed outlier: 3.521A pdb=" N TYR J 96 " --> pdb=" O LYS J 93 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU J 98 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU J 100 " --> pdb=" O ILE J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 108 removed outlier: 4.292A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 116 Processing helix chain 'J' and resid 122 through 132 Processing helix chain 'J' and resid 151 through 155 Processing helix chain 'J' and resid 172 through 178 Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 88 through 94 removed outlier: 3.551A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 131 through 136 Processing helix chain 'I' and resid 142 through 154 Processing helix chain 'I' and resid 159 through 169 Processing helix chain 'I' and resid 178 through 183 removed outlier: 3.577A pdb=" N CYS I 182 " --> pdb=" O ARG I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 203 Processing helix chain 's' and resid 184 through 199 Processing helix chain 's' and resid 205 through 221 removed outlier: 3.551A pdb=" N UNK s 209 " --> pdb=" O UNK s 205 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N UNK s 210 " --> pdb=" O UNK s 206 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N UNK s 221 " --> pdb=" O UNK s 217 " (cutoff:3.500A) Processing helix chain 's' and resid 230 through 241 Processing helix chain 's' and resid 249 through 262 Processing helix chain 's' and resid 265 through 288 Processing helix chain 's' and resid 292 through 310 Processing helix chain 's' and resid 313 through 335 Processing helix chain 's' and resid 338 through 358 Processing helix chain 's' and resid 361 through 381 removed outlier: 3.683A pdb=" N UNK s 381 " --> pdb=" O UNK s 377 " (cutoff:3.500A) Processing helix chain 's' and resid 384 through 405 Processing helix chain 's' and resid 408 through 426 removed outlier: 3.567A pdb=" N UNK s 426 " --> pdb=" O UNK s 422 " (cutoff:3.500A) Processing helix chain 's' and resid 429 through 450 Processing helix chain 's' and resid 453 through 475 Processing helix chain 's' and resid 478 through 496 Processing helix chain 's' and resid 499 through 517 removed outlier: 3.746A pdb=" N UNK s 517 " --> pdb=" O UNK s 513 " (cutoff:3.500A) Processing helix chain 's' and resid 520 through 538 Processing helix chain 's' and resid 542 through 549 Processing helix chain 's' and resid 556 through 567 removed outlier: 3.782A pdb=" N UNK s 567 " --> pdb=" O UNK s 563 " (cutoff:3.500A) Processing helix chain 's' and resid 572 through 590 removed outlier: 3.898A pdb=" N UNK s 590 " --> pdb=" O UNK s 586 " (cutoff:3.500A) Processing helix chain 's' and resid 593 through 613 Processing helix chain 's' and resid 617 through 634 removed outlier: 3.597A pdb=" N UNK s 634 " --> pdb=" O UNK s 630 " (cutoff:3.500A) Processing helix chain 's' and resid 639 through 647 removed outlier: 3.963A pdb=" N UNK s 647 " --> pdb=" O UNK s 643 " (cutoff:3.500A) Processing helix chain 's' and resid 652 through 671 Processing helix chain 's' and resid 675 through 688 Processing helix chain 's' and resid 693 through 714 removed outlier: 3.979A pdb=" N UNK s 714 " --> pdb=" O UNK s 710 " (cutoff:3.500A) Processing helix chain 's' and resid 717 through 734 Processing helix chain 's' and resid 737 through 756 Processing helix chain 's' and resid 761 through 780 Processing helix chain 's' and resid 785 through 802 Processing helix chain 's' and resid 808 through 824 Processing helix chain 's' and resid 829 through 846 Processing helix chain 's' and resid 851 through 870 Processing helix chain 's' and resid 875 through 894 Processing helix chain 's' and resid 899 through 915 Processing helix chain 's' and resid 920 through 934 Processing helix chain 's' and resid 937 through 953 Processing helix chain 's' and resid 958 through 975 Processing helix chain 's' and resid 981 through 995 Processing helix chain 's' and resid 1000 through 1008 Processing helix chain 's' and resid 1011 through 1028 Processing helix chain 'k' and resid 2 through 19 Processing helix chain 'k' and resid 22 through 40 Processing sheet with id=AA1, first strand: chain 'R' and resid 96 through 98 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 41 removed outlier: 7.185A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.092A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER A 75 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 43 through 47 Processing sheet with id=AA5, first strand: chain 'b' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 49 removed outlier: 8.549A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS B 34 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N PHE B 100 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 13.999A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 14.430A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG B 136 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 70 removed outlier: 13.999A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 14.430A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG B 136 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE B 142 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP B 209 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 103 through 116 removed outlier: 5.076A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB1, first strand: chain 'C' and resid 184 through 187 Processing sheet with id=AB2, first strand: chain 'c' and resid 20 through 21 Processing sheet with id=AB3, first strand: chain 'c' and resid 20 through 21 removed outlier: 13.403A pdb=" N ILE c 43 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N ASP F 140 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN c 45 " --> pdb=" O ASP F 140 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR F 126 " --> pdb=" O GLN F 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 9 through 10 removed outlier: 4.165A pdb=" N LEU E 9 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AB6, first strand: chain 'E' and resid 140 through 141 removed outlier: 6.540A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP E 158 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 218 through 220 removed outlier: 6.120A pdb=" N LYS E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 47 through 53 removed outlier: 8.992A pdb=" N VAL H 93 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE H 60 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE H 95 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE H 62 " --> pdb=" O ILE H 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 185 through 188 removed outlier: 7.971A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N GLU H 188 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL H 156 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU H 153 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE H 144 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS H 155 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS H 142 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS H 157 " --> pdb=" O VAL H 140 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.708A pdb=" N LEU G 106 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASP G 57 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL G 108 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY G 55 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASN G 110 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AC3, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AC4, first strand: chain 'Z' and resid 98 through 101 removed outlier: 6.343A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Y' and resid 6 through 15 removed outlier: 5.767A pdb=" N ILE Y 7 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU Y 28 " --> pdb=" O ILE Y 7 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR Y 9 " --> pdb=" O ASP Y 26 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP Y 26 " --> pdb=" O THR Y 9 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS Y 11 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'y' and resid 28 through 29 Processing sheet with id=AC7, first strand: chain 'y' and resid 128 through 129 Processing sheet with id=AC8, first strand: chain 'y' and resid 276 through 277 Processing sheet with id=AC9, first strand: chain 'x' and resid 159 through 164 Processing sheet with id=AD1, first strand: chain 'X' and resid 80 through 84 removed outlier: 5.104A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL X 128 " --> pdb=" O VAL X 125 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AD3, first strand: chain 'W' and resid 71 through 74 removed outlier: 6.616A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'V' and resid 32 through 37 Processing sheet with id=AD5, first strand: chain 'u' and resid 110 through 112 removed outlier: 7.670A pdb=" N LEU u 157 " --> pdb=" O GLN u 84 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU u 86 " --> pdb=" O LEU u 157 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU u 159 " --> pdb=" O LEU u 86 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL u 88 " --> pdb=" O LEU u 159 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N LEU u 221 " --> pdb=" O TYR u 185 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU u 187 " --> pdb=" O LEU u 221 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'u' and resid 252 through 254 Processing sheet with id=AD7, first strand: chain 'u' and resid 257 through 264 removed outlier: 7.860A pdb=" N VAL u 269 " --> pdb=" O SER u 263 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLY u 270 " --> pdb=" O GLU u 564 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU u 564 " --> pdb=" O GLY u 270 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER u 563 " --> pdb=" O MET u 299 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N MET u 299 " --> pdb=" O SER u 563 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'u' and resid 487 through 488 removed outlier: 6.071A pdb=" N HIS u 638 " --> pdb=" O ILE u 694 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ARG u 696 " --> pdb=" O HIS u 638 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU u 640 " --> pdb=" O ARG u 696 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N VAL u 698 " --> pdb=" O LEU u 640 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE u 629 " --> pdb=" O GLN u 641 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'u' and resid 487 through 488 Processing sheet with id=AE1, first strand: chain 'u' and resid 528 through 530 removed outlier: 7.109A pdb=" N GLN u 529 " --> pdb=" O ILE t 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'u' and resid 623 through 625 removed outlier: 6.635A pdb=" N LEU u 667 " --> pdb=" O ILE u 679 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'u' and resid 702 through 707 removed outlier: 7.204A pdb=" N ARG u 714 " --> pdb=" O PRO u 703 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET u 710 " --> pdb=" O PHE u 707 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N HIS u 750 " --> pdb=" O PRO u 744 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LYS u 752 " --> pdb=" O LYS u 742 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 81 through 83 Processing sheet with id=AE5, first strand: chain 'T' and resid 113 through 115 Processing sheet with id=AE6, first strand: chain 'S' and resid 13 through 14 Processing sheet with id=AE7, first strand: chain 'Q' and resid 9 through 15 removed outlier: 6.318A pdb=" N LYS Q 33 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL Q 72 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 16 through 17 Processing sheet with id=AE9, first strand: chain 'P' and resid 76 through 78 Processing sheet with id=AF1, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.643A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY O 29 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LYS O 96 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N CYS O 31 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG O 98 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE O 33 " --> pdb=" O ARG O 98 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU O 93 " --> pdb=" O ILE O 126 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ARG O 128 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE O 95 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 101 through 111 removed outlier: 6.730A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 15.033A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 16.415A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 136 through 137 Processing sheet with id=AF4, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.871A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 37 through 38 removed outlier: 5.384A pdb=" N VAL I 46 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N HIS I 44 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 62 through 67 removed outlier: 7.827A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP I 80 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE I 101 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N CYS I 100 " --> pdb=" O ILE I 175 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE I 175 " --> pdb=" O CYS I 100 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) 2221 hydrogen bonds defined for protein. 6357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.83 Time building geometry restraints manager: 24.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 5998 1.30 - 1.38: 5904 1.38 - 1.46: 13714 1.46 - 1.55: 21621 1.55 - 1.63: 3237 Bond restraints: 50474 Sorted by residual: bond pdb=" CA GLN V 33 " pdb=" CB GLN V 33 " ideal model delta sigma weight residual 1.526 1.444 0.082 1.53e-02 4.27e+03 2.90e+01 bond pdb=" C SER y 371 " pdb=" N PRO y 372 " ideal model delta sigma weight residual 1.337 1.384 -0.047 9.80e-03 1.04e+04 2.32e+01 bond pdb=" C ILE W 75 " pdb=" N SER W 76 " ideal model delta sigma weight residual 1.333 1.265 0.068 1.59e-02 3.96e+03 1.81e+01 bond pdb=" C LEU W 93 " pdb=" N LEU W 94 " ideal model delta sigma weight residual 1.327 1.236 0.091 2.31e-02 1.87e+03 1.56e+01 bond pdb=" CA LYS V 27 " pdb=" CB LYS V 27 " ideal model delta sigma weight residual 1.526 1.467 0.059 1.76e-02 3.23e+03 1.12e+01 ... (remaining 50469 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.01: 6835 106.01 - 112.74: 32925 112.74 - 119.48: 13114 119.48 - 126.21: 20217 126.21 - 132.95: 74 Bond angle restraints: 73165 Sorted by residual: angle pdb=" C LYS c 16 " pdb=" N VAL c 17 " pdb=" CA VAL c 17 " ideal model delta sigma weight residual 121.97 132.95 -10.98 1.80e+00 3.09e-01 3.72e+01 angle pdb=" CA GLY I 63 " pdb=" C GLY I 63 " pdb=" N ASN I 64 " ideal model delta sigma weight residual 114.58 119.82 -5.24 8.60e-01 1.35e+00 3.72e+01 angle pdb=" C LYS Q 16 " pdb=" N LYS Q 17 " pdb=" CA LYS Q 17 " ideal model delta sigma weight residual 121.19 130.68 -9.49 1.59e+00 3.96e-01 3.56e+01 angle pdb=" N ARG R 67 " pdb=" CA ARG R 67 " pdb=" C ARG R 67 " ideal model delta sigma weight residual 114.75 107.45 7.30 1.26e+00 6.30e-01 3.36e+01 angle pdb=" C GLU Z 61 " pdb=" N VAL Z 62 " pdb=" CA VAL Z 62 " ideal model delta sigma weight residual 120.33 124.96 -4.63 8.00e-01 1.56e+00 3.36e+01 ... (remaining 73160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 33642 35.34 - 70.69: 3373 70.69 - 106.03: 282 106.03 - 141.37: 13 141.37 - 176.71: 20 Dihedral angle restraints: 37330 sinusoidal: 20127 harmonic: 17203 Sorted by residual: dihedral pdb=" CA PRO u 81 " pdb=" C PRO u 81 " pdb=" N PRO u 82 " pdb=" CA PRO u 82 " ideal model delta harmonic sigma weight residual 180.00 123.49 56.51 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" C5' U 21371 " pdb=" C4' U 21371 " pdb=" C3' U 21371 " pdb=" O3' U 21371 " ideal model delta sinusoidal sigma weight residual 82.00 163.27 -81.27 1 8.00e+00 1.56e-02 1.27e+02 dihedral pdb=" C4' U 21154 " pdb=" C3' U 21154 " pdb=" C2' U 21154 " pdb=" C1' U 21154 " ideal model delta sinusoidal sigma weight residual 36.00 -43.87 79.87 1 8.00e+00 1.56e-02 1.24e+02 ... (remaining 37327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 10321 0.075 - 0.149: 1262 0.149 - 0.224: 144 0.224 - 0.299: 311 0.299 - 0.374: 59 Chirality restraints: 12097 Sorted by residual: chirality pdb=" C3' U 21304 " pdb=" C4' U 21304 " pdb=" O3' U 21304 " pdb=" C2' U 21304 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C3' U 21154 " pdb=" C4' U 21154 " pdb=" O3' U 21154 " pdb=" C2' U 21154 " both_signs ideal model delta sigma weight residual False -2.48 -2.84 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C2' U 2 591 " pdb=" C3' U 2 591 " pdb=" O2' U 2 591 " pdb=" C1' U 2 591 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 12094 not shown) Planarity restraints: 5911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 228 " 0.036 2.00e-02 2.50e+03 7.17e-02 5.13e+01 pdb=" C ILE E 228 " -0.124 2.00e-02 2.50e+03 pdb=" O ILE E 228 " 0.046 2.00e-02 2.50e+03 pdb=" N GLY E 229 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 85 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.28e+01 pdb=" C ARG A 85 " 0.062 2.00e-02 2.50e+03 pdb=" O ARG A 85 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA A 86 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 84 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.18e+00 pdb=" C GLN A 84 " 0.049 2.00e-02 2.50e+03 pdb=" O GLN A 84 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 85 " -0.017 2.00e-02 2.50e+03 ... (remaining 5908 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 110 2.51 - 3.11: 31772 3.11 - 3.70: 65188 3.70 - 4.30: 77864 4.30 - 4.90: 115539 Nonbonded interactions: 290473 Sorted by model distance: nonbonded pdb=" CB ALA k 19 " pdb=" CB ALA k 21 " model vdw 1.911 3.880 nonbonded pdb=" CA VAL E 131 " pdb=" O ILE E 136 " model vdw 2.223 3.470 nonbonded pdb=" OP1 A 2 983 " pdb=" O2' U 21073 " model vdw 2.243 2.440 nonbonded pdb=" O2' G 2 659 " pdb=" O2' G 2 662 " model vdw 2.245 2.440 nonbonded pdb=" O2' U 2 681 " pdb=" OP1 U 21160 " model vdw 2.245 2.440 ... (remaining 290468 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 12.650 Check model and map are aligned: 0.760 Set scattering table: 0.470 Process input model: 137.220 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 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 : 0.005 0.119 50474 Z= 0.354 Angle : 1.052 11.523 73165 Z= 0.683 Chirality : 0.068 0.374 12097 Planarity : 0.005 0.072 5911 Dihedral : 23.449 176.713 26038 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.60 % Favored : 91.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 2.19 % Twisted General : 0.22 % 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: -3.72 (0.10), residues: 5142 helix: -2.41 (0.09), residues: 1804 sheet: -1.80 (0.17), residues: 758 loop : -2.72 (0.10), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 55 PHE 0.000 0.000 PHE R 28 TYR 0.000 0.000 TYR R 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 4.367 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4291 time to fit residues: 87.4876 Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 629 optimal weight: 0.0670 chunk 565 optimal weight: 0.0870 chunk 313 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 chunk 381 optimal weight: 20.0000 chunk 302 optimal weight: 20.0000 chunk 584 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 355 optimal weight: 10.0000 chunk 435 optimal weight: 5.9990 chunk 677 optimal weight: 20.0000 overall best weight: 3.6302 ------------------------------------------------------------------------------- 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: 0.6815 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 50474 Z= 0.169 Angle : 0.560 10.815 73165 Z= 0.309 Chirality : 0.034 0.223 12097 Planarity : 0.002 0.029 5911 Dihedral : 20.105 179.724 26038 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.11), residues: 5142 helix: 0.00 (0.12), residues: 1877 sheet: -1.50 (0.17), residues: 813 loop : -2.15 (0.11), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 55 PHE 0.000 0.000 PHE R 28 TYR 0.000 0.000 TYR R 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.844 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4178 time to fit residues: 84.9495 Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 376 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 chunk 563 optimal weight: 50.0000 chunk 461 optimal weight: 30.0000 chunk 186 optimal weight: 5.9990 chunk 678 optimal weight: 40.0000 chunk 733 optimal weight: 20.0000 chunk 604 optimal weight: 4.9990 chunk 673 optimal weight: 30.0000 chunk 231 optimal weight: 1.9990 chunk 544 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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: 0.6932 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 50474 Z= 0.231 Angle : 0.593 9.859 73165 Z= 0.337 Chirality : 0.035 0.237 12097 Planarity : 0.003 0.026 5911 Dihedral : 20.565 178.566 26038 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.16 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.12), residues: 5142 helix: 0.90 (0.12), residues: 1913 sheet: -1.26 (0.18), residues: 764 loop : -1.73 (0.12), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 55 PHE 0.000 0.000 PHE R 28 TYR 0.000 0.000 TYR R 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.775 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4278 time to fit residues: 86.2840 Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 670 optimal weight: 50.0000 chunk 510 optimal weight: 20.0000 chunk 352 optimal weight: 40.0000 chunk 75 optimal weight: 10.0000 chunk 323 optimal weight: 20.0000 chunk 455 optimal weight: 20.0000 chunk 681 optimal weight: 30.0000 chunk 721 optimal weight: 40.0000 chunk 355 optimal weight: 6.9990 chunk 645 optimal weight: 8.9990 chunk 194 optimal weight: 30.0000 overall best weight: 13.1996 ------------------------------------------------------------------------------- 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: 0.7036 moved from start: 0.8501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 50474 Z= 0.432 Angle : 0.921 15.842 73165 Z= 0.518 Chirality : 0.042 0.234 12097 Planarity : 0.005 0.033 5911 Dihedral : 22.529 179.685 26038 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.60 % Favored : 89.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -2.11 (0.11), residues: 5142 helix: -0.39 (0.11), residues: 1894 sheet: -1.46 (0.18), residues: 738 loop : -2.20 (0.12), residues: 2510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 55 PHE 0.000 0.000 PHE R 28 TYR 0.000 0.000 TYR R 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.637 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4454 time to fit residues: 89.3109 Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 600 optimal weight: 8.9990 chunk 409 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 536 optimal weight: 30.0000 chunk 297 optimal weight: 8.9990 chunk 615 optimal weight: 30.0000 chunk 498 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 368 optimal weight: 30.0000 chunk 647 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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: 0.7005 moved from start: 0.8698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 50474 Z= 0.234 Angle : 0.531 14.030 73165 Z= 0.301 Chirality : 0.033 0.191 12097 Planarity : 0.003 0.025 5911 Dihedral : 22.365 179.633 26038 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.12), residues: 5142 helix: 0.88 (0.12), residues: 1902 sheet: -1.39 (0.19), residues: 713 loop : -1.90 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 55 PHE 0.000 0.000 PHE R 28 TYR 0.000 0.000 TYR R 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.997 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4249 time to fit residues: 87.1439 Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 242 optimal weight: 0.0980 chunk 649 optimal weight: 20.0000 chunk 142 optimal weight: 40.0000 chunk 423 optimal weight: 0.1980 chunk 178 optimal weight: 9.9990 chunk 721 optimal weight: 40.0000 chunk 599 optimal weight: 40.0000 chunk 334 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 378 optimal weight: 0.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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: 0.6955 moved from start: 0.8663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.027 50474 Z= 0.100 Angle : 0.359 9.938 73165 Z= 0.202 Chirality : 0.029 0.181 12097 Planarity : 0.002 0.025 5911 Dihedral : 21.819 179.622 26038 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 5142 helix: 1.93 (0.13), residues: 1902 sheet: -1.19 (0.19), residues: 735 loop : -1.46 (0.13), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 55 PHE 0.000 0.000 PHE R 28 TYR 0.000 0.000 TYR R 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 4.028 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4518 time to fit residues: 91.9608 Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 695 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 411 optimal weight: 30.0000 chunk 527 optimal weight: 30.0000 chunk 408 optimal weight: 4.9990 chunk 607 optimal weight: 9.9990 chunk 403 optimal weight: 30.0000 chunk 719 optimal weight: 20.0000 chunk 449 optimal weight: 20.0000 chunk 438 optimal weight: 9.9990 chunk 331 optimal weight: 0.9990 overall best weight: 9.1992 ------------------------------------------------------------------------------- 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: 0.7033 moved from start: 0.9442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 50474 Z= 0.286 Angle : 0.642 14.470 73165 Z= 0.359 Chirality : 0.036 0.193 12097 Planarity : 0.003 0.026 5911 Dihedral : 22.529 179.463 26038 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.54 % Favored : 89.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.12), residues: 5142 helix: 1.28 (0.12), residues: 1890 sheet: -1.35 (0.19), residues: 733 loop : -1.74 (0.13), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 55 PHE 0.000 0.000 PHE R 28 TYR 0.000 0.000 TYR R 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.798 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4207 time to fit residues: 86.5782 Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 444 optimal weight: 7.9990 chunk 287 optimal weight: 0.0770 chunk 429 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 141 optimal weight: 30.0000 chunk 139 optimal weight: 20.0000 chunk 457 optimal weight: 0.7980 chunk 489 optimal weight: 9.9990 chunk 355 optimal weight: 0.0570 chunk 67 optimal weight: 20.0000 chunk 565 optimal weight: 20.0000 overall best weight: 1.9860 ------------------------------------------------------------------------------- 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: 0.6965 moved from start: 0.9340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.022 50474 Z= 0.098 Angle : 0.364 10.075 73165 Z= 0.205 Chirality : 0.029 0.181 12097 Planarity : 0.002 0.025 5911 Dihedral : 22.011 178.211 26038 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.13), residues: 5142 helix: 2.31 (0.13), residues: 1905 sheet: -1.15 (0.19), residues: 722 loop : -1.34 (0.13), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 55 PHE 0.000 0.000 PHE R 28 TYR 0.000 0.000 TYR R 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.699 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4230 time to fit residues: 85.9547 Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 654 optimal weight: 50.0000 chunk 688 optimal weight: 30.0000 chunk 628 optimal weight: 50.0000 chunk 670 optimal weight: 50.0000 chunk 403 optimal weight: 30.0000 chunk 291 optimal weight: 40.0000 chunk 526 optimal weight: 0.0000 chunk 205 optimal weight: 10.0000 chunk 605 optimal weight: 20.0000 chunk 633 optimal weight: 6.9990 chunk 667 optimal weight: 40.0000 overall best weight: 13.3998 ------------------------------------------------------------------------------- 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: 0.7071 moved from start: 1.0383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 50474 Z= 0.391 Angle : 0.808 17.193 73165 Z= 0.449 Chirality : 0.040 0.197 12097 Planarity : 0.004 0.027 5911 Dihedral : 23.106 179.213 26038 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.96 % Favored : 87.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.12), residues: 5142 helix: 0.76 (0.12), residues: 1889 sheet: -1.53 (0.19), residues: 741 loop : -1.90 (0.13), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 55 PHE 0.000 0.000 PHE R 28 TYR 0.000 0.000 TYR R 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.876 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4341 time to fit residues: 88.5517 Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 439 optimal weight: 9.9990 chunk 708 optimal weight: 30.0000 chunk 432 optimal weight: 30.0000 chunk 336 optimal weight: 10.0000 chunk 492 optimal weight: 6.9990 chunk 743 optimal weight: 7.9990 chunk 684 optimal weight: 20.0000 chunk 591 optimal weight: 6.9990 chunk 61 optimal weight: 30.0000 chunk 457 optimal weight: 20.0000 chunk 362 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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: 0.7045 moved from start: 1.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 50474 Z= 0.245 Angle : 0.552 15.331 73165 Z= 0.309 Chirality : 0.033 0.187 12097 Planarity : 0.003 0.025 5911 Dihedral : 22.931 179.809 26038 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.12), residues: 5142 helix: 1.39 (0.12), residues: 1898 sheet: -1.44 (0.19), residues: 695 loop : -1.80 (0.13), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 55 PHE 0.000 0.000 PHE R 28 TYR 0.000 0.000 TYR R 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10284 Ramachandran restraints generated. 5142 Oldfield, 0 Emsley, 5142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 4.306 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4342 time to fit residues: 88.7912 Evaluate side-chains 101 residues out of total 4491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 470 optimal weight: 6.9990 chunk 630 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 545 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 164 optimal weight: 2.9990 chunk 592 optimal weight: 0.9990 chunk 248 optimal weight: 50.0000 chunk 608 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 109 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.079979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.068158 restraints weight = 365575.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.069085 restraints weight = 201598.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.068948 restraints weight = 137886.334| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 1.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 50474 Z= 0.180 Angle : 0.459 13.147 73165 Z= 0.255 Chirality : 0.031 0.177 12097 Planarity : 0.002 0.026 5911 Dihedral : 22.521 179.274 26038 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 5142 helix: 2.14 (0.13), residues: 1915 sheet: -1.40 (0.19), residues: 714 loop : -1.61 (0.13), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 55 PHE 0.000 0.000 PHE R 28 TYR 0.000 0.000 TYR R 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5000.37 seconds wall clock time: 93 minutes 1.17 seconds (5581.17 seconds total)