Starting phenix.real_space_refine on Tue Sep 24 21:21:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o31_3731/09_2024/5o31_3731.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o31_3731/09_2024/5o31_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_3731/09_2024/5o31_3731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o31_3731/09_2024/5o31_3731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o31_3731/09_2024/5o31_3731.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o31_3731/09_2024/5o31_3731.cif" } resolution = 4.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 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. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 52703 Number of models: 1 Model: "" Number of chains: 56 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: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 344 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "b" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 175 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'TRANS': 34} 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: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 24} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "i" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 395 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'TRANS': 78} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'UNK:plan-1': 79} Unresolved non-hydrogen planarities: 79 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: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 708 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 87} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "d" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 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: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 705 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 88} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "Z" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 215 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'TRANS': 42} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'UNK:plan-1': 43} Unresolved non-hydrogen planarities: 43 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: 24.11, per 1000 atoms: 0.46 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " UNK Z 99 " - " LYS Z 98 " " UNK b 46 " - " ASN b 45 " " UNK d 98 " - " HIS d 97 " Time building additional restraints: 9.66 Conformation dependent library (CDL) restraints added in 5.8 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... Secondary structure from input PDB file: 311 helices and 32 sheets defined 56.4% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 2 through 23 removed outlier: 3.791A pdb=" N ALA A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) 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 55 through 72 removed outlier: 3.855A pdb=" N ALA A 59 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.838A pdb=" N SER A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 107 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) removed outlier: 4.196A pdb=" N THR A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.749A pdb=" N ARG B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 61 removed outlier: 4.182A pdb=" N GLU B 58 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.558A pdb=" N ASP B 68 " --> pdb=" O PRO B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 107 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 117 through 123 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 160 through 167 Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 24 through 29 Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.749A pdb=" N PHE C 63 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 138 removed outlier: 4.012A pdb=" N TYR C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 14 removed outlier: 3.559A pdb=" N ALA D 11 " --> pdb=" O ASP D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.595A pdb=" N LEU D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 91' Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 99 through 103 removed outlier: 3.507A pdb=" N TYR D 102 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'D' and resid 131 through 162 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 164 through 185 removed outlier: 4.206A pdb=" N PHE D 168 " --> pdb=" O MET D 164 " (cutoff:3.500A) 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 206 through 227 removed outlier: 3.683A pdb=" N ASP D 210 " --> pdb=" O GLY D 206 " (cutoff:3.500A) 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 232 through 239 Processing helix chain 'D' and resid 248 through 254 removed outlier: 3.546A pdb=" N ASN D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 306 removed outlier: 3.813A pdb=" N ARG D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 317 Processing helix chain 'D' and resid 334 through 339 removed outlier: 3.690A pdb=" N LYS D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 352 removed outlier: 3.595A pdb=" N LEU D 345 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D 352 " --> pdb=" O HIS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 406 removed outlier: 4.275A pdb=" N ALA D 397 " --> pdb=" O ALA D 393 " (cutoff:3.500A) 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 410 through 422 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 27 through 38 removed outlier: 4.249A pdb=" N TYR E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 45 removed outlier: 3.918A pdb=" N ALA E 45 " --> pdb=" O HIS E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 42 through 45' Processing helix chain 'E' and resid 46 through 58 removed outlier: 3.576A pdb=" N LEU E 51 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 73 removed outlier: 3.642A pdb=" N MET E 66 " --> pdb=" O PRO E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 87 removed outlier: 3.654A pdb=" N TYR E 87 " --> pdb=" O VAL E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 110 Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 165 through 176 removed outlier: 3.738A pdb=" N GLU E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 40 removed outlier: 3.762A pdb=" N SER F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 51 removed outlier: 3.513A pdb=" N LEU F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 64 removed outlier: 3.505A pdb=" N VAL F 60 " --> pdb=" O ILE F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 79 removed outlier: 3.627A pdb=" N LYS F 78 " --> pdb=" O PRO F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.543A pdb=" N ASN F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS F 84 " --> pdb=" O PHE F 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 80 through 84' Processing helix chain 'F' and resid 105 through 111 removed outlier: 3.654A pdb=" N GLU F 109 " --> pdb=" O CYS F 105 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 130 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 143 through 160 removed outlier: 3.565A pdb=" N ASN F 148 " --> pdb=" O ASN F 144 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY F 160 " --> pdb=" O ALA F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 198 removed outlier: 3.678A pdb=" N ILE F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 237 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 removed outlier: 3.576A pdb=" N ARG F 237 " --> pdb=" O THR F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 245 removed outlier: 4.007A pdb=" N PHE F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE F 245 " --> pdb=" O TRP F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 284 removed outlier: 3.640A pdb=" N GLU F 281 " --> pdb=" O LYS F 277 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS F 283 " --> pdb=" O LEU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 326 Processing helix chain 'F' and resid 342 through 358 removed outlier: 3.534A pdb=" N ALA F 346 " --> pdb=" O ASP F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 368 through 382 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 386 through 402 removed outlier: 4.452A pdb=" N ASP F 390 " --> pdb=" O PRO F 386 " (cutoff:3.500A) 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) removed outlier: 4.028A pdb=" N GLY F 401 " --> pdb=" O LYS F 397 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N HIS F 402 " --> pdb=" O GLN F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 411 Processing helix chain 'F' and resid 412 through 417 Processing helix chain 'F' and resid 423 through 438 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 6 through 9 Processing helix chain 'H' and resid 10 through 19 Processing helix chain 'H' and resid 19 through 31 removed outlier: 3.510A pdb=" N VAL H 23 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU H 28 " --> pdb=" O GLU H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 57 removed outlier: 3.525A pdb=" N PHE H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE H 57 " --> pdb=" O ILE H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 85 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) Processing helix chain 'H' and resid 100 through 111 removed outlier: 4.013A pdb=" N PHE H 104 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER H 109 " --> pdb=" O MET H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 123 removed outlier: 3.735A pdb=" N SER H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER H 123 " --> pdb=" O SER H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 157 removed outlier: 3.691A pdb=" N LEU H 129 " --> pdb=" O SER H 125 " (cutoff:3.500A) 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) removed outlier: 3.720A pdb=" N SER H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 168 removed outlier: 3.938A pdb=" N THR H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 189 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 219 through 242 removed outlier: 3.874A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) 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 277 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 281 through 289 removed outlier: 3.595A pdb=" N LEU H 289 " --> pdb=" O LEU H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 311 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 14 through 26 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 28 through 43 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) removed outlier: 3.604A pdb=" N ARG I 43 " --> pdb=" O SER I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 87 Processing helix chain 'I' and resid 120 through 126 removed outlier: 3.583A pdb=" N GLU I 124 " --> pdb=" O GLY I 120 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS I 126 " --> pdb=" O CYS I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 148 Processing helix chain 'I' and resid 155 through 160 Processing helix chain 'I' and resid 161 through 169 removed outlier: 3.782A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 172 No H-bonds generated for 'chain 'I' and resid 170 through 172' Processing helix chain 'J' and resid 5 through 22 removed outlier: 4.016A pdb=" N LEU J 9 " --> pdb=" O ILE J 5 " (cutoff:3.500A) 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 24 through 31 removed outlier: 4.303A pdb=" N TYR J 28 " --> pdb=" O PRO J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 48 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) removed outlier: 3.733A pdb=" N GLY J 48 " --> pdb=" O VAL J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 54 Processing helix chain 'J' and resid 54 through 59 Processing helix chain 'J' and resid 63 through 75 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 88 through 98 Processing helix chain 'J' and resid 100 through 108 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 150 through 172 removed outlier: 3.848A pdb=" N VAL J 154 " --> pdb=" O GLY J 150 " (cutoff:3.500A) 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 4 through 21 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 26 through 51 removed outlier: 3.808A pdb=" N LEU K 30 " --> pdb=" O LEU K 26 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR K 47 " --> pdb=" O MET K 43 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 57 No H-bonds generated for 'chain 'K' and resid 55 through 57' Processing helix chain 'K' and resid 58 through 85 removed outlier: 3.648A pdb=" N GLU K 70 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA K 72 " --> pdb=" O ALA K 68 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU K 77 " --> pdb=" O LEU K 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 9 removed outlier: 3.970A pdb=" N LEU L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 21 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 31 through 57 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 88 through 107 removed outlier: 3.840A pdb=" N VAL L 92 " --> pdb=" O MET L 88 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 134 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 137 through 151 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 151 through 156 Processing helix chain 'L' and resid 161 through 193 removed outlier: 3.930A pdb=" N ASN L 165 " --> pdb=" O ARG L 161 " (cutoff:3.500A) 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 197 through 202 removed outlier: 3.764A pdb=" N PHE L 202 " --> pdb=" O LEU L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 214 removed outlier: 4.223A pdb=" N ILE L 214 " --> pdb=" O ASN L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 223 removed outlier: 3.569A pdb=" N GLY L 222 " --> pdb=" O LEU L 218 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS L 223 " --> pdb=" O ALA L 219 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 239 removed outlier: 3.713A pdb=" N MET L 237 " --> pdb=" O PRO L 234 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY L 239 " --> pdb=" O ALA L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 248 removed outlier: 3.672A pdb=" N SER L 244 " --> pdb=" O PRO L 240 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS L 248 " --> pdb=" O SER L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 263 removed outlier: 4.336A pdb=" N LEU L 260 " --> pdb=" O GLY L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 270 removed outlier: 3.920A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN L 270 " --> pdb=" O LEU L 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 280 removed outlier: 3.865A pdb=" N LEU L 278 " --> pdb=" O GLN L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 281 through 287 removed outlier: 3.748A pdb=" N THR L 285 " --> pdb=" O GLY L 281 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU L 286 " --> pdb=" O ALA L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 293 removed outlier: 3.912A pdb=" N LEU L 293 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 305 removed outlier: 4.354A pdb=" N ILE L 302 " --> pdb=" O ILE L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 305 through 319 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 324 through 350 removed outlier: 3.754A pdb=" N HIS L 328 " --> pdb=" O LEU L 324 " (cutoff:3.500A) 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 368 through 381 removed outlier: 3.589A pdb=" N THR L 381 " --> pdb=" O SER L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 391 through 401 removed outlier: 3.884A pdb=" N ILE L 395 " --> pdb=" O SER L 391 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 418 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) Processing helix chain 'L' and resid 418 through 428 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 447 through 463 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 467 through 472 Processing helix chain 'L' and resid 488 through 510 removed outlier: 3.833A pdb=" N THR L 494 " --> pdb=" O ALA L 490 " (cutoff:3.500A) Processing helix chain 'L' and resid 528 through 533 Processing helix chain 'L' and resid 536 through 547 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 556 through 572 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 Processing helix chain 'L' and resid 573 through 578 Processing helix chain 'L' and resid 583 through 600 removed outlier: 3.620A pdb=" N TYR L 587 " --> pdb=" O LEU L 583 " (cutoff:3.500A) 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 11 through 18 removed outlier: 3.869A pdb=" N THR M 15 " --> pdb=" O LEU M 11 " (cutoff:3.500A) 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 42 removed outlier: 3.545A pdb=" N THR M 28 " --> pdb=" O TRP M 24 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA M 29 " --> pdb=" O VAL M 25 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER M 31 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE M 34 " --> pdb=" O HIS M 30 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER M 38 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 80 removed outlier: 3.714A pdb=" N LEU M 68 " --> pdb=" O PRO M 64 " (cutoff:3.500A) 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 88 through 112 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 115 through 123 removed outlier: 3.682A pdb=" N TYR M 119 " --> pdb=" O LEU M 115 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE M 120 " --> pdb=" O ILE M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 135 removed outlier: 3.577A pdb=" N THR M 129 " --> pdb=" O THR M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 158 removed outlier: 4.131A pdb=" N ALA M 145 " --> pdb=" O GLU M 141 " (cutoff:3.500A) 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) Processing helix chain 'M' and resid 160 through 171 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 189 through 202 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) Processing helix chain 'M' and resid 214 through 222 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 229 through 238 removed outlier: 3.879A pdb=" N ALA M 233 " --> pdb=" O MET M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 250 removed outlier: 3.985A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 257 through 275 removed outlier: 4.214A pdb=" N PHE M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) 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) removed outlier: 3.657A pdb=" N ILE M 275 " --> pdb=" O MET M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 288 Processing helix chain 'M' and resid 288 through 304 removed outlier: 3.759A pdb=" N SER M 292 " --> pdb=" O TYR M 288 " (cutoff:3.500A) 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) removed outlier: 3.611A pdb=" N GLN M 304 " --> pdb=" O ALA M 300 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 338 removed outlier: 3.673A pdb=" N TYR M 309 " --> pdb=" O THR M 305 " (cutoff:3.500A) 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 354 through 364 removed outlier: 3.752A pdb=" N TRP M 358 " --> pdb=" O LEU M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 373 through 389 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 391 through 403 removed outlier: 3.870A pdb=" N LEU M 395 " --> pdb=" O ILE M 391 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL M 398 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN M 399 " --> pdb=" O LEU M 395 " (cutoff:3.500A) Processing helix chain 'M' and resid 403 through 416 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 430 through 447 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 3 through 22 removed outlier: 4.216A pdb=" N ILE N 7 " --> pdb=" O PRO N 3 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE N 13 " --> pdb=" O ILE N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 46 removed outlier: 3.587A pdb=" N VAL N 29 " --> pdb=" O HIS N 25 " (cutoff:3.500A) 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 49 through 80 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 93 through 106 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 108 through 112 removed outlier: 3.712A pdb=" N HIS N 112 " --> pdb=" O ALA N 109 " (cutoff:3.500A) 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 124 through 133 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) Processing helix chain 'N' and resid 135 through 145 removed outlier: 3.608A pdb=" N MET N 139 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL N 141 " --> pdb=" O ALA N 137 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 153 Processing helix chain 'N' and resid 154 through 168 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 174 through 192 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) Processing helix chain 'N' and resid 200 through 219 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 239 through 252 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) removed outlier: 3.978A pdb=" N GLY N 252 " --> pdb=" O LEU N 248 " (cutoff:3.500A) Processing helix chain 'N' and resid 260 through 272 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) Processing helix chain 'N' and resid 276 through 297 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 297 through 302 removed outlier: 3.634A pdb=" N LEU N 302 " --> pdb=" O TYR N 298 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 332 removed outlier: 4.218A pdb=" N THR N 328 " --> pdb=" O THR N 324 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET N 329 " --> pdb=" O PHE N 325 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU N 332 " --> pdb=" O THR N 328 " (cutoff:3.500A) Processing helix chain 'N' and resid 339 through 345 removed outlier: 3.978A pdb=" N LEU N 343 " --> pdb=" O LEU N 339 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 43 removed outlier: 3.866A pdb=" N ALA O 39 " --> pdb=" O LYS O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 62 Processing helix chain 'O' and resid 70 through 75 removed outlier: 3.916A pdb=" N GLY O 75 " --> pdb=" O VAL O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 85 removed outlier: 3.781A pdb=" N TYR O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP O 85 " --> pdb=" O LYS O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 117 Processing helix chain 'O' and resid 127 through 129 No H-bonds generated for 'chain 'O' and resid 127 through 129' Processing helix chain 'O' and resid 130 through 141 removed outlier: 3.667A pdb=" N PHE O 134 " --> pdb=" O SER O 130 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA O 137 " --> pdb=" O VAL O 133 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET O 138 " --> pdb=" O PHE O 134 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN O 141 " --> pdb=" O ALA O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 160 removed outlier: 3.839A pdb=" N VAL O 149 " --> pdb=" O ARG O 145 " (cutoff:3.500A) 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) Processing helix chain 'O' and resid 178 through 186 removed outlier: 3.924A pdb=" N ARG O 182 " --> pdb=" O GLU O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 208 removed outlier: 3.871A pdb=" N GLY O 208 " --> pdb=" O ASN O 204 " (cutoff:3.500A) Processing helix chain 'O' and resid 209 through 216 removed outlier: 3.587A pdb=" N GLU O 213 " --> pdb=" O THR O 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 230 through 241 removed outlier: 3.544A pdb=" N VAL O 234 " --> pdb=" O ASP O 230 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL O 235 " --> pdb=" O ALA O 231 " (cutoff:3.500A) Processing helix chain 'O' and resid 254 through 265 removed outlier: 3.608A pdb=" N LYS O 258 " --> pdb=" O ARG O 254 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP O 265 " --> pdb=" O MET O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 265 through 270 removed outlier: 3.601A pdb=" N VAL O 269 " --> pdb=" O ASP O 265 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 299 removed outlier: 4.090A pdb=" N GLN O 291 " --> pdb=" O HIS O 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 41 removed outlier: 3.582A pdb=" N UNK P 40 " --> pdb=" O UNK P 36 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N UNK P 41 " --> pdb=" O UNK P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 60 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) removed outlier: 4.061A pdb=" N UNK P 60 " --> pdb=" O UNK P 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 124 removed outlier: 3.554A pdb=" N UNK P 123 " --> pdb=" O UNK P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 148 through 159 Processing helix chain 'P' and resid 176 through 184 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 220 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 237 through 250 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 281 through 290 removed outlier: 4.213A pdb=" N UNK P 290 " --> pdb=" O UNK P 286 " (cutoff:3.500A) Processing helix chain 'P' and resid 313 through 318 Processing helix chain 'S' and resid 31 through 38 Processing helix chain 'S' and resid 39 through 47 removed outlier: 4.078A pdb=" N LYS S 45 " --> pdb=" O VAL S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 95 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 22 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) removed outlier: 3.593A pdb=" N TYR T 22 " --> pdb=" O VAL T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 59 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 63 through 70 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) Processing helix chain 'T' and resid 72 through 82 Processing helix chain 'U' and resid 7 through 21 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 43 through 59 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 63 through 68 removed outlier: 3.838A pdb=" N GLU U 68 " --> pdb=" O ASP U 64 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 85 Processing helix chain 'V' and resid 21 through 35 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) removed outlier: 3.626A pdb=" N GLY V 35 " --> pdb=" O LEU V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 41 through 61 removed outlier: 3.625A pdb=" N LYS V 45 " --> pdb=" O ALA V 41 " (cutoff:3.500A) 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 64 through 69 Processing helix chain 'V' and resid 75 through 85 removed outlier: 4.231A pdb=" N ASN V 85 " --> pdb=" O LEU V 81 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 96 Processing helix chain 'W' and resid 25 through 40 removed outlier: 3.706A pdb=" N ARG W 29 " --> pdb=" O ASN W 25 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG W 40 " --> pdb=" O ARG W 36 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 48 removed outlier: 3.622A pdb=" N LEU W 48 " --> pdb=" O ASN W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 54 through 68 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) removed outlier: 3.799A pdb=" N LYS W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 74 through 89 removed outlier: 3.700A pdb=" N MET W 87 " --> pdb=" O ILE W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 124 removed outlier: 3.674A pdb=" N TYR W 122 " --> pdb=" O LEU W 118 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 8 Processing helix chain 'Y' and resid 19 through 41 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) removed outlier: 3.957A pdb=" N ALA Y 41 " --> pdb=" O ALA Y 37 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 79 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 89 through 97 Processing helix chain 'Y' and resid 98 through 102 removed outlier: 3.746A pdb=" N GLY Y 101 " --> pdb=" O LEU Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 108 through 127 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 11 Proline residue: a 7 - end of helix Processing helix chain 'a' and resid 11 through 16 Processing helix chain 'a' and resid 17 through 26 removed outlier: 3.695A pdb=" N ALA a 24 " --> pdb=" O GLY a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 26 through 31 Processing helix chain 'a' and resid 41 through 54 removed outlier: 3.788A pdb=" N TRP a 45 " --> pdb=" O TYR a 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 14 removed outlier: 4.144A pdb=" N LYS b 9 " --> pdb=" O ALA b 5 " (cutoff:3.500A) 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 16 through 35 removed outlier: 3.843A pdb=" N ALA b 20 " --> pdb=" O PRO b 16 " (cutoff:3.500A) 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 37 through 48 removed outlier: 4.136A pdb=" N SER b 41 " --> pdb=" O TYR b 37 " (cutoff:3.500A) 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 15 through 46 removed outlier: 3.521A pdb=" N LEU c 19 " --> pdb=" O LEU c 15 " (cutoff:3.500A) 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 32 through 43 removed outlier: 3.618A pdb=" N GLU e 36 " --> pdb=" O CYS e 32 " (cutoff:3.500A) 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 55 through 68 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 68 through 85 Processing helix chain 'f' and resid 5 through 10 Processing helix chain 'f' and resid 14 through 27 Processing helix chain 'f' and resid 28 through 32 removed outlier: 3.687A pdb=" N GLU f 32 " --> pdb=" O LYS f 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 50 through 59 removed outlier: 3.778A pdb=" N TRP g 56 " --> pdb=" O ALA g 52 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 68 removed outlier: 3.634A pdb=" N GLY g 65 " --> pdb=" O VAL g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 78 removed outlier: 4.189A pdb=" N ALA g 78 " --> pdb=" O SER g 74 " (cutoff:3.500A) Processing helix chain 'g' and resid 87 through 103 removed outlier: 3.881A pdb=" N ARG g 91 " --> pdb=" O GLU g 87 " (cutoff:3.500A) 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 8 through 24 removed outlier: 3.506A pdb=" N ASP i 24 " --> pdb=" O ARG i 20 " (cutoff:3.500A) Processing helix chain 'i' and resid 42 through 50 Processing helix chain 'i' and resid 60 through 74 removed outlier: 3.581A pdb=" N UNK i 64 " --> pdb=" O UNK i 60 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N UNK i 65 " --> pdb=" O UNK i 61 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 87 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) removed outlier: 3.787A pdb=" N UNK i 87 " --> pdb=" O UNK i 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 20 through 30 removed outlier: 3.873A pdb=" N UNK j 28 " --> pdb=" O UNK j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 30 through 39 removed outlier: 4.081A pdb=" N UNK j 36 " --> pdb=" O UNK j 32 " (cutoff:3.500A) Processing helix chain 'k' and resid 31 through 38 Processing helix chain 'k' and resid 71 through 85 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) removed outlier: 3.963A pdb=" N UNK k 85 " --> pdb=" O UNK k 81 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 28 Processing helix chain 'l' and resid 99 through 119 removed outlier: 3.848A pdb=" N UNK l 107 " --> pdb=" O UNK l 103 " (cutoff:3.500A) Processing helix chain 'o' and resid 61 through 71 removed outlier: 3.694A pdb=" N PHE o 65 " --> pdb=" O TYR o 61 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP o 71 " --> pdb=" O LYS o 67 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 114 removed outlier: 3.571A pdb=" N CYS o 89 " --> pdb=" O ASP o 85 " (cutoff:3.500A) Processing helix chain 'p' and resid 27 through 40 removed outlier: 4.067A pdb=" N UNK p 38 " --> pdb=" O UNK p 34 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N UNK p 40 " --> pdb=" O UNK p 36 " (cutoff:3.500A) Processing helix chain 'p' and resid 40 through 54 Processing helix chain 'p' and resid 80 through 115 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 126 through 141 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 150 through 172 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 17 removed outlier: 3.533A pdb=" N HIS q 17 " --> pdb=" O GLN q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 21 through 30 Processing helix chain 'q' and resid 85 through 90 removed outlier: 3.503A pdb=" N LEU q 90 " --> pdb=" O TRP q 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 34 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 83 through 98 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 114 through 123 removed outlier: 3.680A pdb=" N MET G 122 " --> pdb=" O ASP G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 166 Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 264 through 269 removed outlier: 3.662A pdb=" N PHE G 269 " --> pdb=" O ASP G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 277 removed outlier: 4.226A pdb=" N GLN G 277 " --> pdb=" O GLY G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 308 removed outlier: 4.086A pdb=" N MET G 306 " --> pdb=" O ARG G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 336 removed outlier: 3.534A pdb=" N ASP G 333 " --> pdb=" O ILE G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 363 removed outlier: 3.659A pdb=" N TYR G 362 " --> pdb=" O LEU G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 401 Processing helix chain 'G' and resid 425 through 434 removed outlier: 3.631A pdb=" N LEU G 429 " --> pdb=" O SER G 425 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER G 434 " --> pdb=" O GLN G 430 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 445 Processing helix chain 'G' and resid 455 through 459 Processing helix chain 'G' and resid 462 through 479 removed outlier: 3.515A pdb=" N ILE G 466 " --> pdb=" O ASP G 462 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR G 479 " --> pdb=" O GLN G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 506 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 511 through 517 removed outlier: 3.698A pdb=" N ASN G 517 " --> pdb=" O ALA G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 595 through 607 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 615 through 627 Processing helix chain 'G' and resid 628 through 631 Processing helix chain 'G' and resid 642 through 650 removed outlier: 3.517A pdb=" N LEU G 648 " --> pdb=" O GLN G 644 " (cutoff:3.500A) Processing helix chain 'G' and resid 681 through 693 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 50 through 58 removed outlier: 3.519A pdb=" N LEU s 56 " --> pdb=" O LEU s 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 100 Processing helix chain 'Q' and resid 117 through 122 removed outlier: 3.578A pdb=" N ALA Q 120 " --> pdb=" O SER Q 117 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE Q 122 " --> pdb=" O GLY Q 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 Processing helix chain 'R' and resid 39 through 47 removed outlier: 3.538A pdb=" N LEU R 43 " --> pdb=" O PHE R 39 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN R 47 " --> pdb=" O LEU R 43 " (cutoff:3.500A) Processing helix chain 'r' and resid 3 through 14 removed outlier: 3.520A pdb=" N ILE r 7 " --> pdb=" O ALA r 3 " (cutoff:3.500A) 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 15 through 32 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 33 through 45 removed outlier: 3.561A pdb=" N ALA h 37 " --> pdb=" O GLY h 33 " (cutoff:3.500A) 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 70 through 77 removed outlier: 3.555A pdb=" N ARG h 77 " --> pdb=" O ARG h 73 " (cutoff:3.500A) Processing helix chain 'h' and resid 90 through 115 Processing helix chain 'd' and resid 28 through 42 removed outlier: 3.561A pdb=" N VAL d 34 " --> pdb=" O ARG d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 49 Processing helix chain 'd' and resid 60 through 98 removed outlier: 3.661A pdb=" N TYR d 64 " --> pdb=" O ARG d 60 " (cutoff:3.500A) 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 21 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 29 through 33 Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 56 through 76 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 77 through 91 removed outlier: 3.678A pdb=" N PHE X 81 " --> pdb=" O CYS X 77 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER X 91 " --> pdb=" O CYS X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 99 through 106 removed outlier: 3.834A pdb=" N GLN X 105 " --> pdb=" O LYS X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 109 through 113 removed outlier: 3.571A pdb=" N ASP X 112 " --> pdb=" O CYS X 109 " (cutoff:3.500A) Processing helix chain 'm' and resid 27 through 49 removed outlier: 3.720A pdb=" N ALA m 31 " --> pdb=" O GLU m 27 " (cutoff:3.500A) 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) removed outlier: 3.571A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 61 through 73 removed outlier: 3.545A pdb=" N VAL m 65 " --> pdb=" O ASP m 61 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG m 71 " --> pdb=" O TRP m 67 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 92 removed outlier: 3.593A pdb=" N LEU m 87 " --> pdb=" O THR m 83 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE m 92 " --> pdb=" O LEU m 88 " (cutoff:3.500A) Processing helix chain 'm' and resid 94 through 100 removed outlier: 3.614A pdb=" N TRP m 100 " --> pdb=" O PRO m 96 " (cutoff:3.500A) Processing helix chain 'm' and resid 100 through 117 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 30 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 32 through 52 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) removed outlier: 3.727A pdb=" N ASN n 52 " --> pdb=" O ASP n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 57 through 66 Processing helix chain 'n' and resid 66 through 71 removed outlier: 4.038A pdb=" N PHE n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 114 through 142 removed outlier: 3.938A pdb=" N PHE n 118 " --> pdb=" O TYR n 114 " (cutoff:3.500A) 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) removed outlier: 3.656A pdb=" N GLU n 142 " --> pdb=" O GLN n 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 32 through 70 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 71 through 96 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 126 through 134 removed outlier: 3.616A pdb=" N UNK Z 130 " --> pdb=" O UNK Z 126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.962A pdb=" N MET B 86 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N MET B 116 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 88 " --> pdb=" O MET B 116 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 113 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL B 146 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER B 115 " --> pdb=" O VAL B 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 74 through 82 removed outlier: 5.398A pdb=" N LEU C 75 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU C 97 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP C 77 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 92 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL C 40 " --> pdb=" O CYS C 51 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN C 41 " --> pdb=" O ILE r 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 117 through 118 removed outlier: 6.480A pdb=" N ILE C 117 " --> pdb=" O ALA C 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, 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: 6.858A pdb=" N VAL D 65 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N CYS D 76 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLU D 67 " --> pdb=" O ARG D 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 194 through 195 Processing sheet with id=AA6, 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=AA7, 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=AA8, first strand: chain 'F' and resid 175 through 179 removed outlier: 6.531A pdb=" N LEU F 93 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TYR F 137 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL F 95 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR F 221 " --> pdb=" O TYR F 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 266 through 268 removed outlier: 6.185A pdb=" N ASN F 257 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL F 336 " --> pdb=" O ASN F 257 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER F 259 " --> pdb=" O VAL F 336 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 274 through 275 removed outlier: 3.764A pdb=" N VAL F 274 " --> pdb=" O MET F 317 " (cutoff:3.500A) Processing sheet with id=AB2, 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=AB3, 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=AB4, first strand: chain 'L' and resid 79 through 82 removed outlier: 4.110A pdb=" N GLU L 60 " --> pdb=" O MET L 82 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU L 61 " --> pdb=" O UNK i 97 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N UNK i 97 " --> pdb=" O LEU L 61 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 49 through 51 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) removed outlier: 7.059A pdb=" N THR O 26 " --> pdb=" O TYR O 171 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASP O 173 " --> pdb=" O THR O 26 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ASP O 28 " --> pdb=" O ASP O 173 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 23 through 24 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: 6.334A pdb=" N UNK P 166 " --> pdb=" O UNK P 129 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N UNK P 131 " --> pdb=" O UNK P 166 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N UNK P 168 " --> pdb=" O UNK P 131 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N UNK P 133 " --> pdb=" O UNK P 168 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N UNK P 165 " --> pdb=" O UNK P 228 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N UNK P 230 " --> pdb=" O UNK P 165 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N UNK P 167 " --> pdb=" O UNK P 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 46 through 49 Processing sheet with id=AB8, first strand: chain 'P' and resid 171 through 172 Processing sheet with id=AB9, first strand: chain 'S' and resid 63 through 67 Processing sheet with id=AC1, first strand: chain 'q' and resid 37 through 38 Processing sheet with id=AC2, first strand: chain 'G' and resid 16 through 20 removed outlier: 9.665A pdb=" N ILE G 79 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N PHE G 12 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU G 58 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL G 66 " --> pdb=" O VAL G 57 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 146 through 148 Processing sheet with id=AC4, 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=AC5, 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=AC6, first strand: chain 'G' and resid 291 through 293 removed outlier: 5.990A pdb=" N TYR G 545 " --> pdb=" O LEU G 561 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU G 524 " --> pdb=" O GLN G 546 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 318 through 319 Processing sheet with id=AC8, first strand: chain 'G' and resid 376 through 379 removed outlier: 6.163A pdb=" N VAL G 377 " --> pdb=" O ALA G 407 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 451 through 454 Processing sheet with id=AD1, first strand: chain 'G' and resid 572 through 574 Processing sheet with id=AD2, 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=AD3, first strand: chain 'Q' and resid 65 through 66 removed outlier: 3.726A pdb=" N TRP Q 65 " --> pdb=" O SER Q 74 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 50 through 51 Processing sheet with id=AD5, 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) 2201 hydrogen bonds defined for protein. 6483 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: 19.18 Time building geometry restraints manager: 11.84 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: 22397 1.44 - 1.65: 30796 1.65 - 1.87: 529 1.87 - 2.09: 0 2.09 - 2.30: 80 Bond restraints: 53802 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 53797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 64745 2.01 - 4.02: 8228 4.02 - 6.03: 597 6.03 - 8.04: 176 8.04 - 10.05: 22 Bond angle restraints: 73768 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 73763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.34: 31303 33.34 - 66.69: 616 66.69 - 100.03: 21 100.03 - 133.38: 0 133.38 - 166.72: 1 Dihedral angle restraints: 31941 sinusoidal: 9254 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 31938 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: 21137 2.99 - 3.47: 53735 3.47 - 3.94: 79538 3.94 - 4.42: 85843 4.42 - 4.90: 144556 Nonbonded interactions: 384809 Sorted by model distance: nonbonded pdb=" O MET D 152 " pdb=" OG1 THR D 156 " model vdw 2.512 3.040 nonbonded pdb=" O GLY B 135 " pdb=" N ASP B 137 " model vdw 2.532 3.120 nonbonded pdb=" O LEU H 266 " pdb=" OG SER H 269 " model vdw 2.546 3.040 nonbonded pdb=" OH TYR H 277 " pdb=" O LEU I 30 " model vdw 2.547 3.040 nonbonded pdb=" O ALA L 245 " pdb=" OG SER L 249 " model vdw 2.557 3.040 ... (remaining 384804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 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: 0.090 Extract box with map and model: 1.560 Check model and map are aligned: 0.320 Set scattering table: 0.390 Process input model: 110.910 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 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 53802 Z= 0.547 Angle : 1.367 10.047 73768 Z= 0.881 Chirality : 1.111 21.241 8765 Planarity : 0.005 0.129 9627 Dihedral : 14.052 166.722 17182 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 2.44 % Allowed : 9.28 % Favored : 88.27 % Rotamer: Outliers : 2.22 % Allowed : 7.56 % Favored : 90.22 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 196 HIS 0.007 0.001 HIS R 68 PHE 0.017 0.001 PHE I 139 TYR 0.015 0.001 TYR M 406 ARG 0.005 0.000 ARG D 430 *********************** 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 : 4.420 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 REVERT: A 84 LEU cc_start: 0.8920 (mt) cc_final: 0.8701 (mt) REVERT: B 58 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7675 (tm-30) REVERT: B 62 MET cc_start: 0.8097 (mmp) cc_final: 0.7783 (mtp) REVERT: B 104 TYR cc_start: 0.8424 (t80) cc_final: 0.8194 (t80) REVERT: B 137 ASP cc_start: 0.8225 (m-30) cc_final: 0.7985 (t0) REVERT: B 140 VAL cc_start: 0.9452 (t) cc_final: 0.9198 (m) REVERT: B 143 ASP cc_start: 0.7147 (m-30) cc_final: 0.6826 (m-30) REVERT: C 99 LEU cc_start: 0.8771 (mt) cc_final: 0.8319 (mt) REVERT: C 137 MET cc_start: 0.8209 (mtt) cc_final: 0.7807 (mtp) REVERT: C 153 THR cc_start: 0.8298 (p) cc_final: 0.6117 (p) REVERT: C 154 ASP cc_start: 0.7540 (m-30) cc_final: 0.7303 (m-30) REVERT: C 196 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8125 (pttm) REVERT: C 201 SER cc_start: 0.8586 (t) cc_final: 0.8096 (p) REVERT: D 79 HIS cc_start: 0.6735 (m-70) cc_final: 0.6202 (m170) REVERT: D 97 LEU cc_start: 0.9012 (tt) cc_final: 0.8686 (mt) REVERT: D 103 PHE cc_start: 0.7509 (m-80) cc_final: 0.7304 (m-10) REVERT: D 116 GLN cc_start: 0.8091 (tp40) cc_final: 0.7499 (tp40) REVERT: D 120 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7960 (tt) REVERT: D 140 LEU cc_start: 0.9071 (tt) cc_final: 0.8553 (tt) REVERT: D 156 THR cc_start: 0.8857 (p) cc_final: 0.8224 (t) REVERT: D 167 PHE cc_start: 0.9204 (t80) cc_final: 0.8946 (t80) REVERT: D 193 TYR cc_start: 0.8752 (t80) cc_final: 0.8492 (t80) REVERT: D 217 ASN cc_start: 0.7971 (m-40) cc_final: 0.7422 (t0) REVERT: D 239 THR cc_start: 0.8123 (p) cc_final: 0.7888 (m) REVERT: D 242 ILE cc_start: 0.8850 (mt) cc_final: 0.8510 (pt) REVERT: D 252 ASN cc_start: 0.7785 (m-40) cc_final: 0.7264 (m-40) REVERT: D 293 CYS cc_start: 0.8318 (m) cc_final: 0.7187 (m) REVERT: D 384 SER cc_start: 0.8422 (p) cc_final: 0.8166 (t) REVERT: D 417 ILE cc_start: 0.9231 (mt) cc_final: 0.8974 (mt) REVERT: F 367 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7065 (mt-10) REVERT: F 370 ASP cc_start: 0.6520 (m-30) cc_final: 0.6217 (m-30) REVERT: F 409 ASP cc_start: 0.8045 (m-30) cc_final: 0.7718 (m-30) REVERT: F 415 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8991 (p) REVERT: H 7 LEU cc_start: 0.9359 (mt) cc_final: 0.9055 (tt) REVERT: H 15 LEU cc_start: 0.8964 (mt) cc_final: 0.8717 (mt) REVERT: H 31 MET cc_start: 0.8257 (mmm) cc_final: 0.7969 (mmt) REVERT: H 95 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7510 (mt) REVERT: H 103 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8361 (tp) REVERT: H 116 ILE cc_start: 0.8410 (tt) cc_final: 0.8110 (mp) REVERT: H 149 ILE cc_start: 0.9049 (mt) cc_final: 0.8827 (mt) REVERT: H 184 MET cc_start: 0.8584 (mmm) cc_final: 0.6884 (tpt) REVERT: H 235 ASN cc_start: 0.8484 (m-40) cc_final: 0.8238 (m-40) REVERT: H 271 LEU cc_start: 0.9323 (mt) cc_final: 0.8961 (mp) REVERT: H 280 PHE cc_start: 0.7305 (m-80) cc_final: 0.6922 (m-80) REVERT: H 284 GLN cc_start: 0.8180 (mt0) cc_final: 0.7735 (mt0) REVERT: H 289 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9125 (mt) REVERT: I 32 ARG cc_start: 0.8431 (ttt-90) cc_final: 0.8199 (ttm170) REVERT: I 90 GLN cc_start: 0.8215 (mt0) cc_final: 0.7925 (mt0) REVERT: I 112 ASP cc_start: 0.8214 (p0) cc_final: 0.7721 (p0) REVERT: I 115 LYS cc_start: 0.8860 (mtmm) cc_final: 0.8166 (mttt) REVERT: I 175 TYR cc_start: 0.7228 (m-80) cc_final: 0.6761 (m-80) REVERT: J 28 TYR cc_start: 0.6439 (m-80) cc_final: 0.5948 (m-80) REVERT: J 33 LEU cc_start: 0.9012 (mt) cc_final: 0.8768 (mt) REVERT: J 36 SER cc_start: 0.9145 (p) cc_final: 0.8559 (m) REVERT: J 65 MET cc_start: 0.6760 (tpt) cc_final: 0.6513 (mmm) REVERT: J 70 TYR cc_start: 0.7860 (m-80) cc_final: 0.7606 (m-80) REVERT: J 151 THR cc_start: 0.8240 (p) cc_final: 0.7388 (p) REVERT: J 165 VAL cc_start: 0.9024 (t) cc_final: 0.8797 (t) REVERT: K 24 SER cc_start: 0.6035 (p) cc_final: 0.5751 (p) REVERT: K 29 SER cc_start: 0.9115 (p) cc_final: 0.8885 (t) REVERT: K 30 LEU cc_start: 0.9098 (mt) cc_final: 0.8864 (mp) REVERT: K 31 LEU cc_start: 0.9248 (mt) cc_final: 0.9037 (mt) REVERT: K 55 LEU cc_start: 0.8353 (mt) cc_final: 0.7979 (tp) REVERT: K 66 PHE cc_start: 0.7827 (m-80) cc_final: 0.7609 (m-80) REVERT: K 75 LEU cc_start: 0.9034 (tp) cc_final: 0.8734 (tp) REVERT: K 77 LEU cc_start: 0.8862 (mt) cc_final: 0.8527 (mt) REVERT: K 80 MET cc_start: 0.7453 (mmm) cc_final: 0.7118 (mmm) REVERT: L 22 MET cc_start: 0.6965 (ttm) cc_final: 0.6602 (ttp) REVERT: L 71 ILE cc_start: 0.8237 (mt) cc_final: 0.8034 (tt) REVERT: L 102 GLU cc_start: 0.7955 (tt0) cc_final: 0.7748 (tt0) REVERT: L 109 TYR cc_start: 0.7074 (t80) cc_final: 0.6725 (t80) REVERT: L 130 ILE cc_start: 0.9412 (mt) cc_final: 0.9117 (mm) REVERT: L 133 THR cc_start: 0.8874 (p) cc_final: 0.8624 (t) REVERT: L 179 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7277 (t0) REVERT: L 183 ILE cc_start: 0.8840 (mt) cc_final: 0.8448 (mt) REVERT: L 237 MET cc_start: 0.7605 (mpm) cc_final: 0.7208 (mpm) REVERT: L 278 LEU cc_start: 0.8715 (mt) cc_final: 0.8064 (tp) REVERT: L 286 LEU cc_start: 0.8132 (mt) cc_final: 0.7457 (mt) REVERT: L 356 ILE cc_start: 0.9366 (pt) cc_final: 0.9134 (mt) REVERT: L 375 VAL cc_start: 0.9307 (t) cc_final: 0.9028 (m) REVERT: L 389 PHE cc_start: 0.7159 (t80) cc_final: 0.6742 (t80) REVERT: L 392 LYS cc_start: 0.9184 (tttp) cc_final: 0.8915 (ttpt) REVERT: L 456 ARG cc_start: 0.5360 (mtt90) cc_final: 0.4872 (ptp-110) REVERT: L 532 ILE cc_start: 0.8265 (pt) cc_final: 0.7900 (pt) REVERT: L 540 MET cc_start: 0.7921 (mmm) cc_final: 0.7617 (tmm) REVERT: L 541 ASN cc_start: 0.8818 (m-40) cc_final: 0.8255 (t0) REVERT: L 544 MET cc_start: 0.7430 (mtp) cc_final: 0.6851 (mmp) REVERT: L 564 LYS cc_start: 0.6739 (mttt) cc_final: 0.6360 (mttt) REVERT: M 3 LYS cc_start: 0.7171 (mttt) cc_final: 0.6833 (ptmt) REVERT: M 36 PHE cc_start: 0.7478 (t80) cc_final: 0.6983 (t80) REVERT: M 41 LEU cc_start: 0.8583 (mt) cc_final: 0.7929 (mt) REVERT: M 55 LEU cc_start: 0.6482 (tp) cc_final: 0.6044 (mt) REVERT: M 92 LYS cc_start: 0.7998 (mttt) cc_final: 0.7569 (mttp) REVERT: M 164 LEU cc_start: 0.8435 (mt) cc_final: 0.8235 (mt) REVERT: M 200 MET cc_start: 0.8584 (mmp) cc_final: 0.8354 (mmt) REVERT: M 207 MET cc_start: 0.8595 (mmm) cc_final: 0.8315 (mmm) REVERT: M 249 ILE cc_start: 0.8517 (mm) cc_final: 0.8014 (tp) REVERT: M 250 LEU cc_start: 0.9088 (mt) cc_final: 0.8839 (mt) REVERT: M 259 TYR cc_start: 0.7781 (t80) cc_final: 0.7462 (t80) REVERT: M 269 MET cc_start: 0.8834 (mmm) cc_final: 0.7850 (mmm) REVERT: M 296 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9077 (mt) REVERT: M 304 GLN cc_start: 0.7062 (tt0) cc_final: 0.6805 (tm-30) REVERT: M 310 MET cc_start: 0.8432 (mmt) cc_final: 0.7556 (mmm) REVERT: M 316 MET cc_start: 0.7950 (mmm) cc_final: 0.7526 (mmm) REVERT: M 319 HIS cc_start: 0.6713 (t70) cc_final: 0.6437 (t-90) REVERT: M 354 LEU cc_start: 0.9135 (tt) cc_final: 0.8581 (tp) REVERT: M 379 LEU cc_start: 0.9071 (tp) cc_final: 0.8669 (tt) REVERT: M 409 TYR cc_start: 0.7869 (t80) cc_final: 0.7611 (t80) REVERT: M 441 ILE cc_start: 0.8558 (mt) cc_final: 0.6090 (mt) REVERT: M 446 LEU cc_start: 0.9207 (mt) cc_final: 0.8756 (tp) REVERT: N 14 MET cc_start: 0.7992 (mmm) cc_final: 0.7671 (mmp) REVERT: N 19 ILE cc_start: 0.9374 (mt) cc_final: 0.9148 (mm) REVERT: N 27 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8533 (tp) REVERT: N 63 GLN cc_start: 0.8515 (mt0) cc_final: 0.8312 (mt0) REVERT: N 84 TRP cc_start: 0.8510 (OUTLIER) cc_final: 0.8217 (m-10) REVERT: N 86 VAL cc_start: 0.8382 (t) cc_final: 0.7580 (t) REVERT: N 118 VAL cc_start: 0.9244 (t) cc_final: 0.9023 (p) REVERT: N 120 GLN cc_start: 0.8484 (mt0) cc_final: 0.8254 (mt0) REVERT: N 217 THR cc_start: 0.8593 (p) cc_final: 0.8356 (t) REVERT: N 224 THR cc_start: 0.8276 (p) cc_final: 0.8063 (p) REVERT: O 106 LEU cc_start: 0.9062 (tt) cc_final: 0.8716 (tp) REVERT: O 107 GLN cc_start: 0.9134 (pt0) cc_final: 0.8840 (pt0) REVERT: O 131 ASP cc_start: 0.8503 (m-30) cc_final: 0.8284 (t0) REVERT: O 144 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7789 (mt) REVERT: O 152 TYR cc_start: 0.8788 (t80) cc_final: 0.7559 (t80) REVERT: W 39 TYR cc_start: 0.8615 (t80) cc_final: 0.7684 (t80) REVERT: W 65 MET cc_start: 0.9123 (tpt) cc_final: 0.8713 (ttp) REVERT: W 86 LYS cc_start: 0.8631 (mttt) cc_final: 0.8363 (mtmm) REVERT: W 95 VAL cc_start: 0.9014 (t) cc_final: 0.8809 (p) REVERT: Y 48 PHE cc_start: 0.7689 (m-80) cc_final: 0.6836 (p90) REVERT: Y 89 TYR cc_start: 0.7327 (m-80) cc_final: 0.6909 (m-10) REVERT: a 36 LYS cc_start: 0.8291 (tttp) cc_final: 0.7943 (ttpt) REVERT: b 15 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7747 (mt-10) REVERT: b 18 LEU cc_start: 0.8231 (mt) cc_final: 0.7771 (mt) REVERT: b 22 PHE cc_start: 0.8383 (m-80) cc_final: 0.7804 (m-10) REVERT: b 29 VAL cc_start: 0.9381 (t) cc_final: 0.9142 (p) REVERT: e 38 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7379 (mt-10) REVERT: e 41 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6006 (tm-30) REVERT: f 22 PHE cc_start: 0.8456 (t80) cc_final: 0.8115 (t80) REVERT: f 30 ASN cc_start: 0.8632 (m110) cc_final: 0.8058 (t0) REVERT: g 92 GLU cc_start: 0.8288 (tp30) cc_final: 0.8045 (mm-30) REVERT: g 96 LEU cc_start: 0.8989 (mt) cc_final: 0.8670 (tp) REVERT: g 98 LYS cc_start: 0.8713 (ptmt) cc_final: 0.8154 (pttm) REVERT: i 20 ARG cc_start: 0.8875 (mtm110) cc_final: 0.8395 (mtm180) REVERT: p 88 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6862 (mt-10) REVERT: p 113 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8504 (tp40) REVERT: G 42 TYR cc_start: 0.7951 (t80) cc_final: 0.7600 (t80) REVERT: G 51 ASN cc_start: 0.8754 (m110) cc_final: 0.8054 (t0) REVERT: G 100 ASN cc_start: 0.7252 (m-40) cc_final: 0.6861 (m-40) REVERT: G 107 ILE cc_start: 0.9402 (pt) cc_final: 0.8581 (tp) REVERT: G 118 ASP cc_start: 0.6785 (m-30) cc_final: 0.6269 (m-30) REVERT: R 44 ILE cc_start: 0.9043 (mt) cc_final: 0.8770 (mm) REVERT: R 89 LEU cc_start: 0.8378 (mt) cc_final: 0.8175 (mt) REVERT: r 26 ARG cc_start: 0.7658 (mmt180) cc_final: 0.6090 (ttt180) REVERT: h 25 LEU cc_start: 0.9406 (tt) cc_final: 0.9202 (tp) REVERT: h 40 ILE cc_start: 0.8958 (mt) cc_final: 0.8735 (tp) REVERT: d 30 ARG cc_start: 0.8760 (mtm180) cc_final: 0.8433 (mmt180) REVERT: d 41 SER cc_start: 0.8578 (p) cc_final: 0.8121 (p) REVERT: d 45 ASP cc_start: 0.8218 (p0) cc_final: 0.7918 (p0) REVERT: d 64 TYR cc_start: 0.8494 (m-80) cc_final: 0.8233 (m-10) REVERT: X 31 TYR cc_start: 0.7448 (t80) cc_final: 0.7174 (t80) REVERT: X 56 LEU cc_start: 0.8810 (pp) cc_final: 0.8366 (pt) REVERT: X 57 GLU cc_start: 0.8425 (tt0) cc_final: 0.8161 (tm-30) REVERT: X 79 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8359 (mp0) REVERT: X 96 PHE cc_start: 0.7911 (m-80) cc_final: 0.7675 (m-10) REVERT: X 101 LYS cc_start: 0.8722 (mttp) cc_final: 0.8355 (ttpt) REVERT: X 102 GLN cc_start: 0.8140 (mt0) cc_final: 0.7450 (tm-30) REVERT: m 84 LYS cc_start: 0.6084 (mptt) cc_final: 0.4818 (ptpp) REVERT: n 19 TYR cc_start: 0.8914 (t80) cc_final: 0.8683 (t80) REVERT: n 33 ARG cc_start: 0.8810 (mmm160) cc_final: 0.7613 (mtm180) REVERT: n 46 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7656 (tmt170) REVERT: Z 43 LEU cc_start: 0.9253 (mt) cc_final: 0.8948 (tt) REVERT: Z 59 LEU cc_start: 0.9293 (mt) cc_final: 0.9090 (mp) REVERT: Z 87 ARG cc_start: 0.8249 (ttm170) cc_final: 0.7815 (tpt-90) REVERT: Z 90 LEU cc_start: 0.9450 (mt) cc_final: 0.9196 (mm) outliers start: 88 outliers final: 11 residues processed: 1989 average time/residue: 0.5387 time to fit residues: 1757.1542 Evaluate side-chains 1226 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1205 time to evaluate : 4.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 624 optimal weight: 8.9990 chunk 560 optimal weight: 9.9990 chunk 310 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 377 optimal weight: 6.9990 chunk 299 optimal weight: 0.6980 chunk 579 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 352 optimal weight: 9.9990 chunk 431 optimal weight: 7.9990 chunk 671 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN D 84 HIS D 114 ASN D 116 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 252 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN D 398 HIS F 356 HIS F 398 GLN 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 L 113 ASN L 165 ASN L 205 ASN ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 HIS L 348 HIS L 354 GLN L 580 GLN 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** O 92 ASN O 97 GLN O 151 HIS a 31 ASN a 44 GLN c 35 HIS g 57 ASN G 100 ASN G 119 GLN G 198 ASN G 255 HIS R 51 GLN ** d 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 94 GLN n 13 GLN n 32 HIS n 72 HIS Z 53 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.281 53802 Z= 0.624 Angle : 1.836 52.235 73768 Z= 1.172 Chirality : 0.335 6.926 8765 Planarity : 0.006 0.157 9627 Dihedral : 6.320 166.165 8289 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.77 % Allowed : 8.39 % Favored : 90.85 % Rotamer: Outliers : 0.38 % Allowed : 4.79 % Favored : 94.83 % 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: -3.06 (0.09), residues: 6916 helix: -1.28 (0.08), residues: 3426 sheet: -1.26 (0.30), residues: 278 loop : -2.99 (0.10), residues: 3212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP N 264 HIS 0.010 0.002 HIS a 40 PHE 0.042 0.002 PHE G 215 TYR 0.027 0.002 TYR D 387 ARG 0.011 0.001 ARG X 46 *********************** 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 1369 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1354 time to evaluate : 4.440 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: A 75 LEU cc_start: 0.8714 (mt) cc_final: 0.8408 (tp) REVERT: A 89 THR cc_start: 0.8896 (p) cc_final: 0.8376 (p) REVERT: B 58 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7753 (mm-30) REVERT: B 128 TYR cc_start: 0.8731 (m-80) cc_final: 0.8395 (m-80) REVERT: B 131 SER cc_start: 0.8904 (p) cc_final: 0.8194 (t) REVERT: B 143 ASP cc_start: 0.7081 (m-30) cc_final: 0.6764 (m-30) REVERT: C 193 GLU cc_start: 0.7543 (pp20) cc_final: 0.7271 (pm20) REVERT: C 196 LYS cc_start: 0.8912 (ttpp) cc_final: 0.8253 (pttm) REVERT: D 82 LEU cc_start: 0.9344 (mp) cc_final: 0.8452 (mp) REVERT: D 108 TYR cc_start: 0.7353 (m-10) cc_final: 0.7091 (m-80) REVERT: D 111 MET cc_start: 0.8036 (ptp) cc_final: 0.7667 (ptp) REVERT: D 114 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7682 (m-40) REVERT: D 116 GLN cc_start: 0.8270 (tp-100) cc_final: 0.7814 (tp-100) REVERT: D 189 MET cc_start: 0.8069 (ttm) cc_final: 0.7583 (ttm) REVERT: D 217 ASN cc_start: 0.8424 (m-40) cc_final: 0.7362 (t0) REVERT: D 342 MET cc_start: 0.9081 (tpt) cc_final: 0.8819 (tpt) REVERT: F 352 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7218 (tm-30) REVERT: F 409 ASP cc_start: 0.8008 (m-30) cc_final: 0.7324 (m-30) REVERT: H 11 ILE cc_start: 0.8343 (mm) cc_final: 0.8073 (mm) REVERT: H 15 LEU cc_start: 0.9049 (mt) cc_final: 0.8744 (mt) REVERT: H 31 MET cc_start: 0.8255 (mmm) cc_final: 0.7921 (mmt) REVERT: H 49 ILE cc_start: 0.8337 (tp) cc_final: 0.8100 (tp) REVERT: H 70 MET cc_start: 0.8393 (mmp) cc_final: 0.7954 (mmp) REVERT: H 150 LEU cc_start: 0.9015 (mt) cc_final: 0.8808 (mt) REVERT: H 155 LEU cc_start: 0.9036 (tp) cc_final: 0.8812 (tp) REVERT: H 184 MET cc_start: 0.8696 (mmm) cc_final: 0.8065 (tpp) REVERT: I 103 SER cc_start: 0.8196 (t) cc_final: 0.7549 (m) REVERT: I 113 MET cc_start: 0.8912 (mmm) cc_final: 0.8682 (mmt) REVERT: I 153 LYS cc_start: 0.6125 (mtmt) cc_final: 0.5793 (mtmt) REVERT: I 173 TYR cc_start: 0.7950 (p90) cc_final: 0.7524 (p90) REVERT: J 65 MET cc_start: 0.6116 (tpt) cc_final: 0.5910 (tpt) REVERT: J 70 TYR cc_start: 0.8220 (m-80) cc_final: 0.7788 (m-80) REVERT: J 170 GLU cc_start: 0.8153 (tt0) cc_final: 0.7924 (tt0) REVERT: K 69 CYS cc_start: 0.8457 (p) cc_final: 0.8025 (p) REVERT: K 76 SER cc_start: 0.8944 (p) cc_final: 0.8509 (p) REVERT: L 71 ILE cc_start: 0.8482 (mt) cc_final: 0.8229 (mt) REVERT: L 102 GLU cc_start: 0.8204 (tt0) cc_final: 0.7998 (tt0) REVERT: L 125 LEU cc_start: 0.9168 (tt) cc_final: 0.8930 (tt) REVERT: L 133 THR cc_start: 0.9187 (p) cc_final: 0.8905 (t) REVERT: L 249 SER cc_start: 0.8908 (p) cc_final: 0.8560 (m) REVERT: L 278 LEU cc_start: 0.8578 (mt) cc_final: 0.7996 (tp) REVERT: L 314 MET cc_start: 0.8512 (ttm) cc_final: 0.7996 (ttm) REVERT: L 323 TYR cc_start: 0.8222 (m-80) cc_final: 0.7883 (m-10) REVERT: L 389 PHE cc_start: 0.7296 (t80) cc_final: 0.7094 (t80) REVERT: L 540 MET cc_start: 0.8096 (mmm) cc_final: 0.7787 (tmm) REVERT: L 541 ASN cc_start: 0.8748 (m-40) cc_final: 0.8461 (t0) REVERT: L 564 LYS cc_start: 0.6904 (mttt) cc_final: 0.6544 (mttt) REVERT: M 10 MET cc_start: 0.8142 (tpp) cc_final: 0.7467 (mmm) REVERT: M 36 PHE cc_start: 0.8284 (t80) cc_final: 0.8045 (t80) REVERT: M 70 MET cc_start: 0.8728 (mmm) cc_final: 0.8503 (tpp) REVERT: M 89 LEU cc_start: 0.8345 (mt) cc_final: 0.8009 (mt) REVERT: M 92 LYS cc_start: 0.8451 (mttt) cc_final: 0.7801 (mttm) REVERT: M 103 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8240 (tm-30) REVERT: M 200 MET cc_start: 0.8805 (mmp) cc_final: 0.8516 (mmp) REVERT: M 204 MET cc_start: 0.7798 (mmp) cc_final: 0.7387 (mmp) REVERT: M 249 ILE cc_start: 0.8714 (mm) cc_final: 0.8425 (mm) REVERT: M 269 MET cc_start: 0.8538 (mmm) cc_final: 0.7519 (mtt) REVERT: M 293 HIS cc_start: 0.8306 (m-70) cc_final: 0.8073 (t70) REVERT: M 294 MET cc_start: 0.8543 (mmm) cc_final: 0.8207 (mmm) REVERT: M 304 GLN cc_start: 0.7626 (tt0) cc_final: 0.7164 (tm-30) REVERT: M 379 LEU cc_start: 0.8853 (tp) cc_final: 0.8312 (tt) REVERT: M 446 LEU cc_start: 0.9352 (mt) cc_final: 0.8935 (tp) REVERT: N 40 ILE cc_start: 0.8784 (mm) cc_final: 0.8297 (tt) REVERT: N 54 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7097 (mm-30) REVERT: N 98 MET cc_start: 0.8593 (tpp) cc_final: 0.8293 (tpp) REVERT: N 134 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7795 (tm-30) REVERT: N 143 TYR cc_start: 0.8612 (t80) cc_final: 0.8408 (t80) REVERT: N 144 GLN cc_start: 0.8587 (mt0) cc_final: 0.8378 (mt0) REVERT: N 187 MET cc_start: 0.9040 (mmp) cc_final: 0.8113 (mmm) REVERT: N 190 MET cc_start: 0.8123 (mmm) cc_final: 0.7685 (mtp) REVERT: N 205 LEU cc_start: 0.9034 (mm) cc_final: 0.7786 (mm) REVERT: N 224 THR cc_start: 0.8313 (p) cc_final: 0.8107 (p) REVERT: N 263 LYS cc_start: 0.9118 (mptt) cc_final: 0.8739 (mmtp) REVERT: N 268 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8380 (tm-30) REVERT: N 284 ILE cc_start: 0.8841 (pt) cc_final: 0.8532 (mm) REVERT: N 294 MET cc_start: 0.8800 (mmm) cc_final: 0.8437 (mmm) REVERT: O 106 LEU cc_start: 0.9129 (tt) cc_final: 0.8581 (tp) REVERT: O 131 ASP cc_start: 0.8889 (m-30) cc_final: 0.7954 (t0) REVERT: O 152 TYR cc_start: 0.8856 (t80) cc_final: 0.8137 (t80) REVERT: O 154 GLN cc_start: 0.9337 (mt0) cc_final: 0.8527 (mp10) REVERT: W 65 MET cc_start: 0.8870 (tpt) cc_final: 0.8624 (tmm) REVERT: Y 89 TYR cc_start: 0.7647 (m-80) cc_final: 0.7346 (m-80) REVERT: a 18 ILE cc_start: 0.9426 (mm) cc_final: 0.9159 (mm) REVERT: a 43 TYR cc_start: 0.8695 (t80) cc_final: 0.8062 (t80) REVERT: b 44 ILE cc_start: 0.9214 (pt) cc_final: 0.8939 (pt) REVERT: e 37 LYS cc_start: 0.8315 (mmpt) cc_final: 0.8052 (mmmt) REVERT: e 38 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7690 (mt-10) REVERT: e 41 GLU cc_start: 0.7899 (mt-10) cc_final: 0.6951 (tm-30) REVERT: f 15 LEU cc_start: 0.9152 (mt) cc_final: 0.8907 (mt) REVERT: f 30 ASN cc_start: 0.8785 (m110) cc_final: 0.8277 (t0) REVERT: g 92 GLU cc_start: 0.8422 (tp30) cc_final: 0.7784 (tp30) REVERT: g 96 LEU cc_start: 0.8937 (mt) cc_final: 0.8539 (tp) REVERT: g 98 LYS cc_start: 0.8726 (ptmt) cc_final: 0.8254 (pttm) REVERT: p 136 LYS cc_start: 0.9004 (tmtt) cc_final: 0.8299 (tppp) REVERT: G 42 TYR cc_start: 0.8366 (t80) cc_final: 0.8049 (t80) REVERT: G 179 ASN cc_start: 0.8479 (m-40) cc_final: 0.8090 (m-40) REVERT: G 198 ASN cc_start: 0.9071 (m-40) cc_final: 0.7789 (m-40) REVERT: G 237 ASN cc_start: 0.8686 (m-40) cc_final: 0.8184 (m-40) REVERT: d 87 ASP cc_start: 0.7955 (m-30) cc_final: 0.7541 (m-30) REVERT: X 57 GLU cc_start: 0.8529 (tt0) cc_final: 0.8302 (tm-30) REVERT: X 168 PHE cc_start: 0.7788 (t80) cc_final: 0.7510 (m-80) REVERT: m 49 GLN cc_start: 0.8374 (mt0) cc_final: 0.7934 (tt0) REVERT: m 78 ASN cc_start: 0.6834 (t0) cc_final: 0.6619 (t0) REVERT: m 84 LYS cc_start: 0.6579 (mptt) cc_final: 0.5587 (ptpp) REVERT: m 91 LEU cc_start: 0.7358 (mt) cc_final: 0.7066 (mt) REVERT: m 109 ASP cc_start: 0.8396 (m-30) cc_final: 0.7846 (p0) REVERT: n 19 TYR cc_start: 0.9168 (t80) cc_final: 0.8745 (t80) REVERT: n 23 LEU cc_start: 0.9064 (mt) cc_final: 0.8822 (mt) REVERT: n 33 ARG cc_start: 0.8319 (mmm160) cc_final: 0.7413 (mtm180) REVERT: n 52 ASN cc_start: 0.8153 (m-40) cc_final: 0.7650 (m-40) REVERT: n 69 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7468 (tm-30) REVERT: Z 87 ARG cc_start: 0.8571 (ttm170) cc_final: 0.8175 (tpt-90) REVERT: Z 92 GLU cc_start: 0.8495 (pt0) cc_final: 0.8237 (pt0) outliers start: 15 outliers final: 4 residues processed: 1363 average time/residue: 0.5099 time to fit residues: 1169.1637 Evaluate side-chains 1038 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1033 time to evaluate : 4.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 372 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 558 optimal weight: 8.9990 chunk 456 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 672 optimal weight: 0.0670 chunk 726 optimal weight: 1.9990 chunk 598 optimal weight: 5.9990 chunk 666 optimal weight: 0.9990 chunk 229 optimal weight: 8.9990 chunk 539 optimal weight: 20.0000 overall best weight: 1.4126 ------------------------------------------------------------------------------- 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 106 GLN C 21 GLN ** C 38 GLN ** 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** ** F 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN H 247 HIS H 284 GLN H 292 ASN I 49 ASN ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 GLN I 136 ASN I 144 HIS L 175 ASN ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 HIS ** M 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 192 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 HIS ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 99 GLN G 28 GLN G 237 ASN X 94 GLN X 103 GLN n 11 HIS Z 53 ASN Z 89 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.254 53802 Z= 0.595 Angle : 1.785 51.048 73768 Z= 1.148 Chirality : 0.333 6.564 8765 Planarity : 0.005 0.142 9627 Dihedral : 5.860 166.123 8289 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.18 % Favored : 90.20 % Rotamer: Outliers : 0.13 % Allowed : 3.58 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -2.33 (0.09), residues: 6916 helix: -0.45 (0.08), residues: 3430 sheet: -0.97 (0.31), residues: 287 loop : -2.91 (0.10), residues: 3199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 413 HIS 0.007 0.001 HIS B 127 PHE 0.036 0.002 PHE G 215 TYR 0.028 0.002 TYR M 409 ARG 0.010 0.001 ARG D 105 *********************** 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 1273 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1268 time to evaluate : 4.280 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: A 60 ILE cc_start: 0.9027 (mm) cc_final: 0.8808 (mm) REVERT: A 89 THR cc_start: 0.8933 (p) cc_final: 0.8332 (p) REVERT: B 58 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7544 (mm-30) REVERT: B 60 MET cc_start: 0.8202 (mtt) cc_final: 0.7906 (mtt) REVERT: B 131 SER cc_start: 0.8810 (p) cc_final: 0.7993 (t) REVERT: B 161 LEU cc_start: 0.8970 (mt) cc_final: 0.8719 (mp) REVERT: C 41 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8296 (tm-30) REVERT: C 82 ASP cc_start: 0.8041 (t0) cc_final: 0.7466 (t0) REVERT: C 158 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6893 (tm-30) REVERT: C 196 LYS cc_start: 0.8885 (ttpp) cc_final: 0.8225 (pttm) REVERT: D 82 LEU cc_start: 0.9165 (mp) cc_final: 0.7974 (mp) REVERT: D 111 MET cc_start: 0.7860 (ptp) cc_final: 0.7598 (ptm) REVERT: D 116 GLN cc_start: 0.8123 (tp-100) cc_final: 0.7742 (tp40) REVERT: D 167 PHE cc_start: 0.9198 (t80) cc_final: 0.8684 (t80) REVERT: D 217 ASN cc_start: 0.8387 (m-40) cc_final: 0.7453 (t0) REVERT: D 342 MET cc_start: 0.9023 (tpt) cc_final: 0.8721 (tpt) REVERT: H 11 ILE cc_start: 0.8324 (mm) cc_final: 0.8095 (mm) REVERT: H 15 LEU cc_start: 0.9052 (mt) cc_final: 0.8814 (mt) REVERT: H 49 ILE cc_start: 0.8362 (tp) cc_final: 0.8145 (tp) REVERT: H 183 MET cc_start: 0.7999 (mtp) cc_final: 0.7520 (mtm) REVERT: H 222 LEU cc_start: 0.9201 (pt) cc_final: 0.8983 (pp) REVERT: H 235 ASN cc_start: 0.8357 (m-40) cc_final: 0.7986 (m-40) REVERT: H 277 TYR cc_start: 0.7292 (m-10) cc_final: 0.7034 (m-10) REVERT: I 30 LEU cc_start: 0.7757 (tt) cc_final: 0.7350 (tt) REVERT: I 38 LEU cc_start: 0.9001 (tt) cc_final: 0.8784 (tt) REVERT: I 64 GLU cc_start: 0.7406 (tp30) cc_final: 0.7109 (tp30) REVERT: I 110 ASP cc_start: 0.7424 (m-30) cc_final: 0.7059 (m-30) REVERT: I 153 LYS cc_start: 0.6629 (mtmt) cc_final: 0.6257 (mtmt) REVERT: I 173 TYR cc_start: 0.8012 (p90) cc_final: 0.7562 (p90) REVERT: J 55 MET cc_start: 0.8517 (mmp) cc_final: 0.8063 (mmm) REVERT: J 64 MET cc_start: 0.8362 (tpp) cc_final: 0.8040 (tpp) REVERT: J 70 TYR cc_start: 0.8161 (m-80) cc_final: 0.7744 (m-80) REVERT: J 170 GLU cc_start: 0.8239 (tt0) cc_final: 0.7988 (tt0) REVERT: K 8 ILE cc_start: 0.9188 (pt) cc_final: 0.8969 (mt) REVERT: K 37 MET cc_start: 0.8399 (tpt) cc_final: 0.8095 (tpt) REVERT: K 47 THR cc_start: 0.8636 (p) cc_final: 0.8405 (p) REVERT: K 76 SER cc_start: 0.9039 (p) cc_final: 0.8755 (t) REVERT: K 80 MET cc_start: 0.8297 (mmm) cc_final: 0.8028 (mmm) REVERT: L 53 MET cc_start: 0.8709 (mtm) cc_final: 0.8226 (mtm) REVERT: L 101 MET cc_start: 0.8430 (mmp) cc_final: 0.8060 (mmp) REVERT: L 102 GLU cc_start: 0.8175 (tt0) cc_final: 0.7925 (tt0) REVERT: L 150 MET cc_start: 0.8387 (tpp) cc_final: 0.8152 (tpp) REVERT: L 249 SER cc_start: 0.8823 (p) cc_final: 0.8389 (m) REVERT: L 278 LEU cc_start: 0.8483 (mt) cc_final: 0.7921 (tp) REVERT: L 314 MET cc_start: 0.8499 (ttm) cc_final: 0.7849 (ttm) REVERT: L 323 TYR cc_start: 0.8346 (m-80) cc_final: 0.7949 (m-10) REVERT: L 389 PHE cc_start: 0.7190 (t80) cc_final: 0.6950 (t80) REVERT: L 532 ILE cc_start: 0.8330 (pt) cc_final: 0.7906 (pt) REVERT: L 533 MET cc_start: 0.7958 (mmt) cc_final: 0.7700 (mmm) REVERT: L 540 MET cc_start: 0.8251 (mmm) cc_final: 0.7894 (tmm) REVERT: L 541 ASN cc_start: 0.8725 (m-40) cc_final: 0.8437 (t0) REVERT: L 544 MET cc_start: 0.7624 (mtp) cc_final: 0.7108 (mmp) REVERT: M 3 LYS cc_start: 0.5833 (mttt) cc_final: 0.5089 (mttm) REVERT: M 70 MET cc_start: 0.8762 (mmm) cc_final: 0.8518 (tpp) REVERT: M 89 LEU cc_start: 0.8432 (mt) cc_final: 0.7960 (mt) REVERT: M 92 LYS cc_start: 0.8401 (mttt) cc_final: 0.7809 (mttm) REVERT: M 103 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8004 (tm-30) REVERT: M 269 MET cc_start: 0.8620 (mmm) cc_final: 0.7456 (mtt) REVERT: M 304 GLN cc_start: 0.7667 (tt0) cc_final: 0.6911 (tm-30) REVERT: M 379 LEU cc_start: 0.8961 (tp) cc_final: 0.8346 (tt) REVERT: M 396 MET cc_start: 0.8335 (mmp) cc_final: 0.7610 (mmp) REVERT: M 446 LEU cc_start: 0.9279 (mt) cc_final: 0.8799 (tp) REVERT: N 10 LEU cc_start: 0.8806 (tp) cc_final: 0.8502 (mt) REVERT: N 40 ILE cc_start: 0.8831 (mm) cc_final: 0.8422 (tt) REVERT: N 98 MET cc_start: 0.8517 (tpp) cc_final: 0.8126 (tpp) REVERT: N 134 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7872 (tm-30) REVERT: N 139 MET cc_start: 0.8299 (ttm) cc_final: 0.8078 (ttp) REVERT: N 164 ILE cc_start: 0.9249 (pt) cc_final: 0.8960 (mt) REVERT: N 187 MET cc_start: 0.8767 (mmp) cc_final: 0.8084 (mmm) REVERT: N 190 MET cc_start: 0.8205 (mmm) cc_final: 0.7803 (mtp) REVERT: N 268 GLN cc_start: 0.8550 (tm-30) cc_final: 0.7899 (tm-30) REVERT: N 269 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7237 (tp30) REVERT: N 284 ILE cc_start: 0.8810 (pt) cc_final: 0.8501 (mm) REVERT: N 294 MET cc_start: 0.8716 (mmm) cc_final: 0.8246 (mmm) REVERT: O 106 LEU cc_start: 0.8985 (tt) cc_final: 0.8488 (tp) REVERT: O 107 GLN cc_start: 0.9323 (pt0) cc_final: 0.9065 (pt0) REVERT: O 110 ASP cc_start: 0.8515 (m-30) cc_final: 0.8260 (m-30) REVERT: O 131 ASP cc_start: 0.8556 (m-30) cc_final: 0.7929 (t0) REVERT: O 152 TYR cc_start: 0.8701 (t80) cc_final: 0.7799 (t80) REVERT: V 61 GLU cc_start: 0.8057 (mp0) cc_final: 0.7763 (mp0) REVERT: Y 22 TYR cc_start: 0.7160 (m-80) cc_final: 0.6660 (m-10) REVERT: Y 89 TYR cc_start: 0.7659 (m-80) cc_final: 0.7365 (m-80) REVERT: a 18 ILE cc_start: 0.9431 (mm) cc_final: 0.9201 (mm) REVERT: a 43 TYR cc_start: 0.8534 (t80) cc_final: 0.8113 (t80) REVERT: e 41 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7066 (tm-30) REVERT: f 27 ASP cc_start: 0.8515 (p0) cc_final: 0.8266 (p0) REVERT: f 30 ASN cc_start: 0.8749 (m110) cc_final: 0.8307 (t0) REVERT: g 58 MET cc_start: 0.5547 (mmt) cc_final: 0.5171 (tpp) REVERT: g 76 PHE cc_start: 0.8390 (m-80) cc_final: 0.8106 (m-10) REVERT: g 92 GLU cc_start: 0.8395 (tp30) cc_final: 0.7761 (tp30) REVERT: g 96 LEU cc_start: 0.8830 (mt) cc_final: 0.8472 (tp) REVERT: g 98 LYS cc_start: 0.8779 (ptmt) cc_final: 0.8327 (pttm) REVERT: p 96 LYS cc_start: 0.8423 (tttm) cc_final: 0.8163 (tttt) REVERT: G 42 TYR cc_start: 0.8436 (t80) cc_final: 0.8167 (t80) REVERT: G 51 ASN cc_start: 0.8406 (t0) cc_final: 0.8170 (t0) REVERT: G 107 ILE cc_start: 0.9246 (pt) cc_final: 0.8902 (pt) REVERT: G 179 ASN cc_start: 0.8493 (m-40) cc_final: 0.8134 (m-40) REVERT: G 237 ASN cc_start: 0.8666 (m110) cc_final: 0.8225 (m-40) REVERT: r 26 ARG cc_start: 0.7979 (mmt180) cc_final: 0.6268 (ttt90) REVERT: d 45 ASP cc_start: 0.8789 (p0) cc_final: 0.8388 (p0) REVERT: d 76 LEU cc_start: 0.9103 (tt) cc_final: 0.8883 (tt) REVERT: d 87 ASP cc_start: 0.7957 (m-30) cc_final: 0.7553 (m-30) REVERT: X 31 TYR cc_start: 0.7622 (t80) cc_final: 0.7245 (t80) REVERT: X 56 LEU cc_start: 0.9290 (pp) cc_final: 0.8953 (pt) REVERT: X 105 GLN cc_start: 0.8919 (mp10) cc_final: 0.8621 (mp10) REVERT: X 108 GLU cc_start: 0.8887 (mp0) cc_final: 0.8654 (mp0) REVERT: m 78 ASN cc_start: 0.6813 (t0) cc_final: 0.6522 (t0) REVERT: m 84 LYS cc_start: 0.6602 (mptt) cc_final: 0.5610 (ptpp) REVERT: m 91 LEU cc_start: 0.7274 (mt) cc_final: 0.7050 (mt) REVERT: m 109 ASP cc_start: 0.8409 (m-30) cc_final: 0.7821 (p0) REVERT: n 19 TYR cc_start: 0.9144 (t80) cc_final: 0.8671 (t80) REVERT: n 33 ARG cc_start: 0.8249 (mmm160) cc_final: 0.7349 (mtt180) REVERT: n 52 ASN cc_start: 0.8007 (m-40) cc_final: 0.7567 (m-40) REVERT: Z 92 GLU cc_start: 0.8673 (pt0) cc_final: 0.8381 (pt0) outliers start: 5 outliers final: 0 residues processed: 1270 average time/residue: 0.4870 time to fit residues: 1053.5823 Evaluate side-chains 1011 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1011 time to evaluate : 4.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 664 optimal weight: 40.0000 chunk 505 optimal weight: 5.9990 chunk 348 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 320 optimal weight: 10.0000 chunk 451 optimal weight: 5.9990 chunk 674 optimal weight: 0.9980 chunk 714 optimal weight: 5.9990 chunk 352 optimal weight: 0.1980 chunk 639 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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** D 79 HIS ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 HIS ** F 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN H 292 ASN ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 205 ASN ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 ASN L 348 HIS L 405 ASN M 26 ASN ** M 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 293 HIS ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 415 GLN N 83 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN a 27 HIS ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.266 53802 Z= 0.596 Angle : 1.783 50.787 73768 Z= 1.147 Chirality : 0.333 6.448 8765 Planarity : 0.005 0.145 9627 Dihedral : 5.696 166.019 8289 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.98 % Favored : 90.47 % Rotamer: Outliers : 0.05 % Allowed : 4.13 % Favored : 95.82 % 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: -1.96 (0.10), residues: 6916 helix: -0.06 (0.09), residues: 3441 sheet: -0.80 (0.32), residues: 277 loop : -2.85 (0.10), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 30 HIS 0.008 0.001 HIS F 402 PHE 0.071 0.002 PHE G 215 TYR 0.034 0.002 TYR B 126 ARG 0.008 0.001 ARG F 349 *********************** 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 1222 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1220 time to evaluate : 4.369 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: A 56 PHE cc_start: 0.8835 (t80) cc_final: 0.8612 (t80) REVERT: A 60 ILE cc_start: 0.9089 (mm) cc_final: 0.8752 (mm) REVERT: A 72 LEU cc_start: 0.8843 (mp) cc_final: 0.8630 (mp) REVERT: B 58 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7688 (mm-30) REVERT: B 60 MET cc_start: 0.8177 (mtt) cc_final: 0.7944 (mtm) REVERT: B 62 MET cc_start: 0.8063 (mmp) cc_final: 0.7153 (mtp) REVERT: B 128 TYR cc_start: 0.8338 (m-80) cc_final: 0.8127 (m-80) REVERT: C 41 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8300 (tm-30) REVERT: C 82 ASP cc_start: 0.8029 (t0) cc_final: 0.7543 (t0) REVERT: C 108 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8404 (mttp) REVERT: C 153 THR cc_start: 0.8872 (p) cc_final: 0.8655 (p) REVERT: C 196 LYS cc_start: 0.8762 (ttpp) cc_final: 0.8184 (pttm) REVERT: C 203 TRP cc_start: 0.8994 (m100) cc_final: 0.8642 (m100) REVERT: D 97 LEU cc_start: 0.8915 (tt) cc_final: 0.8560 (mt) REVERT: D 108 TYR cc_start: 0.7510 (m-10) cc_final: 0.7214 (m-80) REVERT: D 111 MET cc_start: 0.7895 (ptp) cc_final: 0.7480 (ptm) REVERT: D 116 GLN cc_start: 0.8095 (tp-100) cc_final: 0.7759 (tp40) REVERT: D 217 ASN cc_start: 0.8381 (m-40) cc_final: 0.7392 (t0) REVERT: D 228 MET cc_start: 0.9034 (tpp) cc_final: 0.8644 (tpp) REVERT: D 338 MET cc_start: 0.8994 (ppp) cc_final: 0.8560 (tmm) REVERT: D 343 GLU cc_start: 0.7442 (pm20) cc_final: 0.7200 (pm20) REVERT: F 352 GLU cc_start: 0.7700 (pp20) cc_final: 0.7373 (tm-30) REVERT: F 409 ASP cc_start: 0.8111 (m-30) cc_final: 0.7876 (m-30) REVERT: H 15 LEU cc_start: 0.9038 (mt) cc_final: 0.8774 (mt) REVERT: H 49 ILE cc_start: 0.8407 (tp) cc_final: 0.8193 (tp) REVERT: H 108 MET cc_start: 0.8380 (mmt) cc_final: 0.7996 (mmp) REVERT: H 183 MET cc_start: 0.8071 (mtp) cc_final: 0.7373 (mtm) REVERT: H 188 SER cc_start: 0.9352 (m) cc_final: 0.8992 (p) REVERT: H 235 ASN cc_start: 0.8172 (m-40) cc_final: 0.7804 (m-40) REVERT: H 268 MET cc_start: 0.8196 (ttp) cc_final: 0.7783 (tmm) REVERT: I 110 ASP cc_start: 0.7469 (m-30) cc_final: 0.7149 (m-30) REVERT: I 153 LYS cc_start: 0.6565 (mtmt) cc_final: 0.6234 (mtmt) REVERT: I 173 TYR cc_start: 0.8013 (p90) cc_final: 0.7679 (p90) REVERT: J 36 SER cc_start: 0.9120 (m) cc_final: 0.8541 (p) REVERT: J 65 MET cc_start: 0.6578 (tpt) cc_final: 0.6329 (tpt) REVERT: J 70 TYR cc_start: 0.8099 (m-80) cc_final: 0.7669 (m-80) REVERT: J 74 MET cc_start: 0.8771 (mmp) cc_final: 0.8404 (mmt) REVERT: J 168 ILE cc_start: 0.9539 (mt) cc_final: 0.9282 (tt) REVERT: J 170 GLU cc_start: 0.8284 (tt0) cc_final: 0.8005 (tt0) REVERT: K 27 MET cc_start: 0.8457 (mmm) cc_final: 0.8005 (mmm) REVERT: K 47 THR cc_start: 0.8612 (p) cc_final: 0.8319 (p) REVERT: K 48 ILE cc_start: 0.9354 (mt) cc_final: 0.9104 (mt) REVERT: K 58 MET cc_start: 0.7057 (ptm) cc_final: 0.6828 (ptm) REVERT: K 63 LEU cc_start: 0.9211 (tp) cc_final: 0.8903 (tp) REVERT: K 70 GLU cc_start: 0.7623 (pt0) cc_final: 0.7329 (tt0) REVERT: K 76 SER cc_start: 0.9078 (p) cc_final: 0.8802 (t) REVERT: K 83 ASN cc_start: 0.8980 (m-40) cc_final: 0.8624 (t0) REVERT: L 53 MET cc_start: 0.8631 (mtm) cc_final: 0.8034 (mtm) REVERT: L 102 GLU cc_start: 0.8192 (tt0) cc_final: 0.7884 (tt0) REVERT: L 201 ILE cc_start: 0.8903 (pt) cc_final: 0.8640 (mt) REVERT: L 249 SER cc_start: 0.8849 (p) cc_final: 0.8567 (m) REVERT: L 278 LEU cc_start: 0.8503 (mt) cc_final: 0.7960 (tp) REVERT: L 313 MET cc_start: 0.8774 (mmt) cc_final: 0.8553 (mmt) REVERT: L 314 MET cc_start: 0.8467 (ttm) cc_final: 0.7858 (ttm) REVERT: L 323 TYR cc_start: 0.8387 (m-80) cc_final: 0.8116 (m-10) REVERT: L 389 PHE cc_start: 0.7163 (t80) cc_final: 0.6960 (t80) REVERT: L 532 ILE cc_start: 0.8445 (pt) cc_final: 0.7982 (pt) REVERT: L 540 MET cc_start: 0.8214 (mmm) cc_final: 0.7761 (tmm) REVERT: M 42 MET cc_start: 0.6861 (ttp) cc_final: 0.6629 (tmm) REVERT: M 70 MET cc_start: 0.8831 (mmm) cc_final: 0.8566 (tpp) REVERT: M 89 LEU cc_start: 0.8460 (mt) cc_final: 0.7860 (mt) REVERT: M 92 LYS cc_start: 0.8532 (mttt) cc_final: 0.7917 (mttm) REVERT: M 103 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8303 (tm-30) REVERT: M 200 MET cc_start: 0.8918 (mmp) cc_final: 0.8572 (mmp) REVERT: M 207 MET cc_start: 0.8459 (mmt) cc_final: 0.8220 (mmm) REVERT: M 236 LEU cc_start: 0.8573 (mm) cc_final: 0.8345 (mm) REVERT: M 269 MET cc_start: 0.8620 (mmm) cc_final: 0.7787 (mtt) REVERT: M 304 GLN cc_start: 0.7733 (tt0) cc_final: 0.6908 (tm-30) REVERT: M 316 MET cc_start: 0.8234 (mmm) cc_final: 0.7863 (mmm) REVERT: M 396 MET cc_start: 0.8298 (mmp) cc_final: 0.7902 (mmp) REVERT: M 446 LEU cc_start: 0.9292 (mt) cc_final: 0.8810 (tp) REVERT: N 40 ILE cc_start: 0.8862 (mm) cc_final: 0.8601 (tt) REVERT: N 98 MET cc_start: 0.8584 (tpp) cc_final: 0.8102 (tpp) REVERT: N 100 MET cc_start: 0.8046 (tpp) cc_final: 0.7831 (tpp) REVERT: N 164 ILE cc_start: 0.9241 (pt) cc_final: 0.8951 (mt) REVERT: N 268 GLN cc_start: 0.8579 (tm-30) cc_final: 0.7905 (tm-30) REVERT: N 269 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7253 (tp30) REVERT: N 282 MET cc_start: 0.8875 (mmm) cc_final: 0.8477 (mmm) REVERT: N 284 ILE cc_start: 0.8732 (pt) cc_final: 0.8532 (mm) REVERT: N 294 MET cc_start: 0.8831 (mmm) cc_final: 0.8412 (mmm) REVERT: O 106 LEU cc_start: 0.8981 (tt) cc_final: 0.8419 (tp) REVERT: O 110 ASP cc_start: 0.8674 (m-30) cc_final: 0.8192 (m-30) REVERT: O 131 ASP cc_start: 0.8536 (m-30) cc_final: 0.7942 (t0) REVERT: O 152 TYR cc_start: 0.8719 (t80) cc_final: 0.7835 (t80) REVERT: Y 22 TYR cc_start: 0.7207 (m-80) cc_final: 0.6678 (m-10) REVERT: Y 89 TYR cc_start: 0.7698 (m-80) cc_final: 0.7409 (m-80) REVERT: a 18 ILE cc_start: 0.9370 (mm) cc_final: 0.9079 (mm) REVERT: a 43 TYR cc_start: 0.8599 (t80) cc_final: 0.8160 (t80) REVERT: b 8 LEU cc_start: 0.8656 (tt) cc_final: 0.8222 (mm) REVERT: e 41 GLU cc_start: 0.7754 (mt-10) cc_final: 0.6927 (tm-30) REVERT: f 27 ASP cc_start: 0.8479 (p0) cc_final: 0.8145 (t0) REVERT: f 30 ASN cc_start: 0.8799 (m110) cc_final: 0.8254 (t0) REVERT: g 76 PHE cc_start: 0.8412 (m-80) cc_final: 0.8131 (m-10) REVERT: g 92 GLU cc_start: 0.8403 (tp30) cc_final: 0.7756 (tp30) REVERT: G 42 TYR cc_start: 0.8411 (t80) cc_final: 0.8141 (t80) REVERT: G 51 ASN cc_start: 0.8375 (t0) cc_final: 0.8078 (t0) REVERT: G 107 ILE cc_start: 0.9147 (pt) cc_final: 0.8926 (pt) REVERT: G 179 ASN cc_start: 0.8319 (m-40) cc_final: 0.7895 (m-40) REVERT: G 237 ASN cc_start: 0.8693 (m110) cc_final: 0.8433 (m-40) REVERT: r 26 ARG cc_start: 0.8146 (mmt180) cc_final: 0.6206 (ttt90) REVERT: d 45 ASP cc_start: 0.8707 (p0) cc_final: 0.8439 (p0) REVERT: X 108 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8573 (mm-30) REVERT: m 45 GLU cc_start: 0.8835 (pt0) cc_final: 0.8635 (pt0) REVERT: m 49 GLN cc_start: 0.8384 (mt0) cc_final: 0.8004 (tt0) REVERT: m 78 ASN cc_start: 0.6793 (t0) cc_final: 0.6558 (t0) REVERT: m 84 LYS cc_start: 0.6517 (mptt) cc_final: 0.5569 (ptpp) REVERT: m 91 LEU cc_start: 0.7472 (mt) cc_final: 0.7263 (mt) REVERT: m 97 LEU cc_start: 0.8732 (mt) cc_final: 0.8523 (mt) REVERT: m 109 ASP cc_start: 0.8306 (m-30) cc_final: 0.7807 (p0) REVERT: n 19 TYR cc_start: 0.9146 (t80) cc_final: 0.8629 (t80) REVERT: n 33 ARG cc_start: 0.8316 (mmm160) cc_final: 0.7265 (mtt180) REVERT: n 52 ASN cc_start: 0.7928 (m-40) cc_final: 0.7521 (m-40) REVERT: Z 92 GLU cc_start: 0.8788 (pt0) cc_final: 0.8340 (pt0) outliers start: 2 outliers final: 1 residues processed: 1221 average time/residue: 0.4848 time to fit residues: 1011.7163 Evaluate side-chains 990 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 989 time to evaluate : 5.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 594 optimal weight: 30.0000 chunk 405 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 531 optimal weight: 10.0000 chunk 294 optimal weight: 2.9990 chunk 609 optimal weight: 0.2980 chunk 493 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 364 optimal weight: 0.9990 chunk 641 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 280 GLN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 ASN ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN H 304 HIS ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 205 ASN L 230 HIS L 348 HIS ** M 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 440 HIS N 83 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 172 GLN V 49 GLN ** p 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN G 100 ASN G 198 ASN R 32 GLN n 13 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.250 53802 Z= 0.613 Angle : 1.798 51.078 73768 Z= 1.154 Chirality : 0.332 6.386 8765 Planarity : 0.005 0.145 9627 Dihedral : 5.747 166.941 8289 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.83 % Favored : 89.71 % Rotamer: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.37 % 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: -1.81 (0.10), residues: 6916 helix: 0.05 (0.09), residues: 3476 sheet: -0.68 (0.32), residues: 283 loop : -2.80 (0.10), residues: 3157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP N 30 HIS 0.010 0.001 HIS I 65 PHE 0.045 0.002 PHE I 139 TYR 0.028 0.002 TYR M 406 ARG 0.007 0.001 ARG i 15 *********************** 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 1174 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1171 time to evaluate : 4.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 60 ILE cc_start: 0.9139 (mm) cc_final: 0.8798 (mm) REVERT: B 48 MET cc_start: 0.7965 (tpp) cc_final: 0.7738 (tpp) REVERT: B 58 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7688 (tm-30) REVERT: B 137 ASP cc_start: 0.8167 (t0) cc_final: 0.7941 (t0) REVERT: B 156 LEU cc_start: 0.8660 (tp) cc_final: 0.8141 (tp) REVERT: C 41 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8261 (tm-30) REVERT: C 82 ASP cc_start: 0.7969 (t0) cc_final: 0.7531 (t0) REVERT: C 154 ASP cc_start: 0.7835 (t0) cc_final: 0.7557 (t0) REVERT: C 196 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8336 (pttm) REVERT: C 203 TRP cc_start: 0.9193 (m100) cc_final: 0.8556 (m100) REVERT: D 82 LEU cc_start: 0.9055 (mp) cc_final: 0.8842 (mp) REVERT: D 97 LEU cc_start: 0.8891 (tt) cc_final: 0.8579 (mt) REVERT: D 111 MET cc_start: 0.7998 (ptp) cc_final: 0.7307 (ptm) REVERT: D 169 TRP cc_start: 0.7834 (m-10) cc_final: 0.7367 (m-10) REVERT: D 217 ASN cc_start: 0.8445 (m-40) cc_final: 0.7413 (t0) REVERT: D 228 MET cc_start: 0.9201 (tpp) cc_final: 0.8604 (tpp) REVERT: D 242 ILE cc_start: 0.9152 (mt) cc_final: 0.8661 (mm) REVERT: D 338 MET cc_start: 0.8919 (ppp) cc_final: 0.8470 (tmm) REVERT: D 427 GLU cc_start: 0.7570 (mt-10) cc_final: 0.6981 (mt-10) REVERT: F 385 ARG cc_start: 0.7603 (mtm-85) cc_final: 0.7384 (ttp-110) REVERT: F 409 ASP cc_start: 0.8184 (m-30) cc_final: 0.7972 (m-30) REVERT: H 15 LEU cc_start: 0.9118 (mt) cc_final: 0.8867 (mt) REVERT: H 49 ILE cc_start: 0.8337 (tp) cc_final: 0.8102 (tp) REVERT: H 93 TYR cc_start: 0.7927 (m-10) cc_final: 0.7559 (m-80) REVERT: H 114 TYR cc_start: 0.8613 (m-80) cc_final: 0.8370 (m-80) REVERT: H 169 GLN cc_start: 0.8081 (mt0) cc_final: 0.7808 (mt0) REVERT: H 183 MET cc_start: 0.8097 (mtp) cc_final: 0.7707 (mtt) REVERT: H 235 ASN cc_start: 0.8138 (m-40) cc_final: 0.7801 (m-40) REVERT: I 110 ASP cc_start: 0.7533 (m-30) cc_final: 0.7136 (m-30) REVERT: I 146 GLU cc_start: 0.7445 (tt0) cc_final: 0.7202 (tt0) REVERT: I 153 LYS cc_start: 0.6771 (mtmt) cc_final: 0.6426 (mtmt) REVERT: I 173 TYR cc_start: 0.7861 (p90) cc_final: 0.7568 (p90) REVERT: J 28 TYR cc_start: 0.7394 (m-80) cc_final: 0.6895 (m-80) REVERT: J 33 LEU cc_start: 0.8677 (tp) cc_final: 0.6761 (tp) REVERT: J 36 SER cc_start: 0.9110 (m) cc_final: 0.8505 (p) REVERT: J 70 TYR cc_start: 0.8206 (m-80) cc_final: 0.7764 (m-80) REVERT: J 74 MET cc_start: 0.8823 (mmp) cc_final: 0.8503 (mmt) REVERT: J 99 MET cc_start: 0.8128 (tpp) cc_final: 0.7614 (tpt) REVERT: J 168 ILE cc_start: 0.9556 (mt) cc_final: 0.9337 (tt) REVERT: K 8 ILE cc_start: 0.9224 (pt) cc_final: 0.8984 (mt) REVERT: K 47 THR cc_start: 0.8743 (p) cc_final: 0.8396 (p) REVERT: K 70 GLU cc_start: 0.7566 (pt0) cc_final: 0.7173 (tt0) REVERT: K 76 SER cc_start: 0.9152 (p) cc_final: 0.8945 (t) REVERT: L 53 MET cc_start: 0.8425 (mtm) cc_final: 0.8052 (mtp) REVERT: L 71 ILE cc_start: 0.8508 (mt) cc_final: 0.8195 (mt) REVERT: L 102 GLU cc_start: 0.8328 (tt0) cc_final: 0.8081 (tt0) REVERT: L 201 ILE cc_start: 0.8928 (pt) cc_final: 0.8642 (mt) REVERT: L 278 LEU cc_start: 0.8511 (mt) cc_final: 0.7959 (tp) REVERT: L 286 LEU cc_start: 0.8957 (mt) cc_final: 0.8309 (mt) REVERT: L 313 MET cc_start: 0.8766 (mmt) cc_final: 0.8529 (mmt) REVERT: L 314 MET cc_start: 0.8536 (ttm) cc_final: 0.7867 (ttm) REVERT: L 323 TYR cc_start: 0.8466 (m-80) cc_final: 0.8165 (m-10) REVERT: L 368 PHE cc_start: 0.8499 (t80) cc_final: 0.7956 (t80) REVERT: L 411 MET cc_start: 0.9034 (mmp) cc_final: 0.8503 (mmt) REVERT: L 532 ILE cc_start: 0.8317 (pt) cc_final: 0.7752 (pt) REVERT: L 540 MET cc_start: 0.8151 (mmm) cc_final: 0.7668 (tmm) REVERT: M 89 LEU cc_start: 0.8468 (mt) cc_final: 0.7889 (mt) REVERT: M 92 LYS cc_start: 0.8459 (mttt) cc_final: 0.7988 (mttt) REVERT: M 103 GLN cc_start: 0.9061 (tm-30) cc_final: 0.8368 (tm-30) REVERT: M 200 MET cc_start: 0.8894 (mmp) cc_final: 0.8451 (mmp) REVERT: M 228 SER cc_start: 0.8843 (m) cc_final: 0.8069 (t) REVERT: M 236 LEU cc_start: 0.8582 (mm) cc_final: 0.8325 (mm) REVERT: M 269 MET cc_start: 0.8624 (mmm) cc_final: 0.7746 (mtt) REVERT: M 304 GLN cc_start: 0.7850 (tt0) cc_final: 0.7263 (tm-30) REVERT: M 310 MET cc_start: 0.8562 (mmt) cc_final: 0.8327 (mmt) REVERT: M 396 MET cc_start: 0.8357 (mmp) cc_final: 0.8078 (mmp) REVERT: M 441 ILE cc_start: 0.8920 (mt) cc_final: 0.8651 (mt) REVERT: M 446 LEU cc_start: 0.9332 (mt) cc_final: 0.8751 (tp) REVERT: N 34 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8343 (mm-30) REVERT: N 98 MET cc_start: 0.8581 (tpp) cc_final: 0.8166 (tpp) REVERT: N 158 SER cc_start: 0.9194 (m) cc_final: 0.8775 (p) REVERT: N 164 ILE cc_start: 0.9270 (pt) cc_final: 0.9021 (mt) REVERT: N 263 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8385 (mptt) REVERT: N 268 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8108 (tm-30) REVERT: N 269 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7370 (mm-30) REVERT: N 282 MET cc_start: 0.8841 (mmm) cc_final: 0.8587 (mmm) REVERT: N 291 TYR cc_start: 0.8578 (t80) cc_final: 0.8163 (t80) REVERT: N 294 MET cc_start: 0.8824 (mmm) cc_final: 0.8504 (mmm) REVERT: O 106 LEU cc_start: 0.9054 (tt) cc_final: 0.8509 (tp) REVERT: O 110 ASP cc_start: 0.8625 (m-30) cc_final: 0.8323 (m-30) REVERT: O 131 ASP cc_start: 0.8661 (m-30) cc_final: 0.8075 (t0) REVERT: O 152 TYR cc_start: 0.8733 (t80) cc_final: 0.7933 (t80) REVERT: V 48 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8188 (mt-10) REVERT: W 26 GLU cc_start: 0.8410 (pm20) cc_final: 0.8162 (pm20) REVERT: Y 22 TYR cc_start: 0.7610 (m-80) cc_final: 0.7043 (m-10) REVERT: Y 89 TYR cc_start: 0.7758 (m-80) cc_final: 0.7342 (m-80) REVERT: a 18 ILE cc_start: 0.9298 (mm) cc_final: 0.9082 (mm) REVERT: a 43 TYR cc_start: 0.8666 (t80) cc_final: 0.8240 (t80) REVERT: e 37 LYS cc_start: 0.8408 (mmpt) cc_final: 0.7905 (mttt) REVERT: e 41 GLU cc_start: 0.7563 (mt-10) cc_final: 0.6912 (tm-30) REVERT: f 30 ASN cc_start: 0.8826 (m110) cc_final: 0.8288 (t0) REVERT: g 76 PHE cc_start: 0.8487 (m-80) cc_final: 0.8186 (m-10) REVERT: g 92 GLU cc_start: 0.8247 (tp30) cc_final: 0.7842 (tp30) REVERT: G 42 TYR cc_start: 0.8486 (t80) cc_final: 0.8260 (t80) REVERT: G 51 ASN cc_start: 0.8436 (t0) cc_final: 0.8123 (t0) REVERT: G 107 ILE cc_start: 0.9079 (pt) cc_final: 0.8813 (pt) REVERT: G 179 ASN cc_start: 0.8497 (m-40) cc_final: 0.8061 (m-40) REVERT: G 237 ASN cc_start: 0.8780 (m110) cc_final: 0.8312 (t0) REVERT: R 32 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7476 (pp30) REVERT: X 108 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8614 (mm-30) REVERT: m 84 LYS cc_start: 0.6501 (mptt) cc_final: 0.5508 (ptpp) REVERT: m 97 LEU cc_start: 0.8806 (mt) cc_final: 0.8519 (mt) REVERT: m 109 ASP cc_start: 0.8435 (m-30) cc_final: 0.7979 (p0) REVERT: n 19 TYR cc_start: 0.9186 (t80) cc_final: 0.8688 (t80) REVERT: n 33 ARG cc_start: 0.8387 (mmm160) cc_final: 0.7339 (mtt180) REVERT: n 52 ASN cc_start: 0.7947 (m-40) cc_final: 0.7541 (m-40) REVERT: n 93 TYR cc_start: 0.5902 (m-10) cc_final: 0.5436 (m-10) REVERT: Z 81 ARG cc_start: 0.7284 (ttt-90) cc_final: 0.6683 (ttt-90) REVERT: Z 92 GLU cc_start: 0.8788 (pt0) cc_final: 0.8491 (pt0) outliers start: 3 outliers final: 0 residues processed: 1173 average time/residue: 0.4835 time to fit residues: 969.7111 Evaluate side-chains 962 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 961 time to evaluate : 5.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 240 optimal weight: 3.9990 chunk 643 optimal weight: 6.9990 chunk 141 optimal weight: 0.1980 chunk 419 optimal weight: 30.0000 chunk 176 optimal weight: 4.9990 chunk 715 optimal weight: 10.0000 chunk 593 optimal weight: 30.0000 chunk 331 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 375 optimal weight: 7.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 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 356 HIS F 373 ASN H 292 ASN ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 GLN ** L 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 HIS ** M 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 172 GLN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.246 53802 Z= 0.620 Angle : 1.806 51.078 73768 Z= 1.157 Chirality : 0.333 6.500 8765 Planarity : 0.005 0.143 9627 Dihedral : 5.818 167.660 8289 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.95 % Favored : 89.63 % Rotamer: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % 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: -1.80 (0.10), residues: 6916 helix: 0.10 (0.09), residues: 3463 sheet: -0.65 (0.32), residues: 274 loop : -2.83 (0.10), residues: 3179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP N 30 HIS 0.008 0.001 HIS F 402 PHE 0.031 0.002 PHE J 57 TYR 0.033 0.002 TYR M 406 ARG 0.012 0.001 ARG n 21 *********************** 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 1146 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1145 time to evaluate : 4.285 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: B 58 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7774 (tm-30) REVERT: B 62 MET cc_start: 0.7779 (mmp) cc_final: 0.7186 (mtm) REVERT: B 69 MET cc_start: 0.8687 (tmm) cc_final: 0.8257 (tmm) REVERT: B 131 SER cc_start: 0.8912 (p) cc_final: 0.8154 (t) REVERT: B 156 LEU cc_start: 0.8664 (tp) cc_final: 0.8043 (tp) REVERT: C 41 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8254 (tm-30) REVERT: C 203 TRP cc_start: 0.9171 (m100) cc_final: 0.8638 (m100) REVERT: D 97 LEU cc_start: 0.8850 (tt) cc_final: 0.8495 (mt) REVERT: D 111 MET cc_start: 0.7597 (ptp) cc_final: 0.7059 (ptp) REVERT: D 116 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7987 (mm-40) REVERT: D 189 MET cc_start: 0.8335 (ttm) cc_final: 0.8041 (ttm) REVERT: D 217 ASN cc_start: 0.8441 (m-40) cc_final: 0.7475 (t0) REVERT: D 242 ILE cc_start: 0.9087 (mt) cc_final: 0.8586 (mm) REVERT: D 276 ASP cc_start: 0.8084 (m-30) cc_final: 0.7840 (m-30) REVERT: D 338 MET cc_start: 0.9018 (ppp) cc_final: 0.8618 (tmm) REVERT: D 427 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6953 (mt-10) REVERT: F 409 ASP cc_start: 0.8149 (m-30) cc_final: 0.7944 (m-30) REVERT: H 15 LEU cc_start: 0.9158 (mt) cc_final: 0.8947 (mt) REVERT: H 183 MET cc_start: 0.8184 (mtp) cc_final: 0.7817 (mtt) REVERT: H 235 ASN cc_start: 0.8298 (m-40) cc_final: 0.7983 (m-40) REVERT: H 284 GLN cc_start: 0.8752 (pt0) cc_final: 0.8063 (pt0) REVERT: I 110 ASP cc_start: 0.7552 (m-30) cc_final: 0.7223 (m-30) REVERT: I 146 GLU cc_start: 0.7594 (tt0) cc_final: 0.7271 (tt0) REVERT: I 153 LYS cc_start: 0.6647 (mtmt) cc_final: 0.6387 (mtmt) REVERT: I 173 TYR cc_start: 0.7898 (p90) cc_final: 0.7637 (p90) REVERT: I 176 ARG cc_start: 0.8073 (mtt-85) cc_final: 0.7753 (mtt-85) REVERT: J 28 TYR cc_start: 0.7090 (m-80) cc_final: 0.6850 (m-80) REVERT: J 36 SER cc_start: 0.9059 (m) cc_final: 0.8569 (p) REVERT: K 47 THR cc_start: 0.8638 (p) cc_final: 0.8312 (p) REVERT: K 70 GLU cc_start: 0.7466 (pt0) cc_final: 0.7148 (tt0) REVERT: L 53 MET cc_start: 0.8566 (mtm) cc_final: 0.8240 (mtp) REVERT: L 71 ILE cc_start: 0.8625 (mt) cc_final: 0.8279 (mt) REVERT: L 101 MET cc_start: 0.8356 (mmp) cc_final: 0.7964 (mmp) REVERT: L 102 GLU cc_start: 0.8318 (tt0) cc_final: 0.8074 (tt0) REVERT: L 186 MET cc_start: 0.7243 (tpt) cc_final: 0.6842 (tpt) REVERT: L 201 ILE cc_start: 0.8993 (pt) cc_final: 0.8630 (mt) REVERT: L 278 LEU cc_start: 0.8525 (mt) cc_final: 0.8025 (tp) REVERT: L 286 LEU cc_start: 0.8907 (mt) cc_final: 0.8317 (mt) REVERT: L 313 MET cc_start: 0.8744 (mmt) cc_final: 0.8528 (mmt) REVERT: L 314 MET cc_start: 0.8677 (ttm) cc_final: 0.7965 (ttm) REVERT: L 323 TYR cc_start: 0.8458 (m-80) cc_final: 0.8164 (m-10) REVERT: L 368 PHE cc_start: 0.8601 (t80) cc_final: 0.7869 (t80) REVERT: L 411 MET cc_start: 0.9031 (mmp) cc_final: 0.8492 (mmt) REVERT: L 540 MET cc_start: 0.8090 (mmm) cc_final: 0.7609 (tmm) REVERT: L 544 MET cc_start: 0.7787 (mtp) cc_final: 0.7586 (mtp) REVERT: M 36 PHE cc_start: 0.8497 (t80) cc_final: 0.8273 (t80) REVERT: M 42 MET cc_start: 0.7122 (tmm) cc_final: 0.6897 (tmm) REVERT: M 89 LEU cc_start: 0.8642 (mt) cc_final: 0.8129 (mt) REVERT: M 92 LYS cc_start: 0.8560 (mttt) cc_final: 0.8065 (mttt) REVERT: M 103 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8764 (tm-30) REVERT: M 200 MET cc_start: 0.8906 (mmp) cc_final: 0.8210 (mmp) REVERT: M 204 MET cc_start: 0.7595 (mmp) cc_final: 0.7304 (mmm) REVERT: M 207 MET cc_start: 0.8520 (mmt) cc_final: 0.8048 (mpp) REVERT: M 228 SER cc_start: 0.8901 (m) cc_final: 0.8007 (t) REVERT: M 257 MET cc_start: 0.6206 (tpt) cc_final: 0.5992 (tpp) REVERT: M 304 GLN cc_start: 0.8012 (tt0) cc_final: 0.7630 (tm-30) REVERT: M 442 LEU cc_start: 0.9236 (pp) cc_final: 0.9034 (pp) REVERT: M 446 LEU cc_start: 0.9389 (mt) cc_final: 0.8687 (tp) REVERT: N 63 GLN cc_start: 0.7996 (mt0) cc_final: 0.7596 (mt0) REVERT: N 86 VAL cc_start: 0.8445 (m) cc_final: 0.8231 (m) REVERT: N 98 MET cc_start: 0.8551 (tpp) cc_final: 0.8138 (tpp) REVERT: N 158 SER cc_start: 0.9280 (m) cc_final: 0.8891 (p) REVERT: N 164 ILE cc_start: 0.9283 (pt) cc_final: 0.9040 (mt) REVERT: N 263 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8658 (mptt) REVERT: N 268 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8161 (tm-30) REVERT: N 269 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7426 (mm-30) REVERT: N 282 MET cc_start: 0.8854 (mmm) cc_final: 0.8521 (mmm) REVERT: N 294 MET cc_start: 0.8783 (mmm) cc_final: 0.8362 (mmm) REVERT: O 106 LEU cc_start: 0.9086 (tt) cc_final: 0.8427 (tp) REVERT: O 110 ASP cc_start: 0.8748 (m-30) cc_final: 0.8248 (m-30) REVERT: O 131 ASP cc_start: 0.8850 (m-30) cc_final: 0.8173 (t0) REVERT: O 152 TYR cc_start: 0.8766 (t80) cc_final: 0.8011 (t80) REVERT: W 26 GLU cc_start: 0.8341 (pm20) cc_final: 0.8089 (pm20) REVERT: W 65 MET cc_start: 0.8348 (ttp) cc_final: 0.8012 (tmm) REVERT: W 92 THR cc_start: 0.8717 (p) cc_final: 0.8471 (p) REVERT: Y 22 TYR cc_start: 0.7775 (m-80) cc_final: 0.7094 (m-10) REVERT: Y 89 TYR cc_start: 0.7810 (m-80) cc_final: 0.7360 (m-80) REVERT: a 43 TYR cc_start: 0.8679 (t80) cc_final: 0.8230 (t80) REVERT: e 41 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7019 (tm-30) REVERT: e 62 PHE cc_start: 0.8980 (t80) cc_final: 0.8762 (t80) REVERT: g 76 PHE cc_start: 0.8442 (m-80) cc_final: 0.8078 (m-10) REVERT: g 92 GLU cc_start: 0.8161 (tp30) cc_final: 0.7652 (tp30) REVERT: p 107 GLU cc_start: 0.7188 (pp20) cc_final: 0.6478 (pp20) REVERT: G 51 ASN cc_start: 0.8531 (t0) cc_final: 0.8207 (t0) REVERT: G 179 ASN cc_start: 0.8574 (m-40) cc_final: 0.8366 (m110) REVERT: Q 81 ASN cc_start: 0.8036 (m-40) cc_final: 0.7682 (m-40) REVERT: d 45 ASP cc_start: 0.8720 (p0) cc_final: 0.8500 (p0) REVERT: X 50 LYS cc_start: 0.5769 (tttt) cc_final: 0.4336 (tmtt) REVERT: X 108 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8687 (mm-30) REVERT: m 84 LYS cc_start: 0.6192 (mptt) cc_final: 0.5575 (ptpt) REVERT: m 97 LEU cc_start: 0.8814 (mt) cc_final: 0.8580 (mt) REVERT: n 19 TYR cc_start: 0.9227 (t80) cc_final: 0.8731 (t80) REVERT: n 33 ARG cc_start: 0.8382 (mmm160) cc_final: 0.7458 (mtt90) REVERT: n 93 TYR cc_start: 0.5749 (m-10) cc_final: 0.5319 (m-10) REVERT: Z 75 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7490 (tm-30) REVERT: Z 81 ARG cc_start: 0.7470 (ttt-90) cc_final: 0.6821 (ttt-90) REVERT: Z 92 GLU cc_start: 0.8762 (pt0) cc_final: 0.8445 (pt0) outliers start: 1 outliers final: 0 residues processed: 1146 average time/residue: 0.4757 time to fit residues: 938.0429 Evaluate side-chains 954 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 954 time to evaluate : 4.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 689 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 407 optimal weight: 10.0000 chunk 522 optimal weight: 30.0000 chunk 404 optimal weight: 10.0000 chunk 601 optimal weight: 0.9980 chunk 399 optimal weight: 20.0000 chunk 712 optimal weight: 10.0000 chunk 445 optimal weight: 6.9990 chunk 434 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** F 373 ASN H 292 ASN ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN ** L 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 HIS ** M 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 440 HIS ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 GLN O 257 HIS G 198 ASN r 51 ASN n 50 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.251 53802 Z= 0.630 Angle : 1.819 51.126 73768 Z= 1.162 Chirality : 0.334 6.429 8765 Planarity : 0.005 0.150 9627 Dihedral : 5.926 168.090 8289 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.48 % Favored : 89.11 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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: -1.82 (0.10), residues: 6916 helix: 0.07 (0.09), residues: 3493 sheet: -0.78 (0.31), residues: 287 loop : -2.85 (0.10), residues: 3136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP N 30 HIS 0.013 0.002 HIS L 332 PHE 0.033 0.002 PHE K 66 TYR 0.045 0.002 TYR D 108 ARG 0.012 0.001 ARG n 21 *********************** 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 1098 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1098 time to evaluate : 4.375 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: B 62 MET cc_start: 0.8088 (mmp) cc_final: 0.7213 (mtm) REVERT: B 69 MET cc_start: 0.8736 (tmm) cc_final: 0.8363 (tmm) REVERT: B 137 ASP cc_start: 0.8203 (t0) cc_final: 0.7996 (t0) REVERT: C 41 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8240 (tm-30) REVERT: C 82 ASP cc_start: 0.8230 (t0) cc_final: 0.7776 (t0) REVERT: C 99 LEU cc_start: 0.8627 (mt) cc_final: 0.8031 (pt) REVERT: C 102 ASN cc_start: 0.9007 (t0) cc_final: 0.8699 (t0) REVERT: C 108 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8459 (mttm) REVERT: C 203 TRP cc_start: 0.9161 (m100) cc_final: 0.8755 (m100) REVERT: D 111 MET cc_start: 0.7882 (ptp) cc_final: 0.7159 (ptp) REVERT: D 115 GLU cc_start: 0.7206 (pt0) cc_final: 0.6725 (pt0) REVERT: D 189 MET cc_start: 0.8134 (ttm) cc_final: 0.7708 (ttm) REVERT: D 217 ASN cc_start: 0.8515 (m-40) cc_final: 0.7499 (t0) REVERT: D 228 MET cc_start: 0.9154 (tpp) cc_final: 0.8085 (tmm) REVERT: D 239 THR cc_start: 0.8290 (m) cc_final: 0.8007 (m) REVERT: D 242 ILE cc_start: 0.9128 (mt) cc_final: 0.8618 (mm) REVERT: D 338 MET cc_start: 0.9035 (ppp) cc_final: 0.8627 (tmm) REVERT: D 427 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6971 (mt-10) REVERT: F 389 ILE cc_start: 0.8886 (mp) cc_final: 0.8677 (mp) REVERT: H 183 MET cc_start: 0.8178 (mtp) cc_final: 0.7873 (mtt) REVERT: H 284 GLN cc_start: 0.8664 (pt0) cc_final: 0.8089 (pt0) REVERT: I 110 ASP cc_start: 0.7553 (m-30) cc_final: 0.7212 (m-30) REVERT: I 146 GLU cc_start: 0.7709 (tt0) cc_final: 0.7339 (tt0) REVERT: I 153 LYS cc_start: 0.6719 (mtmt) cc_final: 0.6352 (mtmt) REVERT: I 176 ARG cc_start: 0.8253 (mtt-85) cc_final: 0.7928 (mtt-85) REVERT: J 36 SER cc_start: 0.9118 (m) cc_final: 0.8652 (p) REVERT: J 99 MET cc_start: 0.8061 (tpp) cc_final: 0.7821 (tpt) REVERT: K 34 GLU cc_start: 0.8503 (tp30) cc_final: 0.7263 (tp30) REVERT: K 70 GLU cc_start: 0.7598 (pt0) cc_final: 0.7183 (tt0) REVERT: L 53 MET cc_start: 0.8587 (mtm) cc_final: 0.8264 (mtp) REVERT: L 101 MET cc_start: 0.8200 (mmp) cc_final: 0.7960 (mmp) REVERT: L 102 GLU cc_start: 0.8303 (tt0) cc_final: 0.8059 (tt0) REVERT: L 201 ILE cc_start: 0.9009 (pt) cc_final: 0.8647 (mt) REVERT: L 278 LEU cc_start: 0.8668 (mt) cc_final: 0.8083 (tp) REVERT: L 286 LEU cc_start: 0.8977 (mt) cc_final: 0.8352 (mt) REVERT: L 313 MET cc_start: 0.8793 (mmt) cc_final: 0.8592 (mmt) REVERT: L 314 MET cc_start: 0.8696 (ttm) cc_final: 0.8039 (ttm) REVERT: L 323 TYR cc_start: 0.8359 (m-80) cc_final: 0.7952 (m-10) REVERT: L 341 MET cc_start: 0.8944 (ppp) cc_final: 0.8420 (ppp) REVERT: L 411 MET cc_start: 0.8969 (mmp) cc_final: 0.8483 (mmt) REVERT: L 532 ILE cc_start: 0.8459 (pt) cc_final: 0.8030 (pt) REVERT: L 540 MET cc_start: 0.8224 (mmm) cc_final: 0.7563 (tmm) REVERT: M 36 PHE cc_start: 0.8565 (t80) cc_final: 0.8348 (t80) REVERT: M 42 MET cc_start: 0.7252 (tmm) cc_final: 0.6987 (tmm) REVERT: M 70 MET cc_start: 0.8976 (mmm) cc_final: 0.8759 (mmp) REVERT: M 89 LEU cc_start: 0.8678 (mt) cc_final: 0.8449 (mt) REVERT: M 92 LYS cc_start: 0.8590 (mttt) cc_final: 0.8201 (mttm) REVERT: M 93 LYS cc_start: 0.8746 (mttp) cc_final: 0.8454 (mttt) REVERT: M 103 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8649 (tm-30) REVERT: M 200 MET cc_start: 0.8880 (mmp) cc_final: 0.8415 (mmp) REVERT: M 228 SER cc_start: 0.8599 (m) cc_final: 0.7911 (t) REVERT: M 257 MET cc_start: 0.6368 (tpt) cc_final: 0.6111 (tpp) REVERT: M 304 GLN cc_start: 0.8024 (tt0) cc_final: 0.7622 (tm-30) REVERT: M 442 LEU cc_start: 0.9270 (pp) cc_final: 0.9026 (pp) REVERT: M 446 LEU cc_start: 0.9383 (mt) cc_final: 0.8773 (tp) REVERT: N 63 GLN cc_start: 0.8091 (mt0) cc_final: 0.7657 (mt0) REVERT: N 79 MET cc_start: 0.8383 (mmm) cc_final: 0.8083 (mmt) REVERT: N 158 SER cc_start: 0.9315 (m) cc_final: 0.9096 (p) REVERT: N 164 ILE cc_start: 0.9270 (pt) cc_final: 0.9044 (mt) REVERT: N 215 MET cc_start: 0.7842 (mmt) cc_final: 0.7523 (mmt) REVERT: N 263 LYS cc_start: 0.8902 (mmtt) cc_final: 0.8548 (mptt) REVERT: N 268 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8256 (tm-30) REVERT: N 269 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7463 (mm-30) REVERT: N 294 MET cc_start: 0.8740 (mmm) cc_final: 0.8422 (mmm) REVERT: O 106 LEU cc_start: 0.9092 (tt) cc_final: 0.8421 (tp) REVERT: O 110 ASP cc_start: 0.8729 (m-30) cc_final: 0.8197 (m-30) REVERT: O 131 ASP cc_start: 0.8669 (m-30) cc_final: 0.8081 (t0) REVERT: O 152 TYR cc_start: 0.8766 (t80) cc_final: 0.8090 (t80) REVERT: W 26 GLU cc_start: 0.8283 (pm20) cc_final: 0.8006 (pm20) REVERT: W 65 MET cc_start: 0.8336 (ttp) cc_final: 0.8015 (tmm) REVERT: Y 22 TYR cc_start: 0.8061 (m-80) cc_final: 0.7701 (m-80) REVERT: Y 89 TYR cc_start: 0.7849 (m-80) cc_final: 0.7385 (m-80) REVERT: a 1 MET cc_start: 0.6761 (mmm) cc_final: 0.6317 (mmm) REVERT: a 43 TYR cc_start: 0.8711 (t80) cc_final: 0.8265 (t80) REVERT: e 41 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7095 (tm-30) REVERT: e 62 PHE cc_start: 0.9024 (t80) cc_final: 0.8764 (t80) REVERT: g 76 PHE cc_start: 0.8429 (m-80) cc_final: 0.8048 (m-10) REVERT: g 85 MET cc_start: 0.9119 (ptp) cc_final: 0.8878 (pmm) REVERT: g 87 GLU cc_start: 0.8660 (pm20) cc_final: 0.8338 (pm20) REVERT: g 92 GLU cc_start: 0.8156 (tp30) cc_final: 0.7651 (tp30) REVERT: p 107 GLU cc_start: 0.6886 (pp20) cc_final: 0.6174 (pp20) REVERT: p 136 LYS cc_start: 0.9124 (tmtt) cc_final: 0.8732 (tppp) REVERT: G 51 ASN cc_start: 0.8492 (t0) cc_final: 0.8205 (t0) REVERT: Q 81 ASN cc_start: 0.8070 (m-40) cc_final: 0.7707 (m-40) REVERT: h 42 LEU cc_start: 0.8940 (mm) cc_final: 0.8721 (tp) REVERT: X 60 LYS cc_start: 0.9115 (pptt) cc_final: 0.8317 (mppt) REVERT: X 61 LEU cc_start: 0.9033 (tt) cc_final: 0.8790 (tt) REVERT: X 108 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8689 (mm-30) REVERT: m 84 LYS cc_start: 0.6586 (mptt) cc_final: 0.5904 (ptpt) REVERT: m 97 LEU cc_start: 0.8721 (mt) cc_final: 0.8468 (mt) REVERT: m 109 ASP cc_start: 0.8333 (m-30) cc_final: 0.7654 (p0) REVERT: n 19 TYR cc_start: 0.9207 (t80) cc_final: 0.8753 (t80) REVERT: n 33 ARG cc_start: 0.8388 (mmm160) cc_final: 0.7396 (mtt90) REVERT: n 93 TYR cc_start: 0.6426 (m-10) cc_final: 0.5816 (m-10) REVERT: Z 81 ARG cc_start: 0.7486 (ttt-90) cc_final: 0.7225 (tmt170) REVERT: Z 85 MET cc_start: 0.8833 (mmp) cc_final: 0.8579 (mmm) REVERT: Z 92 GLU cc_start: 0.8762 (pt0) cc_final: 0.8447 (pt0) outliers start: 0 outliers final: 0 residues processed: 1098 average time/residue: 0.4917 time to fit residues: 927.9281 Evaluate side-chains 913 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 913 time to evaluate : 4.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 440 optimal weight: 1.9990 chunk 284 optimal weight: 0.6980 chunk 425 optimal weight: 30.0000 chunk 214 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 452 optimal weight: 3.9990 chunk 485 optimal weight: 4.9990 chunk 352 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 559 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 356 HIS ** F 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN H 284 GLN H 292 ASN ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN L 348 HIS ** M 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 GLN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.256 53802 Z= 0.595 Angle : 1.795 50.764 73768 Z= 1.151 Chirality : 0.332 6.392 8765 Planarity : 0.005 0.144 9627 Dihedral : 5.696 169.185 8289 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.60 % Favored : 90.02 % Rotamer: Outliers : 0.03 % Allowed : 1.41 % Favored : 98.56 % 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: -1.64 (0.10), residues: 6916 helix: 0.27 (0.09), residues: 3450 sheet: -0.66 (0.32), residues: 273 loop : -2.78 (0.10), residues: 3193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP N 30 HIS 0.009 0.001 HIS L 332 PHE 0.033 0.002 PHE C 142 TYR 0.041 0.002 TYR D 108 ARG 0.014 0.001 ARG D 388 *********************** 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 1142 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1141 time to evaluate : 4.399 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: B 62 MET cc_start: 0.8019 (mmp) cc_final: 0.7292 (mtm) REVERT: B 69 MET cc_start: 0.8598 (tmm) cc_final: 0.8268 (tmm) REVERT: B 131 SER cc_start: 0.8923 (p) cc_final: 0.7929 (t) REVERT: B 137 ASP cc_start: 0.8391 (t0) cc_final: 0.8143 (t0) REVERT: C 41 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8271 (tm-30) REVERT: C 99 LEU cc_start: 0.8598 (mt) cc_final: 0.8007 (pt) REVERT: C 102 ASN cc_start: 0.8934 (t0) cc_final: 0.8598 (t0) REVERT: D 82 LEU cc_start: 0.9247 (mm) cc_final: 0.8868 (mt) REVERT: D 108 TYR cc_start: 0.7175 (m-80) cc_final: 0.6851 (m-80) REVERT: D 189 MET cc_start: 0.7995 (ttm) cc_final: 0.7702 (ttm) REVERT: D 217 ASN cc_start: 0.8410 (m-40) cc_final: 0.7473 (t0) REVERT: D 228 MET cc_start: 0.9089 (tpp) cc_final: 0.7975 (tmm) REVERT: D 242 ILE cc_start: 0.9146 (mt) cc_final: 0.8652 (mm) REVERT: D 338 MET cc_start: 0.8959 (ppp) cc_final: 0.8462 (tmm) REVERT: D 427 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6962 (mt-10) REVERT: H 183 MET cc_start: 0.8109 (mtp) cc_final: 0.7797 (mtt) REVERT: H 235 ASN cc_start: 0.8515 (m-40) cc_final: 0.7993 (m-40) REVERT: H 284 GLN cc_start: 0.8616 (pt0) cc_final: 0.8027 (pt0) REVERT: H 307 LEU cc_start: 0.9214 (mt) cc_final: 0.8894 (tp) REVERT: I 110 ASP cc_start: 0.7473 (m-30) cc_final: 0.7189 (m-30) REVERT: I 146 GLU cc_start: 0.7459 (tt0) cc_final: 0.7145 (tt0) REVERT: I 153 LYS cc_start: 0.6524 (mtmt) cc_final: 0.6126 (mtmt) REVERT: I 176 ARG cc_start: 0.8222 (mtt-85) cc_final: 0.7853 (mtt-85) REVERT: J 36 SER cc_start: 0.9084 (m) cc_final: 0.8576 (p) REVERT: J 170 GLU cc_start: 0.8357 (tt0) cc_final: 0.8096 (tt0) REVERT: K 34 GLU cc_start: 0.8540 (tp30) cc_final: 0.6741 (tp30) REVERT: K 37 MET cc_start: 0.8323 (tmm) cc_final: 0.6606 (tmm) REVERT: K 47 THR cc_start: 0.8601 (p) cc_final: 0.8355 (p) REVERT: K 70 GLU cc_start: 0.7435 (pt0) cc_final: 0.6990 (tt0) REVERT: L 53 MET cc_start: 0.8535 (mtm) cc_final: 0.8273 (mtp) REVERT: L 71 ILE cc_start: 0.8586 (mt) cc_final: 0.8181 (mt) REVERT: L 102 GLU cc_start: 0.8304 (tt0) cc_final: 0.8046 (tt0) REVERT: L 201 ILE cc_start: 0.8984 (pt) cc_final: 0.8572 (mt) REVERT: L 226 GLN cc_start: 0.8201 (mm110) cc_final: 0.7427 (mm-40) REVERT: L 278 LEU cc_start: 0.8553 (mt) cc_final: 0.8096 (tp) REVERT: L 286 LEU cc_start: 0.8908 (mt) cc_final: 0.8312 (mt) REVERT: L 341 MET cc_start: 0.8905 (ppp) cc_final: 0.8417 (ppp) REVERT: L 411 MET cc_start: 0.8998 (mmp) cc_final: 0.8504 (mmt) REVERT: L 540 MET cc_start: 0.7992 (mmm) cc_final: 0.7745 (tmm) REVERT: L 544 MET cc_start: 0.7800 (mtp) cc_final: 0.7469 (mmp) REVERT: M 3 LYS cc_start: 0.6612 (mmtp) cc_final: 0.5419 (mmtm) REVERT: M 36 PHE cc_start: 0.8531 (t80) cc_final: 0.8330 (t80) REVERT: M 42 MET cc_start: 0.7128 (tmm) cc_final: 0.6907 (tmm) REVERT: M 70 MET cc_start: 0.8986 (mmm) cc_final: 0.8604 (mmt) REVERT: M 76 MET cc_start: 0.8825 (mmm) cc_final: 0.8580 (mmt) REVERT: M 89 LEU cc_start: 0.8644 (mt) cc_final: 0.8433 (mt) REVERT: M 92 LYS cc_start: 0.8535 (mttt) cc_final: 0.8185 (mttm) REVERT: M 93 LYS cc_start: 0.8626 (mttp) cc_final: 0.8394 (mttt) REVERT: M 103 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8735 (tm-30) REVERT: M 106 LEU cc_start: 0.9335 (mm) cc_final: 0.9075 (mm) REVERT: M 113 MET cc_start: 0.8418 (mtt) cc_final: 0.8163 (mtt) REVERT: M 200 MET cc_start: 0.8839 (mmp) cc_final: 0.8410 (mmp) REVERT: M 201 MET cc_start: 0.8113 (tpp) cc_final: 0.7699 (tmm) REVERT: M 228 SER cc_start: 0.8477 (m) cc_final: 0.7737 (t) REVERT: M 257 MET cc_start: 0.6385 (tpt) cc_final: 0.5969 (tpp) REVERT: M 304 GLN cc_start: 0.8010 (tt0) cc_final: 0.7587 (tm-30) REVERT: M 446 LEU cc_start: 0.9394 (mt) cc_final: 0.8742 (tp) REVERT: N 58 LYS cc_start: 0.9003 (mttt) cc_final: 0.8703 (mttm) REVERT: N 158 SER cc_start: 0.9367 (m) cc_final: 0.9081 (p) REVERT: N 164 ILE cc_start: 0.9288 (pt) cc_final: 0.8977 (mt) REVERT: N 215 MET cc_start: 0.7851 (mmt) cc_final: 0.7554 (mmt) REVERT: N 268 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8320 (tm-30) REVERT: N 270 MET cc_start: 0.8823 (mmm) cc_final: 0.8567 (tpp) REVERT: N 291 TYR cc_start: 0.8549 (t80) cc_final: 0.8074 (t80) REVERT: N 294 MET cc_start: 0.8651 (mmm) cc_final: 0.8367 (mmm) REVERT: O 106 LEU cc_start: 0.9039 (tt) cc_final: 0.8326 (tp) REVERT: O 110 ASP cc_start: 0.8671 (m-30) cc_final: 0.8094 (m-30) REVERT: O 131 ASP cc_start: 0.8736 (m-30) cc_final: 0.7937 (t0) REVERT: O 152 TYR cc_start: 0.8676 (t80) cc_final: 0.7996 (t80) REVERT: W 26 GLU cc_start: 0.8239 (pm20) cc_final: 0.7957 (pm20) REVERT: W 65 MET cc_start: 0.8301 (ttp) cc_final: 0.7970 (tmm) REVERT: Y 89 TYR cc_start: 0.7800 (m-80) cc_final: 0.7320 (m-80) REVERT: a 18 ILE cc_start: 0.9295 (mm) cc_final: 0.9082 (mm) REVERT: a 43 TYR cc_start: 0.8563 (t80) cc_final: 0.8197 (t80) REVERT: b 8 LEU cc_start: 0.8589 (tt) cc_final: 0.8181 (mm) REVERT: e 41 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7029 (tm-30) REVERT: e 62 PHE cc_start: 0.8939 (t80) cc_final: 0.8661 (t80) REVERT: f 15 LEU cc_start: 0.9124 (mt) cc_final: 0.8913 (mt) REVERT: g 58 MET cc_start: 0.5574 (mmt) cc_final: 0.5269 (mpp) REVERT: g 76 PHE cc_start: 0.8326 (m-80) cc_final: 0.7978 (m-10) REVERT: g 85 MET cc_start: 0.9051 (ptp) cc_final: 0.8785 (pmm) REVERT: g 92 GLU cc_start: 0.8192 (tp30) cc_final: 0.7659 (tp30) REVERT: p 107 GLU cc_start: 0.6637 (pp20) cc_final: 0.6006 (pp20) REVERT: p 136 LYS cc_start: 0.9162 (tmtt) cc_final: 0.8771 (tppp) REVERT: G 51 ASN cc_start: 0.8292 (t0) cc_final: 0.8051 (t0) REVERT: Q 81 ASN cc_start: 0.7902 (m-40) cc_final: 0.7520 (m-40) REVERT: h 28 TYR cc_start: 0.8332 (m-80) cc_final: 0.8131 (m-10) REVERT: h 42 LEU cc_start: 0.8932 (mm) cc_final: 0.8710 (tp) REVERT: d 81 TYR cc_start: 0.9076 (t80) cc_final: 0.8817 (t80) REVERT: X 83 GLU cc_start: 0.8313 (tp30) cc_final: 0.8007 (tp30) REVERT: X 108 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8641 (mm-30) REVERT: m 84 LYS cc_start: 0.6371 (mptt) cc_final: 0.5716 (ptpt) REVERT: m 97 LEU cc_start: 0.8753 (mt) cc_final: 0.8441 (mt) REVERT: m 109 ASP cc_start: 0.8203 (m-30) cc_final: 0.7590 (p0) REVERT: n 19 TYR cc_start: 0.9184 (t80) cc_final: 0.8770 (t80) REVERT: n 33 ARG cc_start: 0.8350 (mmm160) cc_final: 0.7367 (mtt90) REVERT: n 93 TYR cc_start: 0.6369 (m-10) cc_final: 0.5768 (m-10) REVERT: Z 81 ARG cc_start: 0.7520 (ttt-90) cc_final: 0.6750 (ttt-90) REVERT: Z 92 GLU cc_start: 0.8728 (pt0) cc_final: 0.8393 (pt0) outliers start: 1 outliers final: 0 residues processed: 1142 average time/residue: 0.4972 time to fit residues: 977.5526 Evaluate side-chains 947 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 947 time to evaluate : 4.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 647 optimal weight: 0.5980 chunk 682 optimal weight: 20.0000 chunk 622 optimal weight: 40.0000 chunk 663 optimal weight: 3.9990 chunk 399 optimal weight: 20.0000 chunk 289 optimal weight: 5.9990 chunk 521 optimal weight: 20.0000 chunk 203 optimal weight: 0.8980 chunk 599 optimal weight: 30.0000 chunk 627 optimal weight: 50.0000 chunk 661 optimal weight: 7.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 HIS ** 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 373 ASN ** 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 348 HIS ** M 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 440 HIS ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 GLN V 49 GLN G 198 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.251 53802 Z= 0.636 Angle : 1.829 51.099 73768 Z= 1.165 Chirality : 0.333 6.510 8765 Planarity : 0.005 0.147 9627 Dihedral : 5.914 168.900 8289 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.95 % Favored : 88.69 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -1.76 (0.10), residues: 6916 helix: 0.17 (0.09), residues: 3476 sheet: -0.84 (0.31), residues: 284 loop : -2.85 (0.10), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP N 30 HIS 0.009 0.002 HIS L 332 PHE 0.055 0.002 PHE I 139 TYR 0.034 0.002 TYR D 108 ARG 0.015 0.001 ARG F 420 *********************** 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 1062 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1062 time to evaluate : 4.417 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: A 67 LEU cc_start: 0.9223 (mm) cc_final: 0.8988 (mt) REVERT: B 62 MET cc_start: 0.8146 (mmp) cc_final: 0.7286 (mtm) REVERT: B 69 MET cc_start: 0.8649 (tmm) cc_final: 0.8348 (tmm) REVERT: B 131 SER cc_start: 0.9067 (p) cc_final: 0.8381 (t) REVERT: C 38 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8468 (mt0) REVERT: C 41 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8178 (tm-30) REVERT: C 102 ASN cc_start: 0.8973 (t0) cc_final: 0.8603 (t0) REVERT: C 108 LYS cc_start: 0.8649 (mttp) cc_final: 0.8361 (mttm) REVERT: C 203 TRP cc_start: 0.9239 (m100) cc_final: 0.8769 (m100) REVERT: D 82 LEU cc_start: 0.9376 (mm) cc_final: 0.9101 (mm) REVERT: D 189 MET cc_start: 0.8199 (ttm) cc_final: 0.7999 (ttm) REVERT: D 217 ASN cc_start: 0.8561 (m-40) cc_final: 0.7533 (t0) REVERT: D 228 MET cc_start: 0.9118 (tpp) cc_final: 0.8072 (tmm) REVERT: D 242 ILE cc_start: 0.9162 (mt) cc_final: 0.8615 (mt) REVERT: D 338 MET cc_start: 0.8995 (ppp) cc_final: 0.8531 (tmm) REVERT: D 342 MET cc_start: 0.8800 (tpt) cc_final: 0.8504 (tpt) REVERT: D 427 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7213 (mt-10) REVERT: F 373 ASN cc_start: 0.8435 (t0) cc_final: 0.7964 (t0) REVERT: H 170 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7036 (mm-30) REVERT: H 183 MET cc_start: 0.8307 (mtp) cc_final: 0.8047 (mtt) REVERT: H 235 ASN cc_start: 0.8767 (m-40) cc_final: 0.8219 (m-40) REVERT: H 284 GLN cc_start: 0.8451 (pt0) cc_final: 0.8016 (pt0) REVERT: I 110 ASP cc_start: 0.7624 (m-30) cc_final: 0.7248 (m-30) REVERT: I 146 GLU cc_start: 0.7690 (tt0) cc_final: 0.7337 (tt0) REVERT: I 153 LYS cc_start: 0.6754 (mtmt) cc_final: 0.6407 (mtmt) REVERT: I 176 ARG cc_start: 0.8354 (mtt-85) cc_final: 0.7972 (mtt-85) REVERT: J 36 SER cc_start: 0.9165 (m) cc_final: 0.8622 (p) REVERT: J 99 MET cc_start: 0.7950 (tpp) cc_final: 0.7619 (tpt) REVERT: J 170 GLU cc_start: 0.8357 (tt0) cc_final: 0.8089 (tt0) REVERT: K 9 MET cc_start: 0.8577 (mmp) cc_final: 0.8349 (mmm) REVERT: K 27 MET cc_start: 0.8544 (mmm) cc_final: 0.8264 (mmm) REVERT: K 37 MET cc_start: 0.8386 (tmm) cc_final: 0.7246 (tmm) REVERT: K 69 CYS cc_start: 0.7801 (p) cc_final: 0.7353 (p) REVERT: L 53 MET cc_start: 0.8548 (mtm) cc_final: 0.8265 (mtp) REVERT: L 102 GLU cc_start: 0.8347 (tt0) cc_final: 0.8119 (tt0) REVERT: L 186 MET cc_start: 0.7315 (tpt) cc_final: 0.7087 (tpt) REVERT: L 201 ILE cc_start: 0.9033 (pt) cc_final: 0.8653 (mt) REVERT: L 278 LEU cc_start: 0.8553 (mt) cc_final: 0.7984 (tp) REVERT: L 286 LEU cc_start: 0.8854 (mt) cc_final: 0.8239 (mt) REVERT: L 290 MET cc_start: 0.8603 (mmp) cc_final: 0.8338 (mmp) REVERT: L 341 MET cc_start: 0.8854 (ppp) cc_final: 0.8430 (ppp) REVERT: L 411 MET cc_start: 0.9038 (mmp) cc_final: 0.8533 (mmt) REVERT: L 540 MET cc_start: 0.8169 (mmm) cc_final: 0.7569 (tmm) REVERT: M 3 LYS cc_start: 0.6600 (mmtp) cc_final: 0.5366 (mmtm) REVERT: M 36 PHE cc_start: 0.8596 (t80) cc_final: 0.8374 (t80) REVERT: M 42 MET cc_start: 0.7155 (tmm) cc_final: 0.6743 (tmm) REVERT: M 70 MET cc_start: 0.9047 (mmm) cc_final: 0.8653 (mmt) REVERT: M 76 MET cc_start: 0.8847 (mmm) cc_final: 0.8523 (mmt) REVERT: M 89 LEU cc_start: 0.8618 (mt) cc_final: 0.8288 (mt) REVERT: M 92 LYS cc_start: 0.8683 (mttt) cc_final: 0.8321 (mttt) REVERT: M 93 LYS cc_start: 0.8720 (mttp) cc_final: 0.8469 (mttt) REVERT: M 113 MET cc_start: 0.8754 (mtt) cc_final: 0.8284 (mtt) REVERT: M 200 MET cc_start: 0.8874 (mmp) cc_final: 0.8436 (mmp) REVERT: M 228 SER cc_start: 0.8430 (m) cc_final: 0.7875 (t) REVERT: M 257 MET cc_start: 0.6507 (tpt) cc_final: 0.6052 (tpp) REVERT: M 271 MET cc_start: 0.6872 (mtm) cc_final: 0.6635 (mtt) REVERT: M 304 GLN cc_start: 0.8050 (tt0) cc_final: 0.7614 (tm-30) REVERT: M 446 LEU cc_start: 0.9392 (mt) cc_final: 0.8790 (tp) REVERT: N 27 LEU cc_start: 0.9324 (tt) cc_final: 0.9078 (tt) REVERT: N 37 MET cc_start: 0.7942 (mmm) cc_final: 0.7484 (mmm) REVERT: N 58 LYS cc_start: 0.9010 (mttt) cc_final: 0.8700 (mttm) REVERT: N 63 GLN cc_start: 0.8081 (mt0) cc_final: 0.7609 (mt0) REVERT: N 164 ILE cc_start: 0.9301 (pt) cc_final: 0.9035 (mt) REVERT: N 215 MET cc_start: 0.7834 (mmt) cc_final: 0.7369 (mmt) REVERT: N 248 LEU cc_start: 0.7989 (tp) cc_final: 0.7743 (tp) REVERT: N 294 MET cc_start: 0.8780 (mmm) cc_final: 0.8465 (mmm) REVERT: O 106 LEU cc_start: 0.9220 (tt) cc_final: 0.8433 (tp) REVERT: O 110 ASP cc_start: 0.8727 (m-30) cc_final: 0.8208 (m-30) REVERT: O 131 ASP cc_start: 0.8855 (m-30) cc_final: 0.7884 (t0) REVERT: O 152 TYR cc_start: 0.8744 (t80) cc_final: 0.8061 (t80) REVERT: W 65 MET cc_start: 0.8328 (ttp) cc_final: 0.7980 (tmm) REVERT: Y 89 TYR cc_start: 0.7871 (m-80) cc_final: 0.7339 (m-80) REVERT: Y 117 MET cc_start: 0.8568 (tpp) cc_final: 0.8220 (tpt) REVERT: a 18 ILE cc_start: 0.9253 (mm) cc_final: 0.9052 (mm) REVERT: a 43 TYR cc_start: 0.8680 (t80) cc_final: 0.8217 (t80) REVERT: e 36 GLU cc_start: 0.7697 (pp20) cc_final: 0.7276 (pp20) REVERT: e 41 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7219 (tm-30) REVERT: e 62 PHE cc_start: 0.9001 (t80) cc_final: 0.8741 (t80) REVERT: g 58 MET cc_start: 0.5853 (mmt) cc_final: 0.5484 (mmt) REVERT: g 76 PHE cc_start: 0.8396 (m-80) cc_final: 0.8070 (m-10) REVERT: g 87 GLU cc_start: 0.8670 (pm20) cc_final: 0.8361 (pm20) REVERT: g 92 GLU cc_start: 0.8189 (tp30) cc_final: 0.7826 (tp30) REVERT: p 107 GLU cc_start: 0.6779 (pp20) cc_final: 0.6050 (pp20) REVERT: G 51 ASN cc_start: 0.8444 (t0) cc_final: 0.8181 (t0) REVERT: Q 81 ASN cc_start: 0.7947 (m-40) cc_final: 0.7614 (m-40) REVERT: h 42 LEU cc_start: 0.9034 (mm) cc_final: 0.8760 (tp) REVERT: d 64 TYR cc_start: 0.8281 (m-10) cc_final: 0.8072 (m-10) REVERT: X 108 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8635 (mm-30) REVERT: m 84 LYS cc_start: 0.6518 (mptt) cc_final: 0.5597 (mtmt) REVERT: n 19 TYR cc_start: 0.9209 (t80) cc_final: 0.8767 (t80) REVERT: n 33 ARG cc_start: 0.8406 (mmm160) cc_final: 0.7363 (mtt90) REVERT: n 49 GLU cc_start: 0.7590 (pt0) cc_final: 0.7350 (pt0) REVERT: Z 81 ARG cc_start: 0.7325 (ttt-90) cc_final: 0.7090 (tmt170) REVERT: Z 85 MET cc_start: 0.8873 (mmp) cc_final: 0.8587 (mmm) REVERT: Z 92 GLU cc_start: 0.8784 (pt0) cc_final: 0.8448 (pt0) outliers start: 0 outliers final: 0 residues processed: 1062 average time/residue: 0.5514 time to fit residues: 1011.1084 Evaluate side-chains 902 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 902 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 435 optimal weight: 5.9990 chunk 701 optimal weight: 7.9990 chunk 428 optimal weight: 9.9990 chunk 332 optimal weight: 0.0980 chunk 487 optimal weight: 8.9990 chunk 736 optimal weight: 9.9990 chunk 677 optimal weight: 3.9990 chunk 586 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 452 optimal weight: 0.8980 chunk 359 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN ** B 127 HIS ** 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 356 HIS ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN H 284 GLN ** I 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN L 348 HIS ** M 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.260 53802 Z= 0.599 Angle : 1.801 50.758 73768 Z= 1.151 Chirality : 0.332 6.396 8765 Planarity : 0.005 0.144 9627 Dihedral : 5.654 170.399 8289 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.25 % Favored : 90.41 % Rotamer: Outliers : 0.03 % Allowed : 0.43 % Favored : 99.55 % 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: -1.57 (0.10), residues: 6916 helix: 0.31 (0.09), residues: 3454 sheet: -0.61 (0.31), residues: 274 loop : -2.72 (0.11), residues: 3188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP N 30 HIS 0.011 0.001 HIS H 304 PHE 0.042 0.002 PHE I 139 TYR 0.061 0.002 TYR D 108 ARG 0.010 0.001 ARG D 388 ********************** 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 1129 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1128 time to evaluate : 4.302 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: B 60 MET cc_start: 0.8403 (mtt) cc_final: 0.8119 (mtt) REVERT: B 62 MET cc_start: 0.8156 (mmp) cc_final: 0.7445 (mtm) REVERT: B 69 MET cc_start: 0.8541 (tmm) cc_final: 0.8227 (tmm) REVERT: B 131 SER cc_start: 0.8892 (p) cc_final: 0.8153 (t) REVERT: C 38 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8449 (mt0) REVERT: C 41 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8217 (tm-30) REVERT: C 49 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7744 (mt-10) REVERT: C 99 LEU cc_start: 0.8552 (mt) cc_final: 0.7983 (pt) REVERT: C 102 ASN cc_start: 0.8866 (t0) cc_final: 0.8565 (t0) REVERT: D 82 LEU cc_start: 0.9212 (mm) cc_final: 0.8822 (mp) REVERT: D 217 ASN cc_start: 0.8387 (m-40) cc_final: 0.7463 (t0) REVERT: D 228 MET cc_start: 0.9022 (tpp) cc_final: 0.7930 (tmm) REVERT: D 242 ILE cc_start: 0.9119 (mt) cc_final: 0.8647 (mm) REVERT: D 338 MET cc_start: 0.8906 (ppp) cc_final: 0.8425 (tmm) REVERT: D 342 MET cc_start: 0.8684 (tpt) cc_final: 0.8441 (tpt) REVERT: F 373 ASN cc_start: 0.8311 (t0) cc_final: 0.7876 (t0) REVERT: H 93 TYR cc_start: 0.7813 (m-80) cc_final: 0.7417 (m-10) REVERT: H 183 MET cc_start: 0.8282 (mtp) cc_final: 0.8001 (mtt) REVERT: H 235 ASN cc_start: 0.8317 (m110) cc_final: 0.7912 (m-40) REVERT: H 268 MET cc_start: 0.7837 (ttp) cc_final: 0.7225 (tmm) REVERT: I 110 ASP cc_start: 0.7413 (m-30) cc_final: 0.7147 (m-30) REVERT: I 137 PHE cc_start: 0.8201 (m-80) cc_final: 0.7913 (m-10) REVERT: I 146 GLU cc_start: 0.7366 (tt0) cc_final: 0.7019 (tt0) REVERT: I 153 LYS cc_start: 0.6544 (mtmt) cc_final: 0.6245 (mtmt) REVERT: I 176 ARG cc_start: 0.8242 (mtt-85) cc_final: 0.7849 (mtt-85) REVERT: J 36 SER cc_start: 0.9174 (m) cc_final: 0.8666 (p) REVERT: J 170 GLU cc_start: 0.8222 (tt0) cc_final: 0.8007 (tt0) REVERT: K 9 MET cc_start: 0.8494 (mmp) cc_final: 0.8163 (mmm) REVERT: K 27 MET cc_start: 0.8451 (mmm) cc_final: 0.8171 (mmm) REVERT: K 34 GLU cc_start: 0.8505 (tp30) cc_final: 0.6526 (tp30) REVERT: K 37 MET cc_start: 0.8274 (tmm) cc_final: 0.6810 (tmm) REVERT: K 69 CYS cc_start: 0.7752 (p) cc_final: 0.7208 (p) REVERT: L 53 MET cc_start: 0.8489 (mtm) cc_final: 0.8282 (mtp) REVERT: L 71 ILE cc_start: 0.8623 (mt) cc_final: 0.8192 (mt) REVERT: L 201 ILE cc_start: 0.8906 (pt) cc_final: 0.8530 (mt) REVERT: L 278 LEU cc_start: 0.8401 (mt) cc_final: 0.7761 (tp) REVERT: L 286 LEU cc_start: 0.8874 (mt) cc_final: 0.8241 (mt) REVERT: L 341 MET cc_start: 0.8798 (ppp) cc_final: 0.8398 (ppp) REVERT: L 411 MET cc_start: 0.9017 (mmp) cc_final: 0.8361 (mmt) REVERT: L 540 MET cc_start: 0.7965 (mmm) cc_final: 0.7736 (tmm) REVERT: L 544 MET cc_start: 0.7782 (mtp) cc_final: 0.7384 (mmp) REVERT: M 36 PHE cc_start: 0.8508 (t80) cc_final: 0.8305 (t80) REVERT: M 42 MET cc_start: 0.7070 (tmm) cc_final: 0.6728 (tmm) REVERT: M 70 MET cc_start: 0.8952 (mmm) cc_final: 0.8650 (mmt) REVERT: M 76 MET cc_start: 0.8816 (mmm) cc_final: 0.8460 (mmt) REVERT: M 89 LEU cc_start: 0.8658 (mt) cc_final: 0.8442 (mt) REVERT: M 92 LYS cc_start: 0.8500 (mttt) cc_final: 0.8104 (mttm) REVERT: M 93 LYS cc_start: 0.8544 (mttp) cc_final: 0.8331 (mttt) REVERT: M 106 LEU cc_start: 0.9352 (mm) cc_final: 0.8943 (mm) REVERT: M 200 MET cc_start: 0.8864 (mmp) cc_final: 0.8518 (mmp) REVERT: M 228 SER cc_start: 0.8391 (m) cc_final: 0.7710 (t) REVERT: M 257 MET cc_start: 0.6370 (tpt) cc_final: 0.5834 (tpp) REVERT: M 304 GLN cc_start: 0.7985 (tt0) cc_final: 0.7554 (tm-30) REVERT: M 319 HIS cc_start: 0.7627 (t70) cc_final: 0.7221 (t-90) REVERT: M 441 ILE cc_start: 0.8841 (mt) cc_final: 0.8238 (mt) REVERT: M 446 LEU cc_start: 0.9341 (mt) cc_final: 0.8678 (tp) REVERT: N 37 MET cc_start: 0.7898 (mmm) cc_final: 0.7370 (mmm) REVERT: N 63 GLN cc_start: 0.7857 (mt0) cc_final: 0.7535 (mt0) REVERT: N 64 SER cc_start: 0.8650 (t) cc_final: 0.8373 (t) REVERT: N 88 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8027 (ttmm) REVERT: N 164 ILE cc_start: 0.9244 (pt) cc_final: 0.9041 (mt) REVERT: N 176 ARG cc_start: 0.7269 (mtp85) cc_final: 0.6800 (mtp85) REVERT: N 263 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8397 (mptt) REVERT: N 281 PHE cc_start: 0.8698 (t80) cc_final: 0.8431 (t80) REVERT: N 282 MET cc_start: 0.8662 (tpt) cc_final: 0.8302 (mmm) REVERT: N 294 MET cc_start: 0.8611 (mmm) cc_final: 0.8251 (mmm) REVERT: O 131 ASP cc_start: 0.8555 (m-30) cc_final: 0.7823 (t0) REVERT: O 152 TYR cc_start: 0.8642 (t80) cc_final: 0.7978 (t80) REVERT: V 53 GLU cc_start: 0.8536 (tm-30) cc_final: 0.7984 (tm-30) REVERT: W 65 MET cc_start: 0.8299 (ttp) cc_final: 0.7981 (tmm) REVERT: Y 89 TYR cc_start: 0.7774 (m-80) cc_final: 0.7326 (m-80) REVERT: Y 117 MET cc_start: 0.8539 (tpp) cc_final: 0.8191 (tpt) REVERT: a 43 TYR cc_start: 0.8496 (t80) cc_final: 0.8173 (t80) REVERT: b 8 LEU cc_start: 0.8542 (tt) cc_final: 0.8074 (mm) REVERT: e 36 GLU cc_start: 0.7455 (pp20) cc_final: 0.7167 (pp20) REVERT: e 41 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7093 (tm-30) REVERT: e 62 PHE cc_start: 0.8938 (t80) cc_final: 0.8626 (t80) REVERT: g 58 MET cc_start: 0.5411 (mmt) cc_final: 0.5107 (mpp) REVERT: g 76 PHE cc_start: 0.8286 (m-80) cc_final: 0.7959 (m-10) REVERT: g 85 MET cc_start: 0.8980 (ptp) cc_final: 0.8742 (pmm) REVERT: g 92 GLU cc_start: 0.8307 (tp30) cc_final: 0.7903 (tp30) REVERT: p 114 GLN cc_start: 0.7858 (tt0) cc_final: 0.7587 (tm-30) REVERT: p 136 LYS cc_start: 0.9171 (tmtt) cc_final: 0.8759 (tppp) REVERT: G 237 ASN cc_start: 0.8874 (m110) cc_final: 0.8613 (m-40) REVERT: Q 81 ASN cc_start: 0.7731 (m-40) cc_final: 0.7405 (m-40) REVERT: h 42 LEU cc_start: 0.9004 (mm) cc_final: 0.8714 (tp) REVERT: d 48 ILE cc_start: 0.8835 (mm) cc_final: 0.8632 (mm) REVERT: X 83 GLU cc_start: 0.8355 (tp30) cc_final: 0.8106 (tp30) REVERT: X 108 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8594 (mm-30) REVERT: m 84 LYS cc_start: 0.6567 (mptt) cc_final: 0.5910 (ptpt) REVERT: n 19 TYR cc_start: 0.9174 (t80) cc_final: 0.8746 (t80) REVERT: n 33 ARG cc_start: 0.8344 (mmm160) cc_final: 0.7337 (mtt90) REVERT: n 93 TYR cc_start: 0.6428 (m-10) cc_final: 0.5749 (m-10) REVERT: Z 9 MET cc_start: 0.5157 (tpt) cc_final: 0.4947 (tpt) REVERT: Z 81 ARG cc_start: 0.7403 (ttt-90) cc_final: 0.6565 (ttt-90) outliers start: 1 outliers final: 0 residues processed: 1129 average time/residue: 0.4930 time to fit residues: 959.7176 Evaluate side-chains 955 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 955 time to evaluate : 4.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 465 optimal weight: 0.0370 chunk 624 optimal weight: 0.0470 chunk 179 optimal weight: 5.9990 chunk 540 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 587 optimal weight: 30.0000 chunk 245 optimal weight: 0.9990 chunk 602 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 HIS ** L 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 HIS L 546 GLN ** M 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN Z 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.085853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076913 restraints weight = 211454.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.078026 restraints weight = 139505.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.078655 restraints weight = 93764.311| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.257 53802 Z= 0.594 Angle : 1.793 50.676 73768 Z= 1.148 Chirality : 0.332 6.396 8765 Planarity : 0.005 0.141 9627 Dihedral : 5.490 170.608 8289 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.46 % Favored : 90.21 % Rotamer: Outliers : 0.03 % Allowed : 0.53 % Favored : 99.45 % 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: -1.51 (0.10), residues: 6916 helix: 0.35 (0.09), residues: 3453 sheet: -0.59 (0.31), residues: 286 loop : -2.69 (0.11), residues: 3177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP N 30 HIS 0.012 0.001 HIS L 328 PHE 0.038 0.002 PHE I 139 TYR 0.031 0.001 TYR Z 46 ARG 0.015 0.001 ARG n 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15077.73 seconds wall clock time: 258 minutes 24.24 seconds (15504.24 seconds total)