Starting phenix.real_space_refine (version: dev) on Fri Dec 23 03:28:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o31_3731/12_2022/5o31_3731_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o31_3731/12_2022/5o31_3731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o31_3731/12_2022/5o31_3731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o31_3731/12_2022/5o31_3731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o31_3731/12_2022/5o31_3731_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o31_3731/12_2022/5o31_3731_updated.pdb" } resolution = 4.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 52703 Number of models: 1 Model: "" Number of chains: 52 Chain: "A" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 691 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1159 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 10, 'TRANS': 136} Chain: "C" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1678 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 188} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3229 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 26, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 3, 'HIS:plan': 1, 'GLU:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 84 Chain: "E" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1038 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 17, 'TRANS': 168} Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 347 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 10, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 228 Chain: "F" Number of atoms: 2441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 2441 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 243} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 858 Unresolved non-hydrogen angles: 1089 Unresolved non-hydrogen dihedrals: 695 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 12, 'TRP:plan': 4, 'ASP:plan': 17, 'PHE:plan': 9, 'GLU:plan': 26, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 479 Chain: "H" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2312 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 21, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1388 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 165} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1211 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 3, 'TRANS': 167} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "K" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 720 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "L" Number of atoms: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4538 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 27, 'TRANS': 576} Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 5, 'ASN:plan1': 12, 'HIS:plan': 2, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "M" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3549 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 20, 'TRANS': 436} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "N" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2592 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 21, 'TRANS': 322} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "O" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1941 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PTRANS': 14, 'TRANS': 299} Unresolved non-hydrogen bonds: 616 Unresolved non-hydrogen angles: 776 Unresolved non-hydrogen dihedrals: 507 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 11, 'ARG:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 9, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 21, 'ASP:plan': 16} Unresolved non-hydrogen planarities: 328 Chain: "P" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 1415 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 283} Link IDs: {'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 566 Unresolved non-hydrogen angles: 849 Unresolved non-hydrogen dihedrals: 283 Planarities with less than four sites: {'UNK:plan-1': 283} Unresolved non-hydrogen planarities: 283 Chain: "S" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 405 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 4, 'TRANS': 75} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 157 Chain: "T" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 378 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 11, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "U" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 432 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 139 Chain: "V" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 700 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 10, 'ASN:plan1': 1, 'TRP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "W" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "Y" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1011 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "a" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 480 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 60} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "b" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 519 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'UNK:plan-1': 35} Unresolved non-hydrogen planarities: 35 Chain: "c" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 320 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 42} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "e" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 619 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 4, 'TRANS': 84} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 71 Chain: "f" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 350 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 76 Chain: "g" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 677 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 8, 'TRANS': 88} Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "i" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 616 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'UNK:plan-1': 79, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "j" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 260 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'TRANS': 51} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'UNK:plan-1': 52} Unresolved non-hydrogen planarities: 52 Chain: "k" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 370 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'TRANS': 73} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'UNK:plan-1': 74} Unresolved non-hydrogen planarities: 74 Chain: "l" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "o" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 296 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 1, 'TRANS': 56} Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 170 Chain: "p" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1039 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'TRANS': 168} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'UNK:plan-1': 102, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 134 Chain: "q" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 696 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 9, 'TRANS': 128} Unresolved non-hydrogen bonds: 487 Unresolved non-hydrogen angles: 633 Unresolved non-hydrogen dihedrals: 426 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 6, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 308 Chain: "G" Number of atoms: 4151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 4151 Classifications: {'peptide': 688} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 347} Link IDs: {'PTRANS': 32, 'TRANS': 655} Unresolved non-hydrogen bonds: 1155 Unresolved non-hydrogen angles: 1485 Unresolved non-hydrogen dihedrals: 893 Unresolved non-hydrogen chiralities: 151 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 7, 'TYR:plan': 8, 'ASN:plan1': 18, 'TRP:plan': 2, 'ASP:plan': 34, 'PHE:plan': 8, 'GLU:plan': 26, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 583 Chain: "s" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 234 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 3, 'TRANS': 37} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "Q" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 749 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 6, 'TRANS': 116} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 121 Chain: "R" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 638 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 89} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 43 Chain: "r" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 575 Classifications: {'peptide': 88} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 45} Link IDs: {'PTRANS': 11, 'TRANS': 76} Chain breaks: 1 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "h" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 822 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 9, 'TRANS': 124} Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 207 Chain: "d" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 803 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 6, 'TRANS': 106} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'UNK:plan-1': 19, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "X" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1170 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 12, 'TRANS': 151} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 97 Chain: "m" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 904 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 110} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "n" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1124 Classifications: {'peptide': 166} Incomplete info: {'backbone_only': 27, 'truncation_to_alanine': 48} Link IDs: {'PTRANS': 14, 'TRANS': 151} Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 5, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 206 Chain: "Z" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 920 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 131} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 2, 'UNK:plan-1': 43, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1423 SG CYS B 119 93.584 92.750 204.006 1.00 22.96 S ATOM 925 SG CYS B 55 87.645 95.364 204.979 1.00 23.87 S ATOM 919 SG CYS B 54 88.195 89.635 202.118 1.00 23.99 S ATOM 1653 SG CYS B 149 89.771 90.254 208.421 1.00 23.28 S ATOM 7314 SG CYS E 103 103.847 42.809 259.780 1.00 76.23 S ATOM 7342 SG CYS E 108 101.716 39.957 260.822 1.00 77.12 S ATOM 7529 SG CYS E 144 106.853 40.165 256.831 1.00 77.67 S ATOM 7549 SG CYS E 148 105.188 36.926 257.394 1.00 77.41 S ATOM 9676 SG CYS F 362 111.412 48.062 235.872 1.00 42.45 S ATOM 9696 SG CYS F 365 107.518 48.475 240.613 1.00 41.92 S ATOM 10020 SG CYS F 405 111.637 43.317 240.382 1.00 43.10 S ATOM 9657 SG CYS F 359 114.039 49.178 241.640 1.00 42.67 S ATOM 13476 SG CYS I 119 93.196 84.143 214.588 1.00 14.19 S ATOM 13450 SG CYS I 116 94.366 90.719 215.264 1.00 14.25 S ATOM 13497 SG CYS I 122 94.967 86.398 220.197 1.00 14.19 S ATOM 13224 SG CYS I 87 99.119 86.567 215.142 1.00 14.37 S ATOM 13526 SG CYS I 126 96.554 82.601 227.546 1.00 15.60 S ATOM 13197 SG CYS I 83 100.598 84.648 222.839 1.00 15.31 S ATOM 13155 SG CYS I 77 101.569 86.797 228.679 1.00 15.76 S ATOM 13174 SG CYS I 80 102.439 80.534 227.856 1.00 15.48 S ATOM 41303 SG CYS G 114 109.152 67.569 226.740 1.00 22.20 S ATOM 41242 SG CYS G 105 103.792 70.782 228.702 1.00 21.55 S ATOM 41263 SG CYS G 108 109.610 72.372 231.044 1.00 21.60 S ATOM 41635 SG CYS G 156 116.751 60.091 232.287 1.00 26.40 S ATOM 41612 SG CYS G 153 114.265 63.233 237.558 1.00 26.52 S ATOM 41659 SG CYS G 159 120.614 63.349 236.325 1.00 26.78 S ATOM 41989 SG CYS G 203 116.563 66.456 232.372 1.00 26.56 S ATOM 40748 SG CYS G 41 115.965 54.560 230.250 1.00 39.83 S ATOM 40834 SG CYS G 52 112.638 54.486 229.195 1.00 40.42 S ATOM 40859 SG CYS G 55 114.448 50.704 225.134 1.00 41.32 S ATOM 40960 SG CYS G 69 117.698 51.370 226.388 1.00 43.28 S ATOM 46021 SG CYS R 59 97.842 78.231 242.896 1.00 59.04 S ATOM 46175 SG CYS R 84 101.099 79.313 240.903 1.00 56.99 S ATOM 46197 SG CYS R 87 98.014 81.489 240.928 1.00 57.12 S Time building chain proxies: 25.16, per 1000 atoms: 0.48 Number of scatterers: 52703 At special positions: 0 Unit cell: (180.78, 191.82, 292.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 335 16.00 P 4 15.00 O 9467 8.00 N 9294 7.00 C 33574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.03 Simple disulfide: pdb=" SG CYS o 58 " - pdb=" SG CYS o 89 " distance=2.03 Simple disulfide: pdb=" SG CYS o 68 " - pdb=" SG CYS o 79 " distance=2.03 Simple disulfide: pdb=" SG CYS p 76 " - pdb=" SG CYS p 83 " distance=2.03 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.03 Simple disulfide: pdb=" SG CYS X 35 " - pdb=" SG CYS X 65 " distance=2.03 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.03 Simple disulfide: pdb=" SG CYS X 77 " - pdb=" SG CYS X 109 " distance=2.03 Simple disulfide: pdb=" SG CYS X 87 " - pdb=" SG CYS X 99 " distance=2.03 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: 16.17 Conformation dependent library (CDL) restraints added in 6.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb=" FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb=" FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb=" FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb=" FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb=" FES G 803 " pdb=" FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb=" FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb=" FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb=" FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb=" SF4 B 201 " pdb=" FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb=" FE2 SF4 B 201 " - pdb=" SG CYS B 55 " pdb=" FE3 SF4 B 201 " - pdb=" SG CYS B 54 " pdb=" FE4 SF4 B 201 " - pdb=" SG CYS B 149 " pdb=" SF4 F 502 " pdb=" FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb=" FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb=" FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb=" FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb=" SF4 G 801 " pdb=" FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb=" FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb=" FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb=" FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb=" FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb=" FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb=" FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb=" FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb=" SF4 I 201 " pdb=" FE2 SF4 I 201 " - pdb=" SG CYS I 116 " pdb=" FE3 SF4 I 201 " - pdb=" SG CYS I 122 " pdb=" FE4 SF4 I 201 " - pdb=" SG CYS I 87 " pdb=" FE1 SF4 I 201 " - pdb=" SG CYS I 119 " pdb=" SF4 I 202 " pdb=" FE1 SF4 I 202 " - pdb=" SG CYS I 126 " pdb=" FE3 SF4 I 202 " - pdb=" SG CYS I 77 " pdb=" FE4 SF4 I 202 " - pdb=" SG CYS I 80 " pdb=" FE2 SF4 I 202 " - pdb=" SG CYS I 83 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14720 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 293 helices and 25 sheets defined 48.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'A' and resid 3 through 22 removed outlier: 3.684A pdb=" N THR A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 71 removed outlier: 3.514A pdb=" N LEU A 57 " --> pdb=" O LYS A 54 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 62 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 63 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 64 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 66 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 67 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 71 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 Proline residue: A 76 - end of helix No H-bonds generated for 'chain 'A' and resid 73 through 78' Processing helix chain 'A' and resid 84 through 106 removed outlier: 4.235A pdb=" N THR A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.749A pdb=" N ARG B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 94 through 106 Proline residue: B 98 - end of helix removed outlier: 3.753A pdb=" N ARG B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 102 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 153 through 158 removed outlier: 4.162A pdb=" N TYR B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'C' and resid 19 through 22 No H-bonds generated for 'chain 'C' and resid 19 through 22' Processing helix chain 'C' and resid 25 through 32 removed outlier: 4.478A pdb=" N ALA C 30 " --> pdb=" O GLY C 26 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C 32 " --> pdb=" O TYR C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 127 through 137 Processing helix chain 'D' and resid 8 through 13 Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.508A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 93' Processing helix chain 'D' and resid 100 through 104 removed outlier: 4.058A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 104' Processing helix chain 'D' and resid 116 through 126 Processing helix chain 'D' and resid 132 through 161 removed outlier: 3.778A pdb=" N HIS D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N HIS D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 184 removed outlier: 3.664A pdb=" N MET D 170 " --> pdb=" O PRO D 166 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 226 removed outlier: 3.995A pdb=" N TYR D 212 " --> pdb=" O MET D 208 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU D 225 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 249 through 253 Processing helix chain 'D' and resid 293 through 305 removed outlier: 3.813A pdb=" N ARG D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 351 Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.616A pdb=" N ALA D 400 " --> pdb=" O PHE D 396 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 3.784A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 37 Processing helix chain 'E' and resid 43 through 57 removed outlier: 3.647A pdb=" N ALA E 46 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix removed outlier: 3.654A pdb=" N GLN E 55 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG E 56 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN E 57 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 72 Processing helix chain 'E' and resid 77 through 86 Processing helix chain 'E' and resid 106 through 109 No H-bonds generated for 'chain 'E' and resid 106 through 109' Processing helix chain 'E' and resid 114 through 124 Processing helix chain 'E' and resid 166 through 175 removed outlier: 3.738A pdb=" N GLU E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 39 Processing helix chain 'F' and resid 45 through 50 removed outlier: 3.513A pdb=" N LEU F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 63 removed outlier: 3.505A pdb=" N VAL F 60 " --> pdb=" O ILE F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 83 removed outlier: 4.126A pdb=" N SER F 80 " --> pdb=" O GLY F 76 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN F 83 " --> pdb=" O TRP F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 110 Processing helix chain 'F' and resid 116 through 129 removed outlier: 3.715A pdb=" N GLY F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA F 128 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 159 removed outlier: 3.565A pdb=" N ASN F 148 " --> pdb=" O ASN F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 197 removed outlier: 3.678A pdb=" N ILE F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 236 removed outlier: 3.621A pdb=" N VAL F 230 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER F 231 " --> pdb=" O THR F 227 " (cutoff:3.500A) Proline residue: F 232 - end of helix Processing helix chain 'F' and resid 239 through 244 Processing helix chain 'F' and resid 276 through 282 removed outlier: 3.640A pdb=" N GLU F 281 " --> pdb=" O LYS F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 325 removed outlier: 3.841A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 321 through 325' Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 363 through 366 No H-bonds generated for 'chain 'F' and resid 363 through 366' Processing helix chain 'F' and resid 369 through 381 removed outlier: 3.666A pdb=" N LYS F 374 " --> pdb=" O ASP F 370 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG F 378 " --> pdb=" O LYS F 374 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 400 removed outlier: 3.650A pdb=" N TRP F 393 " --> pdb=" O ILE F 389 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU F 394 " --> pdb=" O ASP F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 410 No H-bonds generated for 'chain 'F' and resid 407 through 410' Processing helix chain 'F' and resid 413 through 416 No H-bonds generated for 'chain 'F' and resid 413 through 416' Processing helix chain 'F' and resid 424 through 437 removed outlier: 3.634A pdb=" N ARG F 429 " --> pdb=" O GLU F 425 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE F 433 " --> pdb=" O ARG F 429 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 9 No H-bonds generated for 'chain 'H' and resid 7 through 9' Processing helix chain 'H' and resid 11 through 18 Processing helix chain 'H' and resid 20 through 30 removed outlier: 3.819A pdb=" N LEU H 28 " --> pdb=" O GLU H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 56 removed outlier: 3.525A pdb=" N PHE H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 86 removed outlier: 4.049A pdb=" N LEU H 81 " --> pdb=" O MET H 77 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 110 removed outlier: 3.588A pdb=" N SER H 109 " --> pdb=" O MET H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 122 removed outlier: 4.277A pdb=" N TRP H 118 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER H 119 " --> pdb=" O ILE H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 156 removed outlier: 3.551A pdb=" N ALA H 135 " --> pdb=" O GLY H 131 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN H 138 " --> pdb=" O ARG H 134 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR H 142 " --> pdb=" O GLN H 138 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU H 143 " --> pdb=" O THR H 139 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 167 No H-bonds generated for 'chain 'H' and resid 164 through 167' Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 188 removed outlier: 3.878A pdb=" N MET H 183 " --> pdb=" O TRP H 179 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE H 186 " --> pdb=" O ALA H 182 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE H 187 " --> pdb=" O MET H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 241 removed outlier: 3.756A pdb=" N PHE H 224 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA H 226 " --> pdb=" O LEU H 222 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU H 227 " --> pdb=" O PHE H 223 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA H 229 " --> pdb=" O MET H 225 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE H 231 " --> pdb=" O GLU H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 276 removed outlier: 3.622A pdb=" N ASN H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE H 261 " --> pdb=" O ILE H 257 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU H 266 " --> pdb=" O LYS H 262 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER H 269 " --> pdb=" O LEU H 265 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG H 274 " --> pdb=" O PHE H 270 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA H 275 " --> pdb=" O LEU H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 288 Processing helix chain 'H' and resid 294 through 310 removed outlier: 3.580A pdb=" N ALA H 299 " --> pdb=" O PRO H 295 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER H 306 " --> pdb=" O MET H 302 " (cutoff:3.500A) Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 15 through 25 removed outlier: 4.034A pdb=" N ASP I 19 " --> pdb=" O LYS I 15 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG I 20 " --> pdb=" O SER I 16 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 42 removed outlier: 3.685A pdb=" N MET I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR I 37 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE I 42 " --> pdb=" O LEU I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 144 through 147 No H-bonds generated for 'chain 'I' and resid 144 through 147' Processing helix chain 'I' and resid 156 through 160 Processing helix chain 'I' and resid 162 through 171 removed outlier: 3.782A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN I 170 " --> pdb=" O ALA I 166 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA I 171 " --> pdb=" O ALA I 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 21 removed outlier: 3.533A pdb=" N VAL J 11 " --> pdb=" O PHE J 7 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE J 12 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE J 17 " --> pdb=" O PHE J 13 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY J 19 " --> pdb=" O MET J 15 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.542A pdb=" N GLY J 32 " --> pdb=" O TYR J 28 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU J 33 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL J 44 " --> pdb=" O GLY J 40 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 58 removed outlier: 4.347A pdb=" N VAL J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE J 57 " --> pdb=" O GLY J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 74 removed outlier: 3.533A pdb=" N TYR J 70 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA J 73 " --> pdb=" O GLY J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 97 Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.860A pdb=" N TYR J 105 " --> pdb=" O PHE J 101 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR J 106 " --> pdb=" O PHE J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 removed outlier: 3.722A pdb=" N ILE J 155 " --> pdb=" O THR J 151 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL J 165 " --> pdb=" O LEU J 161 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET J 169 " --> pdb=" O VAL J 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 20 removed outlier: 3.506A pdb=" N MET K 9 " --> pdb=" O TYR K 5 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET K 10 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU K 20 " --> pdb=" O LEU K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 50 removed outlier: 3.680A pdb=" N THR K 47 " --> pdb=" O MET K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 84 Proline residue: K 60 - end of helix removed outlier: 3.533A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS K 69 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU K 70 " --> pdb=" O ALA K 67 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA K 71 " --> pdb=" O ALA K 68 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA K 72 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU K 73 " --> pdb=" O GLU K 70 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY K 74 " --> pdb=" O ALA K 71 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER K 76 " --> pdb=" O LEU K 73 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR K 84 " --> pdb=" O VAL K 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 20 removed outlier: 3.970A pdb=" N LEU L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL L 10 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU L 15 " --> pdb=" O THR L 11 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 56 removed outlier: 3.641A pdb=" N LYS L 37 " --> pdb=" O PRO L 33 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR L 42 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE L 45 " --> pdb=" O SER L 41 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 87 through 106 Proline residue: L 91 - end of helix removed outlier: 4.143A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 removed outlier: 3.744A pdb=" N PHE L 118 " --> pdb=" O ILE L 114 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS L 119 " --> pdb=" O ASN L 115 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR L 120 " --> pdb=" O LYS L 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU L 121 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU L 122 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU L 123 " --> pdb=" O LYS L 119 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 150 removed outlier: 3.833A pdb=" N GLY L 143 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 155 No H-bonds generated for 'chain 'L' and resid 152 through 155' Processing helix chain 'L' and resid 162 through 192 removed outlier: 3.915A pdb=" N ILE L 172 " --> pdb=" O ALA L 168 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN L 175 " --> pdb=" O ALA L 171 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE L 177 " --> pdb=" O LEU L 173 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY L 178 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE L 180 " --> pdb=" O ARG L 176 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU L 190 " --> pdb=" O MET L 186 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR L 191 " --> pdb=" O ALA L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 201 No H-bonds generated for 'chain 'L' and resid 198 through 201' Processing helix chain 'L' and resid 210 through 213 No H-bonds generated for 'chain 'L' and resid 210 through 213' Processing helix chain 'L' and resid 216 through 222 removed outlier: 3.569A pdb=" N GLY L 222 " --> pdb=" O LEU L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 235 through 238 Processing helix chain 'L' and resid 241 through 250 removed outlier: 3.883A pdb=" N HIS L 248 " --> pdb=" O SER L 244 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 262 Processing helix chain 'L' and resid 265 through 269 removed outlier: 3.920A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 265 through 269' Processing helix chain 'L' and resid 271 through 279 removed outlier: 3.865A pdb=" N LEU L 278 " --> pdb=" O GLN L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 283 through 286 No H-bonds generated for 'chain 'L' and resid 283 through 286' Processing helix chain 'L' and resid 289 through 292 Processing helix chain 'L' and resid 298 through 318 removed outlier: 4.354A pdb=" N ILE L 302 " --> pdb=" O ILE L 298 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER L 307 " --> pdb=" O ALA L 303 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER L 308 " --> pdb=" O PHE L 304 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU L 312 " --> pdb=" O SER L 308 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE L 317 " --> pdb=" O MET L 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 349 removed outlier: 3.904A pdb=" N ILE L 329 " --> pdb=" O ALA L 325 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA L 337 " --> pdb=" O ALA L 333 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET L 338 " --> pdb=" O PHE L 334 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU L 339 " --> pdb=" O PHE L 335 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET L 341 " --> pdb=" O ALA L 337 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE L 346 " --> pdb=" O CYS L 342 " (cutoff:3.500A) Processing helix chain 'L' and resid 369 through 380 Processing helix chain 'L' and resid 392 through 400 Processing helix chain 'L' and resid 406 through 427 removed outlier: 3.568A pdb=" N THR L 412 " --> pdb=" O ALA L 408 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA L 415 " --> pdb=" O MET L 411 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER L 417 " --> pdb=" O LEU L 413 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE L 421 " --> pdb=" O SER L 417 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR L 422 " --> pdb=" O PHE L 418 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER L 423 " --> pdb=" O THR L 419 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 462 removed outlier: 3.844A pdb=" N ASN L 452 " --> pdb=" O PRO L 448 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER L 453 " --> pdb=" O LEU L 449 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG L 456 " --> pdb=" O ASN L 452 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE L 459 " --> pdb=" O LYS L 455 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY L 460 " --> pdb=" O ARG L 456 " (cutoff:3.500A) Processing helix chain 'L' and resid 468 through 471 No H-bonds generated for 'chain 'L' and resid 468 through 471' Processing helix chain 'L' and resid 489 through 508 removed outlier: 3.833A pdb=" N THR L 494 " --> pdb=" O ALA L 490 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 532 No H-bonds generated for 'chain 'L' and resid 529 through 532' Processing helix chain 'L' and resid 537 through 546 removed outlier: 3.793A pdb=" N ASN L 541 " --> pdb=" O ALA L 537 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER L 545 " --> pdb=" O ASN L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 577 removed outlier: 4.135A pdb=" N ILE L 561 " --> pdb=" O TRP L 557 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU L 562 " --> pdb=" O LEU L 558 " (cutoff:3.500A) Proline residue: L 563 - end of helix removed outlier: 4.054A pdb=" N SER L 574 " --> pdb=" O GLN L 570 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR L 575 " --> pdb=" O MET L 571 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU L 576 " --> pdb=" O LYS L 572 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 600 removed outlier: 3.626A pdb=" N SER L 590 " --> pdb=" O LEU L 586 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE L 591 " --> pdb=" O TYR L 587 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU L 592 " --> pdb=" O PHE L 588 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE L 593 " --> pdb=" O LEU L 589 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 17 removed outlier: 4.118A pdb=" N TRP M 16 " --> pdb=" O MET M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 41 removed outlier: 3.856A pdb=" N SER M 27 " --> pdb=" O TRP M 24 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR M 28 " --> pdb=" O VAL M 25 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA M 29 " --> pdb=" O ASN M 26 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N HIS M 30 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU M 32 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU M 33 " --> pdb=" O HIS M 30 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE M 36 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER M 38 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU M 39 " --> pdb=" O PHE M 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU M 41 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 79 removed outlier: 3.518A pdb=" N THR M 69 " --> pdb=" O LEU M 65 " (cutoff:3.500A) Proline residue: M 74 - end of helix removed outlier: 5.017A pdb=" N LEU M 77 " --> pdb=" O LEU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 111 removed outlier: 3.742A pdb=" N THR M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET M 98 " --> pdb=" O LEU M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 122 removed outlier: 3.545A pdb=" N ILE M 120 " --> pdb=" O ILE M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 134 Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 142 through 170 removed outlier: 3.679A pdb=" N PHE M 149 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU M 150 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU M 154 " --> pdb=" O LEU M 150 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA M 155 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY M 156 " --> pdb=" O TYR M 152 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 4.032A pdb=" N VAL M 162 " --> pdb=" O LEU M 158 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE M 165 " --> pdb=" O LEU M 161 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR M 166 " --> pdb=" O VAL M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 203 removed outlier: 4.272A pdb=" N PHE M 194 " --> pdb=" O TRP M 190 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET M 195 " --> pdb=" O SER M 191 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS M 199 " --> pdb=" O MET M 195 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 221 removed outlier: 3.822A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA M 219 " --> pdb=" O TRP M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 230 through 237 Processing helix chain 'M' and resid 243 through 249 removed outlier: 3.985A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 274 removed outlier: 3.593A pdb=" N MET M 263 " --> pdb=" O TYR M 259 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP M 267 " --> pdb=" O MET M 263 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N THR M 272 " --> pdb=" O GLY M 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 287 No H-bonds generated for 'chain 'M' and resid 284 through 287' Processing helix chain 'M' and resid 289 through 303 removed outlier: 4.466A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE M 298 " --> pdb=" O MET M 294 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU M 302 " --> pdb=" O ILE M 298 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE M 303 " --> pdb=" O VAL M 299 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.660A pdb=" N MET M 310 " --> pdb=" O PRO M 306 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA M 314 " --> pdb=" O MET M 310 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE M 317 " --> pdb=" O THR M 313 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY M 320 " --> pdb=" O MET M 316 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU M 321 " --> pdb=" O ILE M 317 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER M 324 " --> pdb=" O GLY M 320 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET M 325 " --> pdb=" O LEU M 321 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 355 through 363 Processing helix chain 'M' and resid 374 through 388 removed outlier: 3.988A pdb=" N PHE M 380 " --> pdb=" O ILE M 376 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL M 381 " --> pdb=" O GLY M 377 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER M 387 " --> pdb=" O MET M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 402 removed outlier: 4.191A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY M 397 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL M 398 " --> pdb=" O LEU M 395 " (cutoff:3.500A) Processing helix chain 'M' and resid 404 through 415 removed outlier: 4.284A pdb=" N TYR M 409 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR M 414 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 446 removed outlier: 3.867A pdb=" N MET M 437 " --> pdb=" O GLU M 433 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE M 441 " --> pdb=" O MET M 437 " (cutoff:3.500A) Proline residue: M 443 - end of helix Processing helix chain 'N' and resid 4 through 21 removed outlier: 3.502A pdb=" N ILE N 13 " --> pdb=" O ILE N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 45 removed outlier: 3.524A pdb=" N TRP N 30 " --> pdb=" O TRP N 26 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN N 36 " --> pdb=" O GLY N 32 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU N 38 " --> pdb=" O GLU N 34 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA N 39 " --> pdb=" O MET N 35 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE N 41 " --> pdb=" O MET N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 79 removed outlier: 3.756A pdb=" N THR N 62 " --> pdb=" O LYS N 58 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR N 65 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA N 73 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 105 removed outlier: 3.885A pdb=" N ALA N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS N 105 " --> pdb=" O ALA N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 111 No H-bonds generated for 'chain 'N' and resid 109 through 111' Processing helix chain 'N' and resid 113 through 121 removed outlier: 4.542A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY N 121 " --> pdb=" O GLU N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 132 removed outlier: 3.595A pdb=" N ILE N 129 " --> pdb=" O SER N 125 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU N 130 " --> pdb=" O SER N 126 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU N 131 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR N 132 " --> pdb=" O LEU N 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 125 through 132' Processing helix chain 'N' and resid 134 through 144 Proline residue: N 138 - end of helix removed outlier: 3.528A pdb=" N VAL N 141 " --> pdb=" O PRO N 138 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR N 143 " --> pdb=" O SER N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 153 No H-bonds generated for 'chain 'N' and resid 151 through 153' Processing helix chain 'N' and resid 155 through 166 removed outlier: 3.560A pdb=" N SER N 161 " --> pdb=" O LEU N 157 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE N 162 " --> pdb=" O SER N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 195 removed outlier: 3.521A pdb=" N ILE N 184 " --> pdb=" O ALA N 180 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY N 188 " --> pdb=" O ILE N 184 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA N 192 " --> pdb=" O GLY N 188 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) Proline residue: N 195 - end of helix Processing helix chain 'N' and resid 201 through 218 removed outlier: 3.685A pdb=" N MET N 215 " --> pdb=" O MET N 211 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE N 216 " --> pdb=" O THR N 212 " (cutoff:3.500A) Processing helix chain 'N' and resid 240 through 251 removed outlier: 3.667A pdb=" N THR N 247 " --> pdb=" O LEU N 243 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER N 250 " --> pdb=" O ALA N 246 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 273 removed outlier: 3.858A pdb=" N MET N 265 " --> pdb=" O MET N 261 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE N 267 " --> pdb=" O LYS N 263 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN N 273 " --> pdb=" O GLU N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 296 removed outlier: 3.697A pdb=" N PHE N 281 " --> pdb=" O ILE N 277 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR N 285 " --> pdb=" O PHE N 281 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TYR N 293 " --> pdb=" O ASN N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 298 through 301 No H-bonds generated for 'chain 'N' and resid 298 through 301' Processing helix chain 'N' and resid 325 through 331 removed outlier: 3.914A pdb=" N MET N 329 " --> pdb=" O PHE N 325 " (cutoff:3.500A) Processing helix chain 'N' and resid 340 through 344 Processing helix chain 'O' and resid 36 through 42 Processing helix chain 'O' and resid 58 through 61 No H-bonds generated for 'chain 'O' and resid 58 through 61' Processing helix chain 'O' and resid 71 through 74 No H-bonds generated for 'chain 'O' and resid 71 through 74' Processing helix chain 'O' and resid 80 through 84 Processing helix chain 'O' and resid 95 through 116 Processing helix chain 'O' and resid 128 through 140 removed outlier: 5.477A pdb=" N PHE O 132 " --> pdb=" O TYR O 129 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU O 135 " --> pdb=" O PHE O 132 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU O 136 " --> pdb=" O VAL O 133 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA O 137 " --> pdb=" O PHE O 134 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG O 140 " --> pdb=" O ALA O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 162 removed outlier: 3.684A pdb=" N ASP O 150 " --> pdb=" O LYS O 146 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL O 155 " --> pdb=" O HIS O 151 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL O 158 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE O 160 " --> pdb=" O LYS O 156 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU O 162 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 177 through 185 removed outlier: 4.432A pdb=" N GLN O 180 " --> pdb=" O PRO O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 207 Processing helix chain 'O' and resid 210 through 215 Processing helix chain 'O' and resid 231 through 240 removed outlier: 3.795A pdb=" N VAL O 235 " --> pdb=" O ALA O 231 " (cutoff:3.500A) Processing helix chain 'O' and resid 255 through 264 Processing helix chain 'O' and resid 266 through 269 No H-bonds generated for 'chain 'O' and resid 266 through 269' Processing helix chain 'O' and resid 287 through 298 removed outlier: 4.090A pdb=" N GLN O 291 " --> pdb=" O HIS O 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 40 removed outlier: 3.582A pdb=" N UNK P 40 " --> pdb=" O UNK P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 59 removed outlier: 6.384A pdb=" N UNK P 58 " --> pdb=" O UNK P 54 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N UNK P 59 " --> pdb=" O UNK P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 123 removed outlier: 3.554A pdb=" N UNK P 123 " --> pdb=" O UNK P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 158 Processing helix chain 'P' and resid 177 through 183 removed outlier: 4.355A pdb=" N UNK P 182 " --> pdb=" O UNK P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 219 removed outlier: 3.718A pdb=" N UNK P 212 " --> pdb=" O UNK P 208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N UNK P 218 " --> pdb=" O UNK P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 249 removed outlier: 3.541A pdb=" N UNK P 248 " --> pdb=" O UNK P 244 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N UNK P 249 " --> pdb=" O UNK P 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 282 through 289 Processing helix chain 'P' and resid 314 through 317 No H-bonds generated for 'chain 'P' and resid 314 through 317' Processing helix chain 'S' and resid 32 through 37 Processing helix chain 'S' and resid 40 through 46 removed outlier: 4.078A pdb=" N LYS S 45 " --> pdb=" O VAL S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 94 removed outlier: 3.580A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 21 removed outlier: 3.649A pdb=" N VAL T 15 " --> pdb=" O ILE T 11 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU T 16 " --> pdb=" O LYS T 12 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 58 removed outlier: 3.904A pdb=" N VAL T 48 " --> pdb=" O SER T 44 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE T 58 " --> pdb=" O MET T 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.030A pdb=" N GLU T 68 " --> pdb=" O ASP T 64 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 64 through 69' Processing helix chain 'T' and resid 73 through 81 Processing helix chain 'U' and resid 8 through 20 removed outlier: 3.570A pdb=" N VAL U 15 " --> pdb=" O ILE U 11 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU U 16 " --> pdb=" O LYS U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 58 removed outlier: 4.071A pdb=" N VAL U 48 " --> pdb=" O SER U 44 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE U 58 " --> pdb=" O MET U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 67 No H-bonds generated for 'chain 'U' and resid 64 through 67' Processing helix chain 'U' and resid 73 through 83 Processing helix chain 'V' and resid 22 through 34 removed outlier: 3.731A pdb=" N LEU V 31 " --> pdb=" O TYR V 27 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP V 32 " --> pdb=" O THR V 28 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 removed outlier: 3.614A pdb=" N GLU V 48 " --> pdb=" O ARG V 44 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN V 49 " --> pdb=" O LYS V 45 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE V 50 " --> pdb=" O TYR V 46 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU V 53 " --> pdb=" O GLN V 49 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET V 57 " --> pdb=" O GLU V 53 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA V 60 " --> pdb=" O SER V 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 65 through 68 No H-bonds generated for 'chain 'V' and resid 65 through 68' Processing helix chain 'V' and resid 76 through 84 Processing helix chain 'V' and resid 86 through 95 Processing helix chain 'W' and resid 26 through 39 Processing helix chain 'W' and resid 44 through 47 No H-bonds generated for 'chain 'W' and resid 44 through 47' Processing helix chain 'W' and resid 55 through 67 removed outlier: 3.609A pdb=" N VAL W 62 " --> pdb=" O GLY W 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG W 63 " --> pdb=" O ARG W 59 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET W 65 " --> pdb=" O LYS W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 88 removed outlier: 3.700A pdb=" N MET W 87 " --> pdb=" O ILE W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 123 Processing helix chain 'Y' and resid 2 through 9 removed outlier: 3.975A pdb=" N TRP Y 9 " --> pdb=" O LEU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 20 through 40 removed outlier: 3.626A pdb=" N ILE Y 27 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA Y 30 " --> pdb=" O SER Y 26 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR Y 38 " --> pdb=" O VAL Y 34 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER Y 39 " --> pdb=" O VAL Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 78 removed outlier: 3.807A pdb=" N TYR Y 58 " --> pdb=" O ARG Y 54 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE Y 60 " --> pdb=" O GLY Y 56 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR Y 61 " --> pdb=" O ARG Y 57 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS Y 74 " --> pdb=" O GLY Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 90 through 96 Processing helix chain 'Y' and resid 98 through 101 removed outlier: 3.746A pdb=" N GLY Y 101 " --> pdb=" O LEU Y 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 98 through 101' Processing helix chain 'Y' and resid 109 through 126 removed outlier: 4.181A pdb=" N ALA Y 115 " --> pdb=" O ALA Y 111 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR Y 116 " --> pdb=" O ALA Y 112 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA Y 122 " --> pdb=" O GLY Y 118 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL Y 124 " --> pdb=" O THR Y 120 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS Y 125 " --> pdb=" O ALA Y 121 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 10 Proline residue: a 7 - end of helix Processing helix chain 'a' and resid 12 through 30 removed outlier: 4.920A pdb=" N PHE a 17 " --> pdb=" O GLY a 13 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.695A pdb=" N ALA a 24 " --> pdb=" O GLY a 20 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N HIS a 27 " --> pdb=" O THR a 23 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE a 29 " --> pdb=" O ARG a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 53 Processing helix chain 'b' and resid 6 through 13 removed outlier: 3.818A pdb=" N ASN b 10 " --> pdb=" O ALA b 6 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL b 11 " --> pdb=" O PHE b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 34 removed outlier: 3.604A pdb=" N PHE b 22 " --> pdb=" O LEU b 18 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL b 29 " --> pdb=" O ALA b 25 " (cutoff:3.500A) Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 3.625A pdb=" N LEU b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET b 43 " --> pdb=" O LYS b 39 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE b 44 " --> pdb=" O TYR b 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 45 removed outlier: 3.721A pdb=" N SER c 24 " --> pdb=" O THR c 20 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL c 25 " --> pdb=" O LEU c 21 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN c 34 " --> pdb=" O TYR c 30 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS c 43 " --> pdb=" O VAL c 39 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 42 removed outlier: 3.617A pdb=" N GLU e 38 " --> pdb=" O ALA e 34 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU e 41 " --> pdb=" O LYS e 37 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 67 removed outlier: 3.843A pdb=" N ASP e 61 " --> pdb=" O ILE e 57 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE e 62 " --> pdb=" O GLU e 58 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU e 66 " --> pdb=" O PHE e 62 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 84 Processing helix chain 'f' and resid 6 through 9 No H-bonds generated for 'chain 'f' and resid 6 through 9' Processing helix chain 'f' and resid 15 through 26 Processing helix chain 'f' and resid 29 through 31 No H-bonds generated for 'chain 'f' and resid 29 through 31' Processing helix chain 'g' and resid 51 through 58 removed outlier: 3.778A pdb=" N TRP g 56 " --> pdb=" O ALA g 52 " (cutoff:3.500A) Processing helix chain 'g' and resid 61 through 67 removed outlier: 3.634A pdb=" N GLY g 65 " --> pdb=" O VAL g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 77 No H-bonds generated for 'chain 'g' and resid 74 through 77' Processing helix chain 'g' and resid 88 through 102 removed outlier: 3.863A pdb=" N ARG g 95 " --> pdb=" O ARG g 91 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU g 96 " --> pdb=" O GLU g 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS g 98 " --> pdb=" O GLU g 94 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR g 99 " --> pdb=" O ARG g 95 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 23 Processing helix chain 'i' and resid 43 through 49 Processing helix chain 'i' and resid 61 through 73 removed outlier: 3.637A pdb=" N UNK i 65 " --> pdb=" O UNK i 61 " (cutoff:3.500A) Processing helix chain 'i' and resid 76 through 86 removed outlier: 3.584A pdb=" N UNK i 85 " --> pdb=" O UNK i 81 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N UNK i 86 " --> pdb=" O UNK i 82 " (cutoff:3.500A) Processing helix chain 'j' and resid 21 through 38 removed outlier: 3.873A pdb=" N UNK j 28 " --> pdb=" O UNK j 24 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N UNK j 31 " --> pdb=" O UNK j 27 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N UNK j 32 " --> pdb=" O UNK j 28 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N UNK j 33 " --> pdb=" O UNK j 29 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N UNK j 36 " --> pdb=" O UNK j 32 " (cutoff:3.500A) Processing helix chain 'k' and resid 32 through 37 Processing helix chain 'k' and resid 72 through 84 removed outlier: 3.599A pdb=" N UNK k 77 " --> pdb=" O UNK k 73 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N UNK k 83 " --> pdb=" O UNK k 79 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N UNK k 84 " --> pdb=" O UNK k 80 " (cutoff:3.500A) Processing helix chain 'l' and resid 22 through 27 removed outlier: 3.639A pdb=" N UNK l 26 " --> pdb=" O UNK l 22 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N UNK l 27 " --> pdb=" O UNK l 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 22 through 27' Processing helix chain 'l' and resid 100 through 118 removed outlier: 3.848A pdb=" N UNK l 107 " --> pdb=" O UNK l 103 " (cutoff:3.500A) Processing helix chain 'o' and resid 62 through 70 Processing helix chain 'o' and resid 81 through 113 removed outlier: 3.571A pdb=" N CYS o 89 " --> pdb=" O ASP o 85 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 39 removed outlier: 4.067A pdb=" N UNK p 38 " --> pdb=" O UNK p 34 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 53 Processing helix chain 'p' and resid 81 through 114 removed outlier: 3.528A pdb=" N PHE p 85 " --> pdb=" O VAL p 81 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA p 87 " --> pdb=" O CYS p 83 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU p 100 " --> pdb=" O LYS p 96 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL p 102 " --> pdb=" O ASP p 98 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN p 103 " --> pdb=" O GLN p 99 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN p 114 " --> pdb=" O LYS p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 127 through 140 removed outlier: 3.809A pdb=" N LYS p 136 " --> pdb=" O THR p 132 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA p 137 " --> pdb=" O GLN p 133 " (cutoff:3.500A) Processing helix chain 'p' and resid 151 through 171 removed outlier: 3.529A pdb=" N UNK p 155 " --> pdb=" O UNK p 151 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK p 171 " --> pdb=" O UNK p 167 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 16 Processing helix chain 'q' and resid 22 through 29 Processing helix chain 'q' and resid 86 through 89 No H-bonds generated for 'chain 'q' and resid 86 through 89' Processing helix chain 'G' and resid 26 through 33 removed outlier: 3.770A pdb=" N LYS G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 97 removed outlier: 3.604A pdb=" N LYS G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 122 removed outlier: 3.680A pdb=" N MET G 122 " --> pdb=" O ASP G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 165 Processing helix chain 'G' and resid 199 through 202 No H-bonds generated for 'chain 'G' and resid 199 through 202' Processing helix chain 'G' and resid 265 through 268 No H-bonds generated for 'chain 'G' and resid 265 through 268' Processing helix chain 'G' and resid 272 through 276 removed outlier: 3.912A pdb=" N ARG G 276 " --> pdb=" O GLY G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 307 removed outlier: 4.086A pdb=" N MET G 306 " --> pdb=" O ARG G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 335 removed outlier: 3.534A pdb=" N ASP G 333 " --> pdb=" O ILE G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 362 No H-bonds generated for 'chain 'G' and resid 359 through 362' Processing helix chain 'G' and resid 389 through 400 Processing helix chain 'G' and resid 426 through 433 Processing helix chain 'G' and resid 441 through 444 No H-bonds generated for 'chain 'G' and resid 441 through 444' Processing helix chain 'G' and resid 455 through 458 No H-bonds generated for 'chain 'G' and resid 455 through 458' Processing helix chain 'G' and resid 463 through 478 Processing helix chain 'G' and resid 499 through 505 removed outlier: 3.543A pdb=" N LEU G 503 " --> pdb=" O GLN G 499 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP G 504 " --> pdb=" O VAL G 500 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 596 through 606 removed outlier: 3.848A pdb=" N ILE G 600 " --> pdb=" O ASP G 596 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG G 601 " --> pdb=" O TRP G 597 " (cutoff:3.500A) Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 643 through 649 removed outlier: 3.517A pdb=" N LEU G 648 " --> pdb=" O GLN G 644 " (cutoff:3.500A) Processing helix chain 'G' and resid 682 through 692 removed outlier: 3.689A pdb=" N LYS G 686 " --> pdb=" O GLN G 682 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR G 692 " --> pdb=" O VAL G 688 " (cutoff:3.500A) Processing helix chain 's' and resid 51 through 59 removed outlier: 3.519A pdb=" N LEU s 56 " --> pdb=" O LEU s 52 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER s 59 " --> pdb=" O ASN s 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 99 Processing helix chain 'Q' and resid 118 through 120 No H-bonds generated for 'chain 'Q' and resid 118 through 120' Processing helix chain 'R' and resid 26 through 28 No H-bonds generated for 'chain 'R' and resid 26 through 28' Processing helix chain 'R' and resid 40 through 46 removed outlier: 4.095A pdb=" N ALA R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 4 through 13 removed outlier: 4.020A pdb=" N TRP r 9 " --> pdb=" O ARG r 5 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU r 10 " --> pdb=" O PHE r 6 " (cutoff:3.500A) Processing helix chain 'h' and resid 16 through 31 removed outlier: 3.555A pdb=" N PHE h 21 " --> pdb=" O TYR h 17 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU h 22 " --> pdb=" O ASP h 18 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU h 30 " --> pdb=" O ARG h 26 " (cutoff:3.500A) Processing helix chain 'h' and resid 34 through 44 removed outlier: 3.673A pdb=" N THR h 41 " --> pdb=" O ALA h 37 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE h 43 " --> pdb=" O GLY h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 71 through 76 Processing helix chain 'h' and resid 91 through 114 Processing helix chain 'd' and resid 29 through 48 removed outlier: 3.561A pdb=" N VAL d 34 " --> pdb=" O ARG d 30 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP d 45 " --> pdb=" O SER d 41 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASN d 46 " --> pdb=" O GLY d 42 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA d 47 " --> pdb=" O LEU d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 61 through 97 removed outlier: 3.787A pdb=" N PHE d 68 " --> pdb=" O TYR d 64 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA d 84 " --> pdb=" O ASP d 80 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE d 94 " --> pdb=" O MET d 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 22 through 27 removed outlier: 3.774A pdb=" N ALA X 26 " --> pdb=" O SER X 22 " (cutoff:3.500A) Processing helix chain 'X' and resid 30 through 32 No H-bonds generated for 'chain 'X' and resid 30 through 32' Processing helix chain 'X' and resid 37 through 48 Processing helix chain 'X' and resid 57 through 75 removed outlier: 3.542A pdb=" N LEU X 61 " --> pdb=" O GLU X 57 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU X 67 " --> pdb=" O ASN X 63 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN X 72 " --> pdb=" O GLU X 68 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE X 73 " --> pdb=" O PHE X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 90 Processing helix chain 'X' and resid 100 through 105 removed outlier: 3.834A pdb=" N GLN X 105 " --> pdb=" O LYS X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 110 through 112 No H-bonds generated for 'chain 'X' and resid 110 through 112' Processing helix chain 'm' and resid 28 through 48 removed outlier: 3.841A pdb=" N LEU m 36 " --> pdb=" O GLN m 32 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA m 37 " --> pdb=" O ALA m 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU m 45 " --> pdb=" O ARG m 41 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 72 removed outlier: 3.821A pdb=" N ARG m 71 " --> pdb=" O TRP m 67 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 91 Processing helix chain 'm' and resid 95 through 116 removed outlier: 3.614A pdb=" N TRP m 100 " --> pdb=" O PRO m 96 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR m 101 " --> pdb=" O LEU m 97 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR m 102 " --> pdb=" O VAL m 98 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL m 103 " --> pdb=" O PHE m 99 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS m 105 " --> pdb=" O TYR m 101 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR m 106 " --> pdb=" O TYR m 102 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS m 113 " --> pdb=" O ASP m 109 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU m 114 " --> pdb=" O ARG m 110 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN m 116 " --> pdb=" O GLU m 112 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 29 removed outlier: 3.795A pdb=" N GLU n 27 " --> pdb=" O LEU n 23 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER n 28 " --> pdb=" O ARG n 24 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP n 29 " --> pdb=" O HIS n 25 " (cutoff:3.500A) Processing helix chain 'n' and resid 33 through 51 removed outlier: 4.286A pdb=" N GLU n 49 " --> pdb=" O ALA n 45 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 58 through 65 Processing helix chain 'n' and resid 67 through 70 No H-bonds generated for 'chain 'n' and resid 67 through 70' Processing helix chain 'n' and resid 115 through 141 removed outlier: 3.594A pdb=" N GLN n 123 " --> pdb=" O ALA n 119 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER n 131 " --> pdb=" O LEU n 127 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'Z' and resid 33 through 69 removed outlier: 3.690A pdb=" N LYS Z 51 " --> pdb=" O TRP Z 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP Z 52 " --> pdb=" O SER Z 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU Z 62 " --> pdb=" O ARG Z 58 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG Z 67 " --> pdb=" O ASP Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 95 removed outlier: 3.835A pdb=" N GLU Z 77 " --> pdb=" O LEU Z 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS Z 78 " --> pdb=" O LEU Z 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL Z 82 " --> pdb=" O LYS Z 78 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 133 Processing sheet with id= A, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.370A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE B 144 " --> pdb=" O SER B 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 40 through 44 removed outlier: 4.067A pdb=" N VAL C 40 " --> pdb=" O CYS C 51 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 103 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 92 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP C 77 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU C 97 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LEU C 75 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 47 through 49 removed outlier: 3.569A pdb=" N LEU D 47 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET D 66 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 75 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 361 through 365 removed outlier: 4.000A pdb=" N GLY D 375 " --> pdb=" O LYS D 392 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 137 through 142 removed outlier: 7.226A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N MET E 153 " --> pdb=" O CYS E 103 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 220 through 224 removed outlier: 7.756A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'F' and resid 266 through 268 Processing sheet with id= H, first strand: chain 'I' and resid 64 through 67 removed outlier: 4.006A pdb=" N ALA I 66 " --> pdb=" O VAL I 132 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 92 through 98 removed outlier: 3.517A pdb=" N ARG I 108 " --> pdb=" O GLU I 95 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR I 106 " --> pdb=" O GLU I 97 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 60 through 63 removed outlier: 4.110A pdb=" N GLU L 60 " --> pdb=" O MET L 82 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'O' and resid 219 through 223 removed outlier: 3.627A pdb=" N ASP O 28 " --> pdb=" O TYR O 171 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP O 173 " --> pdb=" O ASP O 28 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N PHE O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'P' and resid 46 through 49 removed outlier: 6.499A pdb=" N UNK P 69 " --> pdb=" O UNK P 47 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N UNK P 49 " --> pdb=" O UNK P 69 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N UNK P 71 " --> pdb=" O UNK P 49 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'P' and resid 91 through 93 removed outlier: 3.678A pdb=" N UNK P 130 " --> pdb=" O UNK P 91 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N UNK P 132 " --> pdb=" O UNK P 93 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N UNK P 228 " --> pdb=" O UNK P 167 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 63 through 67 Processing sheet with id= O, first strand: chain 'G' and resid 9 through 13 Processing sheet with id= P, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= Q, first strand: chain 'G' and resid 173 through 177 removed outlier: 3.508A pdb=" N GLY G 173 " --> pdb=" O GLY G 184 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY G 184 " --> pdb=" O GLY G 173 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP G 180 " --> pdb=" O ARG G 177 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 223 through 228 removed outlier: 3.630A pdb=" N SER G 227 " --> pdb=" O ILE G 238 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= T, first strand: chain 'G' and resid 376 through 379 removed outlier: 7.101A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'G' and resid 451 through 454 Processing sheet with id= V, first strand: chain 'G' and resid 544 through 546 removed outlier: 7.106A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= X, first strand: chain 'Q' and resid 35 through 37 removed outlier: 3.714A pdb=" N GLU Q 58 " --> pdb=" O ARG Q 36 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET Q 57 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU Q 84 " --> pdb=" O MET Q 57 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'R' and resid 56 through 59 removed outlier: 3.705A pdb=" N ILE R 57 " --> pdb=" O ILE R 73 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL R 71 " --> pdb=" O CYS R 59 " (cutoff:3.500A) 1800 hydrogen bonds defined for protein. 5181 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: 16.37 Time building geometry restraints manager: 17.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 22400 1.44 - 1.65: 30796 1.65 - 1.87: 529 1.87 - 2.09: 0 2.09 - 2.30: 80 Bond restraints: 53805 Sorted by residual: bond pdb=" O2B NAP P 501 " pdb=" P2B NAP P 501 " ideal model delta sigma weight residual 1.736 1.615 0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" C5A FMN F 501 " pdb=" C9A FMN F 501 " ideal model delta sigma weight residual 1.390 1.505 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C7 FMN F 501 " pdb=" C8 FMN F 501 " ideal model delta sigma weight residual 1.390 1.501 -0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C10 FMN F 501 " pdb=" C4A FMN F 501 " ideal model delta sigma weight residual 1.390 1.492 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" CA VAL N 115 " pdb=" CB VAL N 115 " ideal model delta sigma weight residual 1.537 1.562 -0.025 5.00e-03 4.00e+04 2.55e+01 ... (remaining 53800 not shown) Histogram of bond angle deviations from ideal: 73.10 - 85.75: 76 85.75 - 98.40: 0 98.40 - 111.05: 17355 111.05 - 123.71: 53157 123.71 - 136.36: 3189 Bond angle restraints: 73777 Sorted by residual: angle pdb=" N PRO N 255 " pdb=" CA PRO N 255 " pdb=" C PRO N 255 " ideal model delta sigma weight residual 110.70 120.32 -9.62 1.22e+00 6.72e-01 6.21e+01 angle pdb=" C HIS C 160 " pdb=" N PRO C 161 " pdb=" CA PRO C 161 " ideal model delta sigma weight residual 119.84 128.96 -9.12 1.25e+00 6.40e-01 5.32e+01 angle pdb=" N PRO F 207 " pdb=" CA PRO F 207 " pdb=" C PRO F 207 " ideal model delta sigma weight residual 110.70 118.75 -8.05 1.22e+00 6.72e-01 4.35e+01 angle pdb=" C MET H 91 " pdb=" N PRO H 92 " pdb=" CA PRO H 92 " ideal model delta sigma weight residual 119.84 127.96 -8.12 1.25e+00 6.40e-01 4.22e+01 angle pdb=" N PHE M 56 " pdb=" CA PHE M 56 " pdb=" C PHE M 56 " ideal model delta sigma weight residual 112.72 104.44 8.28 1.28e+00 6.10e-01 4.19e+01 ... (remaining 73772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.34: 31271 33.34 - 66.69: 596 66.69 - 100.03: 21 100.03 - 133.38: 0 133.38 - 166.72: 1 Dihedral angle restraints: 31889 sinusoidal: 9202 harmonic: 22687 Sorted by residual: dihedral pdb=" CA CYS B 149 " pdb=" C CYS B 149 " pdb=" N PRO B 150 " pdb=" CA PRO B 150 " ideal model delta harmonic sigma weight residual 180.00 -131.57 -48.43 0 5.00e+00 4.00e-02 9.38e+01 dihedral pdb=" CB CYS X 87 " pdb=" SG CYS X 87 " pdb=" SG CYS X 99 " pdb=" CB CYS X 99 " ideal model delta sinusoidal sigma weight residual 93.00 167.05 -74.05 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS X 35 " pdb=" SG CYS X 35 " pdb=" SG CYS X 65 " pdb=" CB CYS X 65 " ideal model delta sinusoidal sigma weight residual 93.00 161.09 -68.09 1 1.00e+01 1.00e-02 6.02e+01 ... (remaining 31886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.248: 8741 4.248 - 8.496: 0 8.496 - 12.745: 0 12.745 - 16.993: 0 16.993 - 21.241: 24 Chirality restraints: 8765 Sorted by residual: chirality pdb=" FE4 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S2 SF4 G 801 " pdb=" S3 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.69 21.24 2.00e-01 2.50e+01 1.13e+04 chirality pdb=" FE3 SF4 F 502 " pdb=" S1 SF4 F 502 " pdb=" S2 SF4 F 502 " pdb=" S4 SF4 F 502 " both_signs ideal model delta sigma weight residual False -10.55 10.68 -21.24 2.00e-01 2.50e+01 1.13e+04 chirality pdb=" FE2 SF4 G 802 " pdb=" S1 SF4 G 802 " pdb=" S3 SF4 G 802 " pdb=" S4 SF4 G 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.68 21.23 2.00e-01 2.50e+01 1.13e+04 ... (remaining 8762 not shown) Planarity restraints: 9630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 149 " 0.085 5.00e-02 4.00e+02 1.29e-01 2.66e+01 pdb=" N PRO B 150 " -0.223 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET H 91 " 0.057 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO H 92 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO H 92 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO H 92 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 6 " -0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO M 7 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO M 7 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO M 7 " -0.048 5.00e-02 4.00e+02 ... (remaining 9627 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 21256 2.99 - 3.47: 54030 3.47 - 3.94: 79964 3.94 - 4.42: 86536 4.42 - 4.90: 144627 Nonbonded interactions: 386413 Sorted by model distance: nonbonded pdb=" O MET D 152 " pdb=" OG1 THR D 156 " model vdw 2.512 2.440 nonbonded pdb=" O GLY B 135 " pdb=" N ASP B 137 " model vdw 2.532 2.520 nonbonded pdb=" O LEU H 266 " pdb=" OG SER H 269 " model vdw 2.546 2.440 nonbonded pdb=" OH TYR H 277 " pdb=" O LEU I 30 " model vdw 2.547 2.440 nonbonded pdb=" O ALA L 245 " pdb=" OG SER L 249 " model vdw 2.557 2.440 ... (remaining 386408 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 'U' and resid 8 through 82) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 4 5.49 5 S 335 5.16 5 C 33574 2.51 5 N 9294 2.21 5 O 9467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 13.940 Check model and map are aligned: 0.590 Convert atoms to be neutral: 0.350 Process input model: 119.450 Find NCS groups from input model: 2.950 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 : 0.008 0.121 53805 Z= 0.546 Angle : 1.367 10.047 73777 Z= 0.881 Chirality : 1.111 21.241 8765 Planarity : 0.005 0.129 9630 Dihedral : 13.963 166.722 17139 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 2.44 % Allowed : 9.28 % Favored : 88.27 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -4.78 (0.07), residues: 6916 helix: -3.22 (0.05), residues: 3279 sheet: -1.87 (0.27), residues: 308 loop : -3.23 (0.09), residues: 3329 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2030 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1942 time to evaluate : 5.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 11 residues processed: 1989 average time/residue: 0.5085 time to fit residues: 1657.9486 Evaluate side-chains 1149 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1138 time to evaluate : 4.448 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3850 time to fit residues: 13.8672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 711 random chunks: chunk 600 optimal weight: 8.9990 chunk 538 optimal weight: 6.9990 chunk 299 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 363 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 557 optimal weight: 0.7980 chunk 215 optimal weight: 0.0980 chunk 338 optimal weight: 0.9980 chunk 414 optimal weight: 7.9990 chunk 645 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 114 ASN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 HIS F 398 GLN ** F 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 HIS ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN H 99 ASN H 169 GLN H 247 HIS H 258 ASN ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN L 113 ASN L 165 ASN L 175 ASN L 205 ASN L 248 HIS L 348 HIS L 354 GLN L 405 ASN M 43 ASN M 144 ASN M 180 GLN ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 415 GLN M 440 HIS ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN O 97 GLN O 107 GLN ** a 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 44 GLN c 35 HIS f 30 ASN G 119 GLN G 198 ASN G 255 HIS R 51 GLN X 94 GLN n 13 GLN n 32 HIS n 72 HIS Z 53 ASN Z 89 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.264 53805 Z= 0.619 Angle : 1.799 51.043 73777 Z= 1.154 Chirality : 0.332 6.565 8765 Planarity : 0.005 0.139 9630 Dihedral : 5.794 165.273 8246 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.72 % Favored : 91.48 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -3.16 (0.09), residues: 6916 helix: -1.40 (0.08), residues: 3313 sheet: -1.20 (0.31), residues: 290 loop : -2.96 (0.09), residues: 3313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1391 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1378 time to evaluate : 4.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 1385 average time/residue: 0.4614 time to fit residues: 1078.4477 Evaluate side-chains 1029 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1026 time to evaluate : 4.440 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3336 time to fit residues: 7.6898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 711 random chunks: chunk 358 optimal weight: 6.9990 chunk 200 optimal weight: 30.0000 chunk 537 optimal weight: 0.0010 chunk 439 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 646 optimal weight: 9.9990 chunk 698 optimal weight: 9.9990 chunk 576 optimal weight: 0.5980 chunk 641 optimal weight: 10.0000 chunk 220 optimal weight: 0.9990 chunk 518 optimal weight: 9.9990 overall best weight: 2.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS C 21 GLN ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 HIS F 356 HIS ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN H 171 GLN H 247 HIS H 292 ASN ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN L 348 HIS L 580 GLN ** M 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 180 GLN M 192 ASN M 293 HIS ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 273 ASN O 114 HIS ** a 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 ASN f 30 ASN g 57 ASN ** i 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 99 GLN G 28 GLN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 GLN X 39 ASN X 94 GLN X 103 GLN n 13 GLN ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.273 53805 Z= 0.628 Angle : 1.779 51.231 73777 Z= 1.146 Chirality : 0.332 6.415 8765 Planarity : 0.005 0.143 9630 Dihedral : 5.554 165.939 8246 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.44 % Favored : 89.85 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.09), residues: 6916 helix: -0.57 (0.08), residues: 3351 sheet: -0.92 (0.31), residues: 296 loop : -2.80 (0.10), residues: 3269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1234 time to evaluate : 4.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 1240 average time/residue: 0.4443 time to fit residues: 935.7581 Evaluate side-chains 991 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 989 time to evaluate : 3.984 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3069 time to fit residues: 6.3800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 711 random chunks: chunk 639 optimal weight: 1.9990 chunk 486 optimal weight: 3.9990 chunk 335 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 308 optimal weight: 3.9990 chunk 434 optimal weight: 1.9990 chunk 649 optimal weight: 7.9990 chunk 687 optimal weight: 5.9990 chunk 339 optimal weight: 2.9990 chunk 615 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 116 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN I 49 ASN ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 GLN K 7 ASN ** L 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 HIS M 138 ASN ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 415 GLN N 144 GLN O 107 GLN O 151 HIS W 57 GLN ** a 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 30 ASN g 86 GLN ** i 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.246 53805 Z= 0.625 Angle : 1.780 50.874 73777 Z= 1.146 Chirality : 0.331 6.350 8765 Planarity : 0.005 0.147 9630 Dihedral : 5.481 165.708 8246 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.72 % Favored : 90.69 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.10), residues: 6916 helix: -0.16 (0.09), residues: 3368 sheet: -0.80 (0.31), residues: 291 loop : -2.77 (0.10), residues: 3257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1190 time to evaluate : 4.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 1192 average time/residue: 0.4408 time to fit residues: 899.0293 Evaluate side-chains 974 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 972 time to evaluate : 3.961 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3108 time to fit residues: 6.3427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 711 random chunks: chunk 572 optimal weight: 0.8980 chunk 390 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 511 optimal weight: 20.0000 chunk 283 optimal weight: 0.0030 chunk 586 optimal weight: 8.9990 chunk 475 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 350 optimal weight: 20.0000 chunk 616 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 overall best weight: 2.9892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 HIS ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 116 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 HIS ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 HIS M 26 ASN M 293 HIS ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 440 HIS V 49 GLN W 57 GLN ** a 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 30 ASN ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN X 94 GLN ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.244 53805 Z= 0.636 Angle : 1.791 51.050 73777 Z= 1.151 Chirality : 0.332 6.390 8765 Planarity : 0.005 0.146 9630 Dihedral : 5.533 165.368 8246 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.79 % Favored : 89.66 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -1.86 (0.10), residues: 6916 helix: 0.02 (0.09), residues: 3410 sheet: -0.83 (0.30), residues: 296 loop : -2.77 (0.10), residues: 3210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1158 time to evaluate : 4.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1159 average time/residue: 0.4247 time to fit residues: 839.8823 Evaluate side-chains 945 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 945 time to evaluate : 3.933 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 711 random chunks: chunk 231 optimal weight: 8.9990 chunk 618 optimal weight: 0.2980 chunk 135 optimal weight: 5.9990 chunk 403 optimal weight: 30.0000 chunk 169 optimal weight: 4.9990 chunk 687 optimal weight: 5.9990 chunk 571 optimal weight: 20.0000 chunk 318 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 361 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 HIS ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 HIS M 168 GLN ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN W 57 GLN a 27 HIS f 30 ASN ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN ** d 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.247 53805 Z= 0.624 Angle : 1.784 51.021 73777 Z= 1.146 Chirality : 0.332 6.496 8765 Planarity : 0.005 0.148 9630 Dihedral : 5.432 164.386 8246 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.40 % Favored : 90.14 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -1.75 (0.10), residues: 6916 helix: 0.14 (0.09), residues: 3394 sheet: -0.84 (0.30), residues: 301 loop : -2.73 (0.10), residues: 3221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1156 time to evaluate : 4.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1157 average time/residue: 0.4276 time to fit residues: 846.5535 Evaluate side-chains 919 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 918 time to evaluate : 3.961 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3740 time to fit residues: 5.9102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 711 random chunks: chunk 663 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 391 optimal weight: 10.0000 chunk 502 optimal weight: 20.0000 chunk 389 optimal weight: 20.0000 chunk 579 optimal weight: 10.0000 chunk 384 optimal weight: 10.0000 chunk 685 optimal weight: 10.0000 chunk 428 optimal weight: 7.9990 chunk 417 optimal weight: 20.0000 chunk 316 optimal weight: 7.9990 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN D 79 HIS ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN D 357 GLN F 356 HIS H 235 ASN H 247 HIS ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 HIS ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 440 HIS ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 GLN ** e 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 30 ASN ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 113 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 79 GLN X 39 ASN n 11 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.237 53805 Z= 0.741 Angle : 1.886 51.173 73777 Z= 1.190 Chirality : 0.333 6.432 8765 Planarity : 0.006 0.155 9630 Dihedral : 6.245 164.659 8246 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.41 % Favored : 88.11 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.03 % 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: -2.19 (0.10), residues: 6916 helix: -0.29 (0.09), residues: 3385 sheet: -1.21 (0.29), residues: 304 loop : -2.84 (0.10), residues: 3227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1052 time to evaluate : 4.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1054 average time/residue: 0.4170 time to fit residues: 753.6850 Evaluate side-chains 870 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 870 time to evaluate : 3.747 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 711 random chunks: chunk 423 optimal weight: 0.0370 chunk 273 optimal weight: 5.9990 chunk 409 optimal weight: 20.0000 chunk 206 optimal weight: 8.9990 chunk 134 optimal weight: 0.9990 chunk 132 optimal weight: 40.0000 chunk 435 optimal weight: 0.9980 chunk 466 optimal weight: 9.9990 chunk 338 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 538 optimal weight: 8.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN D 116 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN ** F 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 HIS ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN I 136 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 HIS M 88 ASN ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 279 GLN ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 273 ASN O 257 HIS f 30 ASN g 57 ASN i 12 GLN ** p 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.260 53805 Z= 0.625 Angle : 1.793 51.071 73777 Z= 1.149 Chirality : 0.333 6.581 8765 Planarity : 0.005 0.145 9630 Dihedral : 5.666 165.198 8246 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.17 % Favored : 90.38 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.77 (0.10), residues: 6916 helix: 0.13 (0.09), residues: 3367 sheet: -0.99 (0.30), residues: 299 loop : -2.71 (0.10), residues: 3250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1137 time to evaluate : 4.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1137 average time/residue: 0.4181 time to fit residues: 812.0544 Evaluate side-chains 907 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 907 time to evaluate : 3.764 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 711 random chunks: chunk 623 optimal weight: 9.9990 chunk 656 optimal weight: 0.6980 chunk 598 optimal weight: 4.9990 chunk 638 optimal weight: 1.9990 chunk 384 optimal weight: 10.0000 chunk 278 optimal weight: 0.0980 chunk 501 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 577 optimal weight: 9.9990 chunk 603 optimal weight: 9.9990 chunk 636 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 HIS ** F 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 HIS ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 230 HIS ** L 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 HIS ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 279 GLN ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 273 ASN f 30 ASN p 113 GLN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.249 53805 Z= 0.624 Angle : 1.790 50.747 73777 Z= 1.148 Chirality : 0.332 6.402 8765 Planarity : 0.005 0.141 9630 Dihedral : 5.501 164.416 8246 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.80 % Favored : 89.78 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.65 (0.10), residues: 6916 helix: 0.21 (0.09), residues: 3369 sheet: -0.88 (0.29), residues: 297 loop : -2.63 (0.10), residues: 3250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1076 time to evaluate : 4.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1078 average time/residue: 0.4081 time to fit residues: 750.8199 Evaluate side-chains 903 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 903 time to evaluate : 3.732 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 711 random chunks: chunk 419 optimal weight: 30.0000 chunk 675 optimal weight: 1.9990 chunk 412 optimal weight: 10.0000 chunk 320 optimal weight: 1.9990 chunk 469 optimal weight: 0.3980 chunk 708 optimal weight: 0.3980 chunk 651 optimal weight: 0.0970 chunk 564 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 435 optimal weight: 5.9990 chunk 345 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN D 217 ASN D 237 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 HIS ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 279 GLN ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN f 30 ASN p 113 GLN G 110 GLN G 119 GLN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.255 53805 Z= 0.623 Angle : 1.789 50.696 73777 Z= 1.146 Chirality : 0.332 6.404 8765 Planarity : 0.005 0.219 9630 Dihedral : 5.415 164.438 8246 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.44 % Favored : 90.18 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.65 (0.10), residues: 6916 helix: 0.21 (0.09), residues: 3386 sheet: -0.75 (0.30), residues: 301 loop : -2.66 (0.10), residues: 3229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13832 Ramachandran restraints generated. 6916 Oldfield, 0 Emsley, 6916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1094 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1095 average time/residue: 0.4318 time to fit residues: 814.6346 Evaluate side-chains 899 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 899 time to evaluate : 3.801 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 711 random chunks: chunk 448 optimal weight: 7.9990 chunk 600 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 520 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 564 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 chunk 580 optimal weight: 30.0000 chunk 71 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 116 GLN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN F 356 HIS F 373 ASN F 402 HIS H 235 ASN ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN I 144 HIS K 52 HIS ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 HIS M 82 HIS ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 279 GLN ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 30 ASN p 113 GLN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.083326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.074459 restraints weight = 214393.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.074940 restraints weight = 126198.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.075216 restraints weight = 96037.566| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.243 53805 Z= 0.646 Angle : 1.808 50.957 73777 Z= 1.157 Chirality : 0.333 6.392 8765 Planarity : 0.005 0.142 9630 Dihedral : 5.569 164.047 8246 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.57 % Favored : 89.07 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.69 (0.10), residues: 6916 helix: 0.17 (0.09), residues: 3380 sheet: -0.88 (0.30), residues: 291 loop : -2.65 (0.10), residues: 3245 =============================================================================== Job complete usr+sys time: 12684.82 seconds wall clock time: 220 minutes 14.22 seconds (13214.22 seconds total)