Starting phenix.real_space_refine on Tue Sep 24 14:44:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ldw_4040/09_2024/5ldw_4040.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ldw_4040/09_2024/5ldw_4040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ldw_4040/09_2024/5ldw_4040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ldw_4040/09_2024/5ldw_4040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ldw_4040/09_2024/5ldw_4040.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ldw_4040/09_2024/5ldw_4040.cif" } resolution = 4.27 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= 0.027 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 325 5.16 5 C 32427 2.51 5 N 9078 2.21 5 O 9318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 51181 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 687 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 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: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1684 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 189} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 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: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 959 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PTRANS': 17, 'TRANS': 168} Unresolved non-hydrogen bonds: 530 Unresolved non-hydrogen angles: 677 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 5, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 294 Chain: "F" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 2356 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 256} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 957 Unresolved non-hydrogen angles: 1224 Unresolved non-hydrogen dihedrals: 797 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 9, 'ASN:plan1': 12, 'TRP:plan': 6, 'ASP:plan': 17, 'PHE:plan': 13, 'GLU:plan': 26, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 561 Chain: "G" Number of atoms: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1199 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 343 Unresolved non-hydrogen angles: 435 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 154 Chain: "G" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 2415 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 483} Link IDs: {'TRANS': 482} Unresolved non-hydrogen bonds: 966 Unresolved non-hydrogen angles: 1449 Unresolved non-hydrogen dihedrals: 483 Planarities with less than four sites: {'UNK:plan-1': 483} Unresolved non-hydrogen planarities: 483 Chain: "H" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2306 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "I" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 165} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 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: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3536 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 20, 'TRANS': 436} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 65 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: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1851 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 208} Link IDs: {'PTRANS': 10, 'TRANS': 303} Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 882 Unresolved non-hydrogen dihedrals: 498 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 10, 'ASN:plan1': 6, 'ASP:plan': 10, 'TYR:plan': 8, 'UNK:plan-1': 86, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 390 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: "Q" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 Chain: "R" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 501 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 1, 'TRANS': 87} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 54, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 64 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: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 685 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 10, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 109 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: {'PCIS': 2, 'PTRANS': 3, '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: "X" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 858 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "X" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 275 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'UNK:plan-1': 55} Unresolved non-hydrogen planarities: 55 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: "Z" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 706 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 1, 'TRANS': 93} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 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: "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: "d" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 695 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 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: "e" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 616 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 4, 'TRANS': 84} Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 75 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: "h" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 295 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 36} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "h" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 475 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'TRANS': 94} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 95 Planarities with less than four sites: {'UNK:plan-1': 95} Unresolved non-hydrogen planarities: 95 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: "m" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 887 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 21, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "n" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 893 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 7, 'TRANS': 119} Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 6, 'TRP:plan': 4, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 182 Chain: "n" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 195 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'TRANS': 38} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'UNK:plan-1': 39} Unresolved non-hydrogen planarities: 39 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: "r" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 435 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'UNK:plan-1': 87} Unresolved non-hydrogen planarities: 87 Chain: "s" 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: "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: "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: "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: "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 1419 SG CYS B 119 95.296 89.866 205.246 1.00 29.57 S ATOM 921 SG CYS B 55 89.532 92.524 206.741 1.00 32.08 S ATOM 915 SG CYS B 54 89.601 86.746 204.004 1.00 32.26 S ATOM 1649 SG CYS B 149 91.938 87.493 210.063 1.00 30.40 S ATOM 7257 SG CYS E 103 111.044 42.876 261.793 1.00 99.40 S ATOM 7285 SG CYS E 108 109.250 39.856 263.008 1.00100.21 S ATOM 7466 SG CYS E 144 114.265 40.167 258.861 1.00101.54 S ATOM 7486 SG CYS E 148 112.770 36.921 259.808 1.00 99.96 S ATOM 9514 SG CYS F 362 117.200 47.341 237.285 1.00 66.03 S ATOM 9534 SG CYS F 365 113.373 47.984 242.238 1.00 63.63 S ATOM 9858 SG CYS F 405 117.384 42.759 241.864 1.00 67.04 S ATOM 9495 SG CYS F 359 119.908 48.632 242.942 1.00 65.78 S ATOM 10740 SG CYS G 114 113.979 66.174 228.021 1.00 32.69 S ATOM 10679 SG CYS G 105 108.335 69.209 229.057 1.00 31.43 S ATOM 10700 SG CYS G 108 113.573 71.097 232.269 1.00 31.93 S ATOM 10988 SG CYS G 156 121.458 58.903 233.455 1.00 33.87 S ATOM 10965 SG CYS G 153 119.157 62.858 238.224 1.00 33.69 S ATOM 11012 SG CYS G 159 125.426 62.876 236.425 1.00 33.88 S ATOM 11242 SG CYS G 203 120.918 65.264 232.448 1.00 32.99 S ATOM 10258 SG CYS G 41 121.275 53.753 230.602 1.00 49.30 S ATOM 10335 SG CYS G 52 117.637 52.749 230.715 1.00 49.63 S ATOM 10360 SG CYS G 55 118.961 49.326 226.470 1.00 49.23 S ATOM 10433 SG CYS G 69 122.361 50.606 226.833 1.00 50.26 S ATOM 16900 SG CYS I 119 95.864 82.284 215.164 1.00 23.44 S ATOM 16874 SG CYS I 116 96.862 88.457 216.491 1.00 23.12 S ATOM 16921 SG CYS I 122 97.766 84.053 221.235 1.00 23.28 S ATOM 16648 SG CYS I 87 101.803 84.447 216.027 1.00 23.18 S ATOM 16950 SG CYS I 126 100.323 80.870 228.677 1.00 25.71 S ATOM 16621 SG CYS I 83 103.893 82.841 223.564 1.00 25.04 S ATOM 16579 SG CYS I 77 105.162 85.310 229.284 1.00 26.58 S ATOM 16598 SG CYS I 80 106.409 79.094 228.492 1.00 25.63 S ATOM 34064 SG CYS R 59 102.607 77.022 244.252 1.00 59.19 S ATOM 34215 SG CYS R 84 105.503 77.768 241.702 1.00 58.54 S ATOM 34237 SG CYS R 87 102.705 80.262 242.234 1.00 57.98 S Time building chain proxies: 21.66, per 1000 atoms: 0.42 Number of scatterers: 51181 At special positions: 0 Unit cell: (183.54, 184.87, 292.6, 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 325 16.00 P 4 15.00 O 9318 8.00 N 9078 7.00 C 32427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 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 Simple disulfide: pdb=" SG CYS Y 17 " - pdb=" SG CYS Y 74 " distance=2.03 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 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 G 210 " - " THR G 209 " " UNK X 114 " - " LYS X 113 " " UNK Z 100 " - " ASP Z 99 " " UNK b 46 " - " ASN b 45 " " UNK d 98 " - " HIS d 97 " " UNK h 46 " - " VAL h 45 " " UNK n 137 " - " VAL n 136 " Time building additional restraints: 8.87 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " 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="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " 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="FE3 SF4 B 201 " - pdb=" SG CYS B 54 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 55 " 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="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " 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="FE4 SF4 I 201 " - pdb=" SG CYS I 87 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 116 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 122 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 119 " pdb="FE2 SF4 I 201 " - pdb=" NE2 HIS I 65 " pdb=" SF4 I 202 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 126 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 80 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 83 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 77 " 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 59 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " Number of angles added : 3 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14896 Finding SS restraints... Secondary structure from input PDB file: 247 helices and 23 sheets defined 63.1% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 removed outlier: 3.560A pdb=" N THR A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 77 removed outlier: 3.569A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.328A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 106 removed outlier: 4.187A pdb=" N THR A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.657A pdb=" N ASP B 34 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 63 removed outlier: 3.635A pdb=" N GLU B 58 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA B 63 " --> pdb=" O MET B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 Proline residue: B 98 - end of helix removed outlier: 3.758A pdb=" N ARG B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS B 102 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 No H-bonds generated for 'chain 'B' and resid 118 through 121' Processing helix chain 'B' and resid 154 through 166 removed outlier: 3.979A pdb=" N TYR B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 29 removed outlier: 3.622A pdb=" N ALA C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 Processing helix chain 'C' and resid 126 through 138 removed outlier: 3.902A pdb=" N TYR C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 133 " --> pdb=" O TRP C 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 14 removed outlier: 3.836A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 4.219A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 removed outlier: 3.508A pdb=" N LEU D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) Proline residue: D 101 - end of helix removed outlier: 4.203A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.066A pdb=" N GLN D 116 " --> pdb=" O MET D 112 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA D 117 " --> pdb=" O CYS D 113 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 161 removed outlier: 3.852A pdb=" N TRP D 136 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 154 " --> pdb=" O HIS D 150 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N HIS D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 182 removed outlier: 3.598A pdb=" N MET D 170 " --> pdb=" O PRO D 166 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 229 removed outlier: 3.591A pdb=" N ASP D 210 " --> pdb=" O GLY D 206 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR D 212 " --> pdb=" O MET D 208 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU D 225 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 227 " --> pdb=" O ASP D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 249 through 253 removed outlier: 3.917A pdb=" N TYR D 253 " --> pdb=" O ASP D 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 249 through 253' Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 294 through 317 removed outlier: 4.399A pdb=" N ARG D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE D 308 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ARG D 309 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 352 removed outlier: 3.519A pdb=" N TYR D 352 " --> pdb=" O HIS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.605A pdb=" N ALA D 400 " --> pdb=" O PHE D 396 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.911A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 37 removed outlier: 4.965A pdb=" N ARG E 30 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 4.019A pdb=" N ASP E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 removed outlier: 3.814A pdb=" N ASN E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 72 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU E 73 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 86 removed outlier: 3.754A pdb=" N ALA E 84 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR E 85 " --> pdb=" O TYR E 81 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 111 removed outlier: 5.049A pdb=" N ARG E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 123 removed outlier: 3.515A pdb=" N LYS E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 178 removed outlier: 4.012A pdb=" N LYS E 177 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA E 178 " --> pdb=" O ASP E 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 39 removed outlier: 4.260A pdb=" N GLN F 37 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG F 39 " --> pdb=" O GLY F 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 33 through 39' Processing helix chain 'F' and resid 44 through 50 Processing helix chain 'F' and resid 53 through 63 removed outlier: 4.098A pdb=" N VAL F 60 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 81 Processing helix chain 'F' and resid 105 through 112 removed outlier: 3.671A pdb=" N GLU F 109 " --> pdb=" O CYS F 105 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG F 112 " --> pdb=" O ARG F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 129 removed outlier: 3.619A pdb=" N LEU F 118 " --> pdb=" O PRO F 115 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL F 119 " --> pdb=" O HIS F 116 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU F 120 " --> pdb=" O LYS F 117 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS F 122 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL F 124 " --> pdb=" O GLY F 121 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY F 125 " --> pdb=" O CYS F 122 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY F 126 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG F 127 " --> pdb=" O VAL F 124 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA F 128 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET F 129 " --> pdb=" O GLY F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 159 removed outlier: 3.646A pdb=" N ASN F 148 " --> pdb=" O ASN F 144 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG F 154 " --> pdb=" O GLN F 150 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 187 No H-bonds generated for 'chain 'F' and resid 184 through 187' Processing helix chain 'F' and resid 189 through 197 removed outlier: 4.056A pdb=" N ILE F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU F 194 " --> pdb=" O THR F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 236 removed outlier: 3.850A pdb=" N SER F 231 " --> pdb=" O THR F 227 " (cutoff:3.500A) Proline residue: F 232 - end of helix Processing helix chain 'F' and resid 239 through 243 removed outlier: 3.807A pdb=" N PHE F 242 " --> pdb=" O GLY F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 283 removed outlier: 3.551A pdb=" N HIS F 283 " --> pdb=" O LEU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 324 removed outlier: 4.462A pdb=" N GLN F 324 " --> pdb=" O ASP F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 356 removed outlier: 3.666A pdb=" N TYR F 354 " --> pdb=" O LEU F 350 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 381 removed outlier: 3.553A pdb=" N GLU F 367 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY F 368 " --> pdb=" O PRO F 364 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TRP F 371 " --> pdb=" O GLU F 367 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS F 374 " --> pdb=" O ASP F 370 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG F 378 " --> pdb=" O LYS F 374 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE F 379 " --> pdb=" O VAL F 375 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL F 380 " --> pdb=" O MET F 376 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 401 removed outlier: 3.882A pdb=" N ILE F 389 " --> pdb=" O PRO F 386 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER F 391 " --> pdb=" O GLU F 388 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU F 392 " --> pdb=" O ILE F 389 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP F 393 " --> pdb=" O ASP F 390 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER F 396 " --> pdb=" O TRP F 393 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS F 397 " --> pdb=" O GLU F 394 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE F 399 " --> pdb=" O SER F 396 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU F 400 " --> pdb=" O LYS F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 419 Proline residue: F 414 - end of helix removed outlier: 3.785A pdb=" N LEU F 418 " --> pdb=" O PRO F 414 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE F 419 " --> pdb=" O VAL F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 438 removed outlier: 3.847A pdb=" N ARG F 429 " --> pdb=" O GLU F 425 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET F 430 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE F 433 " --> pdb=" O ARG F 429 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN F 435 " --> pdb=" O GLN F 431 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 32 removed outlier: 4.024A pdb=" N LYS G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 99 removed outlier: 3.709A pdb=" N GLY G 92 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET G 94 " --> pdb=" O ARG G 90 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 122 removed outlier: 3.863A pdb=" N MET G 121 " --> pdb=" O GLN G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 166 removed outlier: 3.711A pdb=" N SER G 164 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 202 removed outlier: 4.082A pdb=" N ILE G 200 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 275 removed outlier: 3.562A pdb=" N UNK G 270 " --> pdb=" O UNK G 267 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N UNK G 271 " --> pdb=" O UNK G 268 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N UNK G 272 " --> pdb=" O UNK G 269 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N UNK G 274 " --> pdb=" O UNK G 271 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N UNK G 275 " --> pdb=" O UNK G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 removed outlier: 3.540A pdb=" N UNK G 301 " --> pdb=" O UNK G 297 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N UNK G 307 " --> pdb=" O UNK G 303 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N UNK G 309 " --> pdb=" O UNK G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 337 removed outlier: 3.800A pdb=" N UNK G 333 " --> pdb=" O UNK G 329 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N UNK G 334 " --> pdb=" O UNK G 330 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N UNK G 335 " --> pdb=" O UNK G 331 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N UNK G 336 " --> pdb=" O UNK G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 400 removed outlier: 3.542A pdb=" N UNK G 395 " --> pdb=" O UNK G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 433 removed outlier: 4.670A pdb=" N UNK G 430 " --> pdb=" O UNK G 426 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N UNK G 431 " --> pdb=" O UNK G 427 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N UNK G 433 " --> pdb=" O UNK G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 445 removed outlier: 4.631A pdb=" N UNK G 442 " --> pdb=" O UNK G 438 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N UNK G 445 " --> pdb=" O UNK G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 473 removed outlier: 3.589A pdb=" N UNK G 468 " --> pdb=" O UNK G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 504 removed outlier: 3.965A pdb=" N UNK G 503 " --> pdb=" O UNK G 500 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N UNK G 504 " --> pdb=" O UNK G 501 " (cutoff:3.500A) Processing helix chain 'G' and resid 552 through 556 removed outlier: 3.720A pdb=" N UNK G 555 " --> pdb=" O UNK G 552 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N UNK G 556 " --> pdb=" O UNK G 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 552 through 556' Processing helix chain 'G' and resid 596 through 607 removed outlier: 3.750A pdb=" N UNK G 600 " --> pdb=" O UNK G 596 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N UNK G 601 " --> pdb=" O UNK G 597 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N UNK G 603 " --> pdb=" O UNK G 599 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N UNK G 604 " --> pdb=" O UNK G 600 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N UNK G 605 " --> pdb=" O UNK G 601 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N UNK G 606 " --> pdb=" O UNK G 602 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N UNK G 607 " --> pdb=" O UNK G 603 " (cutoff:3.500A) Processing helix chain 'G' and resid 616 through 626 removed outlier: 3.837A pdb=" N UNK G 620 " --> pdb=" O UNK G 616 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N UNK G 621 " --> pdb=" O UNK G 617 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N UNK G 624 " --> pdb=" O UNK G 620 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N UNK G 625 " --> pdb=" O UNK G 621 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N UNK G 626 " --> pdb=" O UNK G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 642 through 653 removed outlier: 4.438A pdb=" N UNK G 647 " --> pdb=" O UNK G 643 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N UNK G 648 " --> pdb=" O UNK G 644 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N UNK G 650 " --> pdb=" O UNK G 646 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N UNK G 651 " --> pdb=" O UNK G 647 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N UNK G 652 " --> pdb=" O UNK G 648 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N UNK G 653 " --> pdb=" O UNK G 649 " (cutoff:3.500A) Processing helix chain 'G' and resid 683 through 691 removed outlier: 4.489A pdb=" N UNK G 687 " --> pdb=" O UNK G 683 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N UNK G 688 " --> pdb=" O UNK G 684 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 31 removed outlier: 3.538A pdb=" N MET H 8 " --> pdb=" O ILE H 4 " (cutoff:3.500A) Proline residue: H 12 - end of helix removed outlier: 4.313A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL H 23 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG H 25 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU H 28 " --> pdb=" O GLU H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 57 removed outlier: 3.768A pdb=" N ILE H 49 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP H 51 " --> pdb=" O PRO H 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE H 53 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS H 54 " --> pdb=" O ASP H 51 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU H 55 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE H 56 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE H 57 " --> pdb=" O LYS H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 87 Proline residue: H 75 - end of helix removed outlier: 3.596A pdb=" N MET H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.579A pdb=" N SER H 109 " --> pdb=" O MET H 105 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY H 120 " --> pdb=" O ILE H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 156 removed outlier: 3.713A pdb=" N THR H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR H 142 " --> pdb=" O GLN H 138 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL H 153 " --> pdb=" O ILE H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 169 removed outlier: 3.978A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 190 Proline residue: H 180 - end of helix removed outlier: 3.889A pdb=" N MET H 183 " --> pdb=" O TRP H 179 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP H 185 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE H 186 " --> pdb=" O ALA H 182 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE H 187 " --> pdb=" O MET H 183 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR H 189 " --> pdb=" O TRP H 185 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU H 190 " --> pdb=" O PHE H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 241 removed outlier: 3.519A pdb=" N MET H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA H 229 " --> pdb=" O MET H 225 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE H 231 " --> pdb=" O GLU H 227 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 274 removed outlier: 3.702A pdb=" N THR H 256 " --> pdb=" O GLU H 253 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE H 257 " --> pdb=" O LEU H 254 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE H 259 " --> pdb=" O THR H 256 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE H 261 " --> pdb=" O ASN H 258 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS H 262 " --> pdb=" O PHE H 259 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER H 263 " --> pdb=" O THR H 260 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU H 265 " --> pdb=" O LYS H 262 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET H 268 " --> pdb=" O LEU H 265 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE H 273 " --> pdb=" O PHE H 270 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG H 274 " --> pdb=" O LEU H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 Processing helix chain 'H' and resid 293 through 311 removed outlier: 3.643A 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 24 removed outlier: 4.003A pdb=" N ASP I 19 " --> pdb=" O LYS I 15 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG I 20 " --> pdb=" O SER I 16 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 42 removed outlier: 3.519A pdb=" N ARG I 32 " --> pdb=" O GLU I 29 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR I 37 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER I 39 " --> pdb=" O MET I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 153 through 156 No H-bonds generated for 'chain 'I' and resid 153 through 156' Processing helix chain 'I' and resid 158 through 171 removed outlier: 5.011A pdb=" N ALA I 163 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE I 165 " --> pdb=" O GLU I 162 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA I 166 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE I 169 " --> pdb=" O ALA I 166 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN I 170 " --> pdb=" O ALA I 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 22 removed outlier: 4.161A pdb=" N LEU J 9 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL J 11 " --> pdb=" O PHE J 7 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE J 12 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE J 17 " --> pdb=" O PHE J 13 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLY J 19 " --> pdb=" O MET J 15 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER J 21 " --> pdb=" O PHE J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 45 removed outlier: 3.523A pdb=" N GLY J 32 " --> pdb=" O TYR J 28 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU J 33 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE J 43 " --> pdb=" O VAL J 39 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL J 44 " --> pdb=" O GLY J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 59 removed outlier: 3.859A pdb=" N LEU J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE J 57 " --> pdb=" O GLY J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 74 removed outlier: 3.629A pdb=" N TYR J 70 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA J 73 " --> pdb=" O GLY J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 108 removed outlier: 3.523A pdb=" N GLY J 91 " --> pdb=" O ALA J 88 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL J 94 " --> pdb=" O GLY J 91 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR J 95 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU J 97 " --> pdb=" O VAL J 94 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET J 99 " --> pdb=" O GLY J 96 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE J 101 " --> pdb=" O LEU J 98 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE J 102 " --> pdb=" O MET J 99 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR J 105 " --> pdb=" O PHE J 102 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU J 108 " --> pdb=" O TYR J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 170 removed outlier: 3.879A pdb=" N VAL J 165 " --> pdb=" O LEU J 161 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET J 169 " --> pdb=" O VAL J 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 20 removed outlier: 4.287A pdb=" N ASN K 7 " --> pdb=" O MET K 3 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE K 8 " --> pdb=" O VAL K 4 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET K 10 " --> pdb=" O MET K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 50 removed outlier: 4.317A pdb=" N LEU K 30 " --> pdb=" O LEU K 26 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR K 47 " --> pdb=" O MET K 43 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE K 48 " --> pdb=" O ALA K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 83 Proline residue: K 60 - end of helix removed outlier: 3.610A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU K 70 " --> pdb=" O ALA K 67 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA K 72 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU K 73 " --> pdb=" O GLU K 70 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLY K 74 " --> pdb=" O ALA K 71 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER K 76 " --> pdb=" O LEU K 73 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL K 79 " --> pdb=" O SER K 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 23 removed outlier: 4.061A pdb=" N LEU L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL L 10 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU L 15 " --> pdb=" O THR L 11 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Proline residue: L 18 - end of helix removed outlier: 4.027A pdb=" N SER L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 56 removed outlier: 3.549A pdb=" N VAL L 36 " --> pdb=" O TYR L 32 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS L 37 " --> pdb=" O PRO L 33 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR L 42 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE L 45 " --> pdb=" O SER L 41 " (cutoff:3.500A) removed outlier: 3.806A 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 86 through 106 removed outlier: 3.815A pdb=" N ILE L 90 " --> pdb=" O SER L 86 " (cutoff:3.500A) Proline residue: L 91 - end of helix removed outlier: 3.670A pdb=" N SER L 99 " --> pdb=" O PHE L 95 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU L 102 " --> pdb=" O TRP L 98 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 removed outlier: 4.053A pdb=" N PHE L 118 " --> pdb=" O ILE L 114 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS L 119 " --> pdb=" O ASN L 115 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR L 120 " --> pdb=" O LYS L 116 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU L 121 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU L 123 " --> pdb=" O LYS L 119 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 156 removed outlier: 3.725A pdb=" N ILE L 142 " --> pdb=" O PHE L 138 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY L 143 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE L 152 " --> pdb=" O GLY L 148 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU L 153 " --> pdb=" O ILE L 149 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU L 154 " --> pdb=" O MET L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 190 removed outlier: 4.230A pdb=" N ALA L 167 " --> pdb=" O ASP L 163 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA L 168 " --> pdb=" O ALA L 164 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE L 172 " --> pdb=" O ALA L 168 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN L 175 " --> pdb=" O ALA L 171 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE L 180 " --> pdb=" O ARG L 176 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE L 189 " --> pdb=" O ALA L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 202 removed outlier: 5.025A pdb=" N PHE L 202 " --> pdb=" O LEU L 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 198 through 202' Processing helix chain 'L' and resid 209 through 221 removed outlier: 3.670A pdb=" N LEU L 213 " --> pdb=" O SER L 209 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE L 214 " --> pdb=" O ASN L 210 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY L 215 " --> pdb=" O MET L 211 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA L 217 " --> pdb=" O LEU L 213 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU L 218 " --> pdb=" O ILE L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 237 Proline residue: L 234 - end of helix removed outlier: 4.199A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 230 through 237' Processing helix chain 'L' and resid 241 through 247 Processing helix chain 'L' and resid 253 through 262 removed outlier: 5.009A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU L 259 " --> pdb=" O ALA L 255 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU L 260 " --> pdb=" O GLY L 256 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG L 262 " --> pdb=" O PHE L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 268 removed outlier: 3.502A pdb=" N GLU L 268 " --> pdb=" O TYR L 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 264 through 268' Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.576A pdb=" N SER L 275 " --> pdb=" O LYS L 271 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU L 278 " --> pdb=" O GLN L 274 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE L 283 " --> pdb=" O CYS L 279 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR L 284 " --> pdb=" O LEU L 280 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR L 285 " --> pdb=" O GLY L 281 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU L 286 " --> pdb=" O ALA L 282 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE L 287 " --> pdb=" O ILE L 283 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR L 288 " --> pdb=" O THR L 284 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS L 291 " --> pdb=" O PHE L 287 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA L 292 " --> pdb=" O THR L 288 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 319 removed outlier: 4.263A pdb=" N ILE L 302 " --> pdb=" O ILE L 298 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR L 306 " --> pdb=" O ILE L 302 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER L 307 " --> pdb=" O ALA L 303 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU L 312 " --> pdb=" O SER L 308 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE L 317 " --> pdb=" O MET L 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.769A pdb=" N PHE L 326 " --> pdb=" O PRO L 322 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU L 327 " --> pdb=" O TYR L 323 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS L 328 " --> pdb=" O LEU L 324 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE L 329 " --> pdb=" O ALA L 325 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N MET L 338 " --> pdb=" O PHE L 334 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N MET L 341 " --> pdb=" O ALA L 337 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER L 343 " --> pdb=" O LEU L 339 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE L 346 " --> pdb=" O CYS L 342 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE L 347 " --> pdb=" O SER L 343 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS L 348 " --> pdb=" O GLY L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 367 through 380 removed outlier: 4.226A pdb=" N THR L 371 " --> pdb=" O PRO L 367 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA L 372 " --> pdb=" O PHE L 368 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU L 373 " --> pdb=" O THR L 369 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU L 380 " --> pdb=" O GLY L 376 " (cutoff:3.500A) Processing helix chain 'L' and resid 388 through 401 removed outlier: 3.962A pdb=" N ASP L 393 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE L 395 " --> pdb=" O SER L 391 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE L 396 " --> pdb=" O LYS L 392 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN L 400 " --> pdb=" O ILE L 396 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.578A pdb=" N LEU L 413 " --> pdb=" O LEU L 409 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE L 414 " --> pdb=" O LEU L 410 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA L 415 " --> pdb=" O MET L 411 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER L 417 " --> pdb=" O LEU L 413 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE L 421 " --> pdb=" O SER L 417 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR L 422 " --> pdb=" O PHE L 418 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER L 423 " --> pdb=" O THR L 419 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE L 426 " --> pdb=" O TYR L 422 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE L 427 " --> pdb=" O SER L 423 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE L 429 " --> pdb=" O ARG L 425 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA L 430 " --> pdb=" O ILE L 426 " (cutoff:3.500A) Processing helix chain 'L' and resid 449 through 463 removed outlier: 3.662A pdb=" N SER L 453 " --> pdb=" O LEU L 449 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG L 456 " --> pdb=" O ASN L 452 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE L 459 " --> pdb=" O LYS L 455 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY L 460 " --> pdb=" O ARG L 456 " (cutoff:3.500A) Processing helix chain 'L' and resid 464 through 471 removed outlier: 3.519A pdb=" N ILE L 468 " --> pdb=" O ALA L 464 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER L 469 " --> pdb=" O GLY L 465 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN L 470 " --> pdb=" O TYR L 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 487 through 510 removed outlier: 4.524A pdb=" N LEU L 491 " --> pdb=" O LYS L 487 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR L 494 " --> pdb=" O ALA L 490 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE L 495 " --> pdb=" O LEU L 491 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET L 507 " --> pdb=" O GLU L 503 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 531 through 563 removed outlier: 4.458A pdb=" N ARG L 535 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU L 536 " --> pdb=" O ILE L 532 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ALA L 537 " --> pdb=" O MET L 533 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.526A pdb=" N ASN L 541 " --> pdb=" O ALA L 537 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET L 544 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER L 545 " --> pdb=" O ASN L 541 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER L 548 " --> pdb=" O MET L 544 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA L 549 " --> pdb=" O SER L 545 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N SER L 550 " --> pdb=" O GLN L 546 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER L 551 " --> pdb=" O LYS L 547 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU L 552 " --> pdb=" O SER L 548 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP L 554 " --> pdb=" O SER L 550 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU L 555 " --> pdb=" O SER L 551 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE L 556 " --> pdb=" O LEU L 552 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU L 558 " --> pdb=" O ASP L 554 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU L 559 " --> pdb=" O LEU L 555 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE L 561 " --> pdb=" O TRP L 557 " (cutoff:3.500A) removed outlier: 6.321A 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 564 through 577 removed outlier: 3.685A pdb=" N LEU L 568 " --> pdb=" O LYS L 564 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA L 569 " --> pdb=" O THR L 565 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET L 571 " --> pdb=" O SER L 567 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR L 575 " --> pdb=" O MET L 571 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU L 576 " --> pdb=" O LYS L 572 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 599 removed outlier: 3.528A pdb=" N PHE L 591 " --> pdb=" O TYR L 587 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU L 592 " --> pdb=" O PHE L 588 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE L 593 " --> pdb=" O LEU L 589 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE L 595 " --> pdb=" O PHE L 591 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 17 removed outlier: 3.928A pdb=" N THR M 8 " --> pdb=" O TYR M 4 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE M 9 " --> pdb=" O ILE M 5 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU M 11 " --> pdb=" O PRO M 7 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix removed outlier: 3.901A pdb=" N TRP M 16 " --> pdb=" O MET M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 41 removed outlier: 3.984A pdb=" N SER M 31 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE M 34 " --> pdb=" O HIS M 30 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 80 removed outlier: 3.571A pdb=" N LEU M 72 " --> pdb=" O THR M 69 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU M 73 " --> pdb=" O MET M 70 " (cutoff:3.500A) Proline residue: M 74 - end of helix removed outlier: 3.506A pdb=" N MET M 78 " --> pdb=" O LEU M 75 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ALA M 79 " --> pdb=" O MET M 76 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER M 80 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 111 removed outlier: 3.632A pdb=" N LEU M 94 " --> pdb=" O ARG M 91 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE M 95 " --> pdb=" O LYS M 92 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE M 96 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N MET M 98 " --> pdb=" O PHE M 95 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER M 101 " --> pdb=" O MET M 98 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU M 106 " --> pdb=" O GLN M 103 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE M 107 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR M 109 " --> pdb=" O LEU M 106 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR M 111 " --> pdb=" O MET M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 136 removed outlier: 4.004A pdb=" N ILE M 120 " --> pdb=" O ILE M 116 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU M 121 " --> pdb=" O LEU M 117 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA M 124 " --> pdb=" O ILE M 120 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR M 125 " --> pdb=" O LEU M 121 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix removed outlier: 3.514A pdb=" N ILE M 131 " --> pdb=" O VAL M 127 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP M 136 " --> pdb=" O ILE M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 171 removed outlier: 4.884A pdb=" N TYR M 148 " --> pdb=" O ASN M 144 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU M 150 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR M 152 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA M 155 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY M 156 " --> pdb=" O TYR M 152 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 4.280A pdb=" N VAL M 162 " --> pdb=" O LEU M 158 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE M 165 " --> pdb=" O LEU M 161 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR M 166 " --> pdb=" O VAL M 162 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR M 170 " --> pdb=" O TYR M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.837A pdb=" N PHE M 194 " --> pdb=" O TRP M 190 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N MET M 195 " --> pdb=" O SER M 191 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP M 196 " --> pdb=" O ASN M 192 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS M 199 " --> pdb=" O MET M 195 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL M 205 " --> pdb=" O MET M 201 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS M 206 " --> pdb=" O ALA M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 220 removed outlier: 3.847A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA M 219 " --> pdb=" O TRP M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 230 through 250 removed outlier: 3.691A pdb=" N LYS M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TYR M 241 " --> pdb=" O LYS M 237 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLY M 242 " --> pdb=" O LEU M 238 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET M 243 " --> pdb=" O GLY M 239 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU M 244 " --> pdb=" O GLY M 240 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG M 245 " --> pdb=" O TYR M 241 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR M 247 " --> pdb=" O MET M 243 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 277 removed outlier: 3.609A pdb=" N TYR M 259 " --> pdb=" O PHE M 256 " (cutoff:3.500A) Proline residue: M 260 - end of helix removed outlier: 3.648A pdb=" N LEU M 264 " --> pdb=" O PHE M 261 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU M 266 " --> pdb=" O MET M 263 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET M 269 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE M 270 " --> pdb=" O TRP M 267 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N MET M 271 " --> pdb=" O GLY M 268 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR M 272 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER M 274 " --> pdb=" O MET M 271 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE M 275 " --> pdb=" O THR M 272 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU M 277 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.626A pdb=" N LEU M 285 " --> pdb=" O LEU M 282 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR M 288 " --> pdb=" O LEU M 285 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER M 290 " --> pdb=" O ALA M 287 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER M 292 " --> pdb=" O SER M 289 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N HIS M 293 " --> pdb=" O SER M 290 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET M 294 " --> pdb=" O VAL M 291 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU M 296 " --> pdb=" O HIS M 293 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL M 299 " --> pdb=" O LEU M 296 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE M 301 " --> pdb=" O ILE M 298 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE M 303 " --> pdb=" O ALA M 300 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 337 removed outlier: 3.771A pdb=" N ILE M 317 " --> pdb=" O THR M 313 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER M 324 " --> pdb=" O GLY M 320 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET M 325 " --> pdb=" O LEU M 321 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 355 through 366 removed outlier: 3.520A pdb=" N THR M 365 " --> pdb=" O LEU M 361 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN M 366 " --> pdb=" O ALA M 362 " (cutoff:3.500A) Processing helix chain 'M' and resid 373 through 388 removed outlier: 3.695A pdb=" N LEU M 379 " --> pdb=" O LEU M 375 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE M 380 " --> pdb=" O ILE M 376 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL M 381 " --> pdb=" O GLY M 377 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE M 386 " --> pdb=" O VAL M 382 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER M 387 " --> pdb=" O MET M 383 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP M 388 " --> pdb=" O SER M 384 " (cutoff:3.500A) Processing helix chain 'M' and resid 392 through 415 removed outlier: 3.997A pdb=" N VAL M 398 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN M 399 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA M 404 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU M 405 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER M 407 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR M 409 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR M 414 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 449 removed outlier: 3.759A pdb=" N MET M 437 " --> pdb=" O GLU M 433 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE M 441 " --> pdb=" O MET M 437 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 3.691A pdb=" N THR M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU M 449 " --> pdb=" O LEU M 445 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 21 removed outlier: 3.501A pdb=" N ILE N 9 " --> pdb=" O PHE N 6 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE N 13 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU N 15 " --> pdb=" O THR N 12 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR N 17 " --> pdb=" O MET N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 45 removed outlier: 3.786A pdb=" N TRP N 30 " --> pdb=" O TRP N 26 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN N 36 " --> pdb=" O GLY N 32 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA N 39 " --> pdb=" O MET N 35 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE N 41 " --> pdb=" O MET N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 79 removed outlier: 3.656A pdb=" N GLU N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR N 62 " --> pdb=" O LYS N 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN N 63 " --> pdb=" O TYR N 59 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR N 65 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA N 66 " --> pdb=" O THR N 62 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET N 72 " --> pdb=" O MET N 68 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA N 73 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 105 removed outlier: 3.758A pdb=" N MET N 100 " --> pdb=" O MET N 96 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS N 105 " --> pdb=" O ALA N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 121 removed outlier: 5.103A pdb=" N HIS N 112 " --> pdb=" O ALA N 109 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE N 113 " --> pdb=" O PRO N 110 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TRP N 114 " --> pdb=" O PHE N 111 " (cutoff:3.500A) Proline residue: N 116 - end of helix removed outlier: 4.476A pdb=" N THR N 119 " --> pdb=" O PRO N 116 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN N 120 " --> pdb=" O GLU N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 144 removed outlier: 3.871A pdb=" N ILE N 129 " --> pdb=" O SER N 125 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU N 130 " --> pdb=" O SER N 126 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU N 131 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR N 132 " --> pdb=" O LEU N 128 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.994A pdb=" N VAL N 141 " --> pdb=" O ALA N 137 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 170 removed outlier: 4.164A pdb=" N THR N 156 " --> pdb=" O ASN N 152 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU N 157 " --> pdb=" O LEU N 153 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER N 161 " --> pdb=" O LEU N 157 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE N 162 " --> pdb=" O SER N 158 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU N 163 " --> pdb=" O VAL N 159 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 194 removed outlier: 3.802A pdb=" N ILE N 184 " --> pdb=" O ALA N 180 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA N 192 " --> pdb=" O GLY N 188 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 219 removed outlier: 3.591A pdb=" N ASN N 204 " --> pdb=" O THR N 201 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE N 207 " --> pdb=" O ASN N 204 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE N 209 " --> pdb=" O ILE N 206 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE N 210 " --> pdb=" O ILE N 207 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER N 213 " --> pdb=" O ILE N 210 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR N 214 " --> pdb=" O MET N 211 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE N 216 " --> pdb=" O SER N 213 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR N 217 " --> pdb=" O THR N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.712A pdb=" N SER N 231 " --> pdb=" O THR N 227 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 227 through 235' Processing helix chain 'N' and resid 238 through 252 removed outlier: 4.132A pdb=" N VAL N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU N 243 " --> pdb=" O ILE N 239 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY N 252 " --> pdb=" O LEU N 248 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix removed outlier: 4.125A pdb=" N ILE N 266 " --> pdb=" O LYS N 263 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE N 267 " --> pdb=" O TRP N 264 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU N 269 " --> pdb=" O ILE N 266 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR N 271 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS N 272 " --> pdb=" O GLU N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 297 removed outlier: 3.859A pdb=" N PHE N 281 " --> pdb=" O ILE N 277 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR N 293 " --> pdb=" O ASN N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 323 through 332 removed outlier: 5.721A pdb=" N LEU N 326 " --> pdb=" O MET N 323 " (cutoff:3.500A) Proline residue: N 327 - end of helix removed outlier: 3.858A pdb=" N VAL N 331 " --> pdb=" O THR N 328 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU N 332 " --> pdb=" O MET N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 340 through 345 removed outlier: 3.552A pdb=" N SER N 344 " --> pdb=" O THR N 340 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL N 345 " --> pdb=" O PRO N 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 340 through 345' Processing helix chain 'O' and resid 34 through 44 removed outlier: 4.872A pdb=" N UNK O 38 " --> pdb=" O UNK O 34 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N UNK O 39 " --> pdb=" O UNK O 35 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N UNK O 41 " --> pdb=" O UNK O 37 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N UNK O 42 " --> pdb=" O UNK O 38 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N UNK O 44 " --> pdb=" O UNK O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 116 removed outlier: 4.636A pdb=" N GLN O 97 " --> pdb=" O SER O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 62 removed outlier: 4.513A pdb=" N UNK O 61 " --> pdb=" O UNK O 57 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N UNK O 62 " --> pdb=" O UNK O 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 57 through 62' Processing helix chain 'O' and resid 130 through 140 removed outlier: 3.595A pdb=" N PHE O 134 " --> pdb=" O SER O 130 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N MET O 138 " --> pdb=" O PHE O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 162 removed outlier: 3.569A pdb=" N ASP O 150 " --> pdb=" O LYS O 146 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL O 155 " --> pdb=" O HIS O 151 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL O 158 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE O 160 " --> pdb=" O LYS O 156 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N CYS O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU O 162 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 178 through 185 removed outlier: 4.179A pdb=" N ARG O 182 " --> pdb=" O GLU O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 215 removed outlier: 3.652A pdb=" N GLY O 208 " --> pdb=" O ASN O 204 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU O 211 " --> pdb=" O LYS O 207 " (cutoff:3.500A) Proline residue: O 212 - end of helix Processing helix chain 'O' and resid 232 through 240 Processing helix chain 'O' and resid 253 through 264 removed outlier: 4.001A pdb=" N HIS O 257 " --> pdb=" O ASP O 253 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS O 258 " --> pdb=" O ARG O 254 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET O 261 " --> pdb=" O HIS O 257 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU O 262 " --> pdb=" O LYS O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 271 Processing helix chain 'O' and resid 286 through 298 removed outlier: 3.737A pdb=" N GLN O 291 " --> pdb=" O HIS O 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 40 removed outlier: 4.901A pdb=" N UNK P 33 " --> pdb=" O UNK P 29 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N UNK P 34 " --> pdb=" O UNK P 30 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N UNK P 40 " --> pdb=" O UNK P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 61 removed outlier: 3.856A pdb=" N UNK P 59 " --> pdb=" O UNK P 55 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N UNK P 60 " --> pdb=" O UNK P 56 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N UNK P 61 " --> pdb=" O UNK P 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 55 through 61' Processing helix chain 'P' and resid 79 through 85 removed outlier: 3.809A pdb=" N UNK P 85 " --> pdb=" O UNK P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 123 removed outlier: 4.248A pdb=" N UNK P 112 " --> pdb=" O UNK P 108 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N UNK P 113 " --> pdb=" O UNK P 109 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N UNK P 114 " --> pdb=" O UNK P 110 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N UNK P 123 " --> pdb=" O UNK P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 157 removed outlier: 5.630A pdb=" N UNK P 151 " --> pdb=" O UNK P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 219 removed outlier: 4.232A pdb=" N UNK P 212 " --> pdb=" O UNK P 208 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N UNK P 215 " --> pdb=" O UNK P 211 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 249 removed outlier: 3.528A pdb=" N UNK P 243 " --> pdb=" O UNK P 239 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N UNK P 248 " --> pdb=" O UNK P 244 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N UNK P 249 " --> pdb=" O UNK P 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 312 through 315 No H-bonds generated for 'chain 'P' and resid 312 through 315' Processing helix chain 'P' and resid 178 through 186 removed outlier: 4.276A pdb=" N UNK P 182 " --> pdb=" O UNK P 178 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N UNK P 183 " --> pdb=" O UNK P 179 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N UNK P 186 " --> pdb=" O UNK P 182 " (cutoff:3.500A) Processing helix chain 'P' and resid 280 through 289 removed outlier: 3.514A pdb=" N UNK P 286 " --> pdb=" O UNK P 282 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N UNK P 287 " --> pdb=" O UNK P 283 " (cutoff:3.500A) Processing helix chain 'P' and resid 312 through 319 removed outlier: 5.784A pdb=" N UNK P 316 " --> pdb=" O UNK P 312 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N UNK P 317 " --> pdb=" O UNK P 313 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 98 removed outlier: 3.756A pdb=" N UNK Q 93 " --> pdb=" O UNK Q 89 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N UNK Q 94 " --> pdb=" O UNK Q 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 removed outlier: 4.114A pdb=" N UNK R 45 " --> pdb=" O UNK R 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 45 removed outlier: 3.569A pdb=" N ASP S 34 " --> pdb=" O GLN S 30 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG S 39 " --> pdb=" O PHE S 35 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR S 40 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU S 42 " --> pdb=" O LYS S 38 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS S 45 " --> pdb=" O VAL S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 94 removed outlier: 3.625A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 21 removed outlier: 3.553A pdb=" N VAL T 15 " --> pdb=" O ILE T 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR T 17 " --> pdb=" O ASP T 13 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL T 18 " --> pdb=" O ARG T 14 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU T 21 " --> pdb=" O TYR T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 58 removed outlier: 4.445A pdb=" N VAL T 48 " --> pdb=" O SER T 44 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE T 50 " --> pdb=" O ASP T 46 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE T 51 " --> pdb=" O GLN T 47 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA T 53 " --> pdb=" O GLU T 49 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET T 54 " --> pdb=" O ILE T 50 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP T 56 " --> pdb=" O MET T 52 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU T 57 " --> pdb=" O ALA T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 69 removed outlier: 3.893A pdb=" N GLU T 68 " --> pdb=" O ASP T 64 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 64 through 69' Processing helix chain 'T' and resid 73 through 79 removed outlier: 3.967A pdb=" N ASP T 78 " --> pdb=" O GLN T 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 21 removed outlier: 3.520A pdb=" N ASP U 13 " --> pdb=" O GLU U 9 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL U 18 " --> pdb=" O ARG U 14 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU U 21 " --> pdb=" O TYR U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 57 removed outlier: 4.793A pdb=" N VAL U 48 " --> pdb=" O SER U 44 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU U 49 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU U 57 " --> pdb=" O ALA U 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.522A pdb=" N GLU U 68 " --> pdb=" O ASP U 64 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 64 through 69' Processing helix chain 'U' and resid 73 through 81 removed outlier: 3.587A pdb=" N ASP U 78 " --> pdb=" O GLN U 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 21 through 35 removed outlier: 3.618A pdb=" N LEU V 26 " --> pdb=" O ARG V 22 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU V 31 " --> pdb=" O TYR V 27 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP V 32 " --> pdb=" O THR V 28 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL V 33 " --> pdb=" O LYS V 29 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 removed outlier: 4.727A pdb=" N GLN V 49 " --> pdb=" O LYS V 45 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE V 50 " --> pdb=" O TYR V 46 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET V 57 " --> pdb=" O GLU V 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL V 58 " --> pdb=" O LYS V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 70 removed outlier: 3.686A pdb=" N GLU V 68 " --> pdb=" O VAL V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 95 removed outlier: 3.527A pdb=" N LEU V 81 " --> pdb=" O GLU V 77 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU V 86 " --> pdb=" O GLN V 82 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU V 87 " --> pdb=" O ALA V 83 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER V 88 " --> pdb=" O GLU V 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 46 removed outlier: 3.895A pdb=" N ARG W 29 " --> pdb=" O ASN W 25 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL W 31 " --> pdb=" O ALA W 27 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA W 37 " --> pdb=" O GLU W 33 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU W 41 " --> pdb=" O ALA W 37 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL W 42 " --> pdb=" O TRP W 38 " (cutoff:3.500A) Proline residue: W 43 - end of helix removed outlier: 4.435A pdb=" N VAL W 46 " --> pdb=" O VAL W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 69 removed outlier: 3.663A pdb=" N VAL W 62 " --> pdb=" O GLY W 58 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG W 63 " --> pdb=" O ARG W 59 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET W 65 " --> pdb=" O LYS W 61 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN W 69 " --> pdb=" O MET W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 93 removed outlier: 3.614A pdb=" N MET W 87 " --> pdb=" O ILE W 83 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU W 89 " --> pdb=" O GLY W 85 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLU W 90 " --> pdb=" O LYS W 86 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N THR W 92 " --> pdb=" O GLU W 88 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 100 through 103 removed outlier: 7.423A pdb=" N MET W 103 " --> pdb=" O THR W 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 100 through 103' Processing helix chain 'W' and resid 117 through 122 removed outlier: 4.549A pdb=" N PHE W 121 " --> pdb=" O PHE W 117 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR W 122 " --> pdb=" O LEU W 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 117 through 122' Processing helix chain 'X' and resid 22 through 26 removed outlier: 4.953A pdb=" N LYS X 25 " --> pdb=" O SER X 22 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 47 Processing helix chain 'X' and resid 52 through 76 removed outlier: 3.560A pdb=" N LEU X 56 " --> pdb=" O PRO X 52 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLU X 57 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU X 58 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY X 59 " --> pdb=" O CYS X 55 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU X 61 " --> pdb=" O GLU X 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU X 68 " --> pdb=" O GLN X 64 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE X 70 " --> pdb=" O ALA X 66 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN X 72 " --> pdb=" O GLU X 68 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE X 73 " --> pdb=" O PHE X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 91 removed outlier: 3.572A pdb=" N ASP X 89 " --> pdb=" O TRP X 85 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER X 91 " --> pdb=" O CYS X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 99 through 113 removed outlier: 4.361A pdb=" N GLN X 105 " --> pdb=" O LYS X 101 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE X 106 " --> pdb=" O GLN X 102 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP X 107 " --> pdb=" O GLN X 103 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU X 108 " --> pdb=" O ALA X 104 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS X 109 " --> pdb=" O GLN X 105 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL X 110 " --> pdb=" O PHE X 106 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP X 112 " --> pdb=" O GLU X 108 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS X 113 " --> pdb=" O CYS X 109 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 12 removed outlier: 3.716A pdb=" N TYR Y 8 " --> pdb=" O VAL Y 4 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP Y 9 " --> pdb=" O LEU Y 5 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP Y 10 " --> pdb=" O ARG Y 6 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE Y 11 " --> pdb=" O GLN Y 7 " (cutoff:3.500A) Proline residue: Y 12 - end of helix Processing helix chain 'Y' and resid 18 through 42 removed outlier: 4.368A pdb=" N TYR Y 22 " --> pdb=" O HIS Y 18 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR Y 25 " --> pdb=" O THR Y 21 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER Y 26 " --> pdb=" O TYR Y 22 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE Y 27 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL Y 34 " --> pdb=" O ALA Y 30 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL Y 35 " --> pdb=" O ALA Y 31 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL Y 40 " --> pdb=" O SER Y 36 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA Y 41 " --> pdb=" O ALA Y 37 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU Y 42 " --> pdb=" O TYR Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 78 removed outlier: 3.635A pdb=" N THR Y 55 " --> pdb=" O GLY Y 51 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG Y 57 " --> pdb=" O ALA Y 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR Y 58 " --> pdb=" O ARG Y 54 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE Y 60 " --> pdb=" O GLY Y 56 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR Y 61 " --> pdb=" O ARG Y 57 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY Y 66 " --> pdb=" O ALA Y 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS Y 74 " --> pdb=" O GLY Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 87 through 102 removed outlier: 3.726A pdb=" N ILE Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY Y 92 " --> pdb=" O ASN Y 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA Y 95 " --> pdb=" O ILE Y 91 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE Y 99 " --> pdb=" O ALA Y 95 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU Y 100 " --> pdb=" O GLY Y 96 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLY Y 101 " --> pdb=" O GLY Y 97 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA Y 102 " --> pdb=" O LEU Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 110 through 125 removed outlier: 5.143A pdb=" N ALA Y 115 " --> pdb=" O ALA Y 111 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR Y 116 " --> pdb=" O ALA Y 112 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL Y 124 " --> pdb=" O THR Y 120 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS Y 125 " --> pdb=" O ALA Y 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 95 removed outlier: 3.941A pdb=" N PHE Z 35 " --> pdb=" O GLY Z 31 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA Z 36 " --> pdb=" O TYR Z 32 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL Z 37 " --> pdb=" O SER Z 33 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU Z 42 " --> pdb=" O GLY Z 38 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP Z 47 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS Z 51 " --> pdb=" O TRP Z 47 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP Z 52 " --> pdb=" O SER Z 48 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG Z 58 " --> pdb=" O ARG Z 54 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU Z 59 " --> pdb=" O GLU Z 55 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU Z 62 " --> pdb=" O ARG Z 58 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA Z 66 " --> pdb=" O GLU Z 62 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG Z 67 " --> pdb=" O ASP Z 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE Z 68 " --> pdb=" O PHE Z 64 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N MET Z 71 " --> pdb=" O ARG Z 67 " (cutoff:3.500A) Proline residue: Z 72 - end of helix removed outlier: 3.684A pdb=" N GLU Z 77 " --> pdb=" O LEU Z 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS Z 78 " --> pdb=" O LEU Z 74 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG Z 80 " --> pdb=" O ALA Z 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 135 Processing helix chain 'a' and resid 42 through 53 removed outlier: 3.662A pdb=" N LEU a 47 " --> pdb=" O TYR a 43 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG a 52 " --> pdb=" O MET a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 1 through 29 removed outlier: 3.943A pdb=" N VAL a 5 " --> pdb=" O MET a 1 " (cutoff:3.500A) Proline residue: a 7 - end of helix removed outlier: 3.922A pdb=" N MET a 12 " --> pdb=" O GLY a 8 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL a 14 " --> pdb=" O ALA a 10 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE a 17 " --> pdb=" O GLY a 13 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.643A pdb=" N THR a 23 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA a 24 " --> pdb=" O GLY a 20 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE a 26 " --> pdb=" O ALA a 22 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N HIS a 27 " --> pdb=" O THR a 23 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE a 29 " --> pdb=" O ARG a 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 13 removed outlier: 4.761A pdb=" N ALA b 6 " --> pdb=" O GLU b 2 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE b 7 " --> pdb=" O ARG b 3 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU b 8 " --> pdb=" O VAL b 4 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS b 9 " --> pdb=" O ALA b 5 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN b 10 " --> pdb=" O ALA b 6 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL b 11 " --> pdb=" O PHE b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 32 removed outlier: 4.363A pdb=" N ALA b 20 " --> pdb=" O PRO b 16 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE b 22 " --> pdb=" O LEU b 18 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL b 29 " --> pdb=" O ALA b 25 " (cutoff:3.500A) Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 46 removed outlier: 3.621A pdb=" N LEU b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET b 43 " --> pdb=" O LYS b 39 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE b 44 " --> pdb=" O TYR b 40 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN b 45 " --> pdb=" O SER b 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 38 through 46' Processing helix chain 'c' and resid 15 through 44 removed outlier: 4.461A pdb=" N LEU c 19 " --> pdb=" O LEU c 15 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER c 24 " --> pdb=" O THR c 20 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL c 25 " --> pdb=" O LEU c 21 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR c 30 " --> pdb=" O PHE c 26 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN c 34 " --> pdb=" O TYR c 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 48 removed outlier: 3.514A pdb=" N PHE d 33 " --> pdb=" O PRO d 29 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL d 34 " --> pdb=" O ARG d 30 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY d 42 " --> pdb=" O GLY d 38 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP d 45 " --> pdb=" O SER d 41 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASN d 46 " --> pdb=" O GLY d 42 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA d 47 " --> pdb=" O LEU d 43 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE d 48 " --> pdb=" O ILE d 44 " (cutoff:3.500A) Processing helix chain 'd' and resid 60 through 97 removed outlier: 3.954A pdb=" N TYR d 64 " --> pdb=" O ARG d 60 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE d 68 " --> pdb=" O TYR d 64 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET d 90 " --> pdb=" O ARG d 86 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE d 94 " --> pdb=" O MET d 90 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 43 removed outlier: 4.283A pdb=" N GLU e 38 " --> pdb=" O ALA e 34 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP e 39 " --> pdb=" O PHE e 35 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 67 removed outlier: 3.776A pdb=" N LEU e 66 " --> pdb=" O PHE e 62 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 84 removed outlier: 3.558A pdb=" N ARG e 74 " --> pdb=" O LYS e 70 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE e 78 " --> pdb=" O ARG e 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 4 through 9 removed outlier: 3.512A pdb=" N ARG f 8 " --> pdb=" O LEU f 4 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP f 9 " --> pdb=" O GLN f 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 4 through 9' Processing helix chain 'f' and resid 12 through 33 removed outlier: 4.209A pdb=" N VAL f 16 " --> pdb=" O VAL f 12 " (cutoff:3.500A) Proline residue: f 17 - end of helix removed outlier: 3.504A pdb=" N ARG f 28 " --> pdb=" O TYR f 24 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN f 30 " --> pdb=" O LEU f 26 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASP f 31 " --> pdb=" O ASP f 27 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU f 32 " --> pdb=" O ARG f 28 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS f 33 " --> pdb=" O LYS f 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 51 through 74 removed outlier: 3.798A pdb=" N TRP g 56 " --> pdb=" O ALA g 52 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG g 59 " --> pdb=" O ILE g 55 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL g 60 " --> pdb=" O TRP g 56 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N PHE g 62 " --> pdb=" O MET g 58 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE g 63 " --> pdb=" O ARG g 59 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY g 65 " --> pdb=" O VAL g 61 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE g 66 " --> pdb=" O PHE g 62 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU g 70 " --> pdb=" O PHE g 66 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL g 71 " --> pdb=" O SER g 67 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU g 72 " --> pdb=" O ILE g 68 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY g 73 " --> pdb=" O VAL g 69 " (cutoff:3.500A) Processing helix chain 'h' and resid 17 through 43 removed outlier: 3.695A pdb=" N PHE h 21 " --> pdb=" O TYR h 17 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU h 22 " --> pdb=" O ASP h 18 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR h 28 " --> pdb=" O LEU h 24 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR h 32 " --> pdb=" O TYR h 28 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE h 34 " --> pdb=" O LEU h 30 " (cutoff:3.500A) Proline residue: h 35 - end of helix removed outlier: 3.629A pdb=" N THR h 41 " --> pdb=" O ALA h 37 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE h 43 " --> pdb=" O GLY h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 70 through 78 removed outlier: 3.936A pdb=" N UNK h 78 " --> pdb=" O UNK h 74 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 116 removed outlier: 3.979A pdb=" N UNK h 88 " --> pdb=" O UNK h 84 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N UNK h 100 " --> pdb=" O UNK h 96 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N UNK h 116 " --> pdb=" O UNK h 112 " (cutoff:3.500A) Processing helix chain 'i' and resid 6 through 23 removed outlier: 5.837A pdb=" N ARG i 10 " --> pdb=" O GLU i 6 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU i 11 " --> pdb=" O GLU i 7 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN i 13 " --> pdb=" O LEU i 9 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU i 16 " --> pdb=" O GLN i 12 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU i 17 " --> pdb=" O GLN i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 42 through 51 removed outlier: 3.606A pdb=" N UNK i 49 " --> pdb=" O UNK i 45 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N UNK i 50 " --> pdb=" O UNK i 46 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N UNK i 51 " --> pdb=" O UNK i 47 " (cutoff:3.500A) Processing helix chain 'i' and resid 57 through 86 removed outlier: 5.818A pdb=" N UNK i 61 " --> pdb=" O UNK i 57 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N UNK i 62 " --> pdb=" O UNK i 58 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N UNK i 64 " --> pdb=" O UNK i 60 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N UNK i 65 " --> pdb=" O UNK i 61 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N UNK i 68 " --> pdb=" O UNK i 64 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N UNK i 72 " --> pdb=" O UNK i 68 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N UNK i 75 " --> pdb=" O UNK i 71 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N UNK i 76 " --> pdb=" O UNK i 72 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N UNK i 77 " --> pdb=" O UNK i 73 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N UNK i 78 " --> pdb=" O UNK i 74 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N UNK i 80 " --> pdb=" O UNK i 76 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N UNK i 85 " --> pdb=" O UNK i 81 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N UNK i 86 " --> pdb=" O UNK i 82 " (cutoff:3.500A) Processing helix chain 'j' and resid 19 through 40 removed outlier: 3.870A pdb=" N UNK j 23 " --> pdb=" O UNK j 19 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N UNK j 26 " --> pdb=" O UNK j 22 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N UNK j 27 " --> pdb=" O UNK j 23 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N UNK j 31 " --> pdb=" O UNK j 27 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N UNK j 32 " --> pdb=" O UNK j 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N UNK j 33 " --> pdb=" O UNK j 29 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N UNK j 36 " --> pdb=" O UNK j 32 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N UNK j 39 " --> pdb=" O UNK j 35 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N UNK j 40 " --> pdb=" O UNK j 36 " (cutoff:3.500A) Processing helix chain 'k' and resid 15 through 21 removed outlier: 5.097A pdb=" N UNK k 19 " --> pdb=" O UNK k 15 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 72 removed outlier: 4.682A pdb=" N UNK k 59 " --> pdb=" O UNK k 55 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N UNK k 60 " --> pdb=" O UNK k 56 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N UNK k 65 " --> pdb=" O UNK k 61 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N UNK k 68 " --> pdb=" O UNK k 64 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N UNK k 69 " --> pdb=" O UNK k 65 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N UNK k 70 " --> pdb=" O UNK k 66 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N UNK k 71 " --> pdb=" O UNK k 67 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N UNK k 72 " --> pdb=" O UNK k 68 " (cutoff:3.500A) Processing helix chain 'l' and resid 17 through 25 removed outlier: 3.911A pdb=" N UNK l 20 " --> pdb=" O UNK l 17 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N UNK l 21 " --> pdb=" O UNK l 18 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N UNK l 22 " --> pdb=" O UNK l 19 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N UNK l 23 " --> pdb=" O UNK l 20 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N UNK l 24 " --> pdb=" O UNK l 21 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N UNK l 25 " --> pdb=" O UNK l 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 17 through 25' Processing helix chain 'l' and resid 98 through 118 removed outlier: 3.839A pdb=" N UNK l 102 " --> pdb=" O UNK l 98 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N UNK l 103 " --> pdb=" O UNK l 99 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N UNK l 107 " --> pdb=" O UNK l 103 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N UNK l 109 " --> pdb=" O UNK l 105 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N UNK l 112 " --> pdb=" O UNK l 108 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N UNK l 115 " --> pdb=" O UNK l 111 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N UNK l 116 " --> pdb=" O UNK l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 49 removed outlier: 3.559A pdb=" N UNK m 30 " --> pdb=" O UNK m 26 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA m 33 " --> pdb=" O UNK m 29 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE m 38 " --> pdb=" O GLU m 34 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG m 41 " --> pdb=" O ALA m 37 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU m 45 " --> pdb=" O ARG m 41 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR m 46 " --> pdb=" O LEU m 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 63 through 72 removed outlier: 4.120A pdb=" N ARG m 71 " --> pdb=" O TRP m 67 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 116 removed outlier: 3.671A pdb=" N GLY m 95 " --> pdb=" O LEU m 91 " (cutoff:3.500A) Proline residue: m 96 - end of helix removed outlier: 3.621A pdb=" N TRP m 100 " --> pdb=" O PRO m 96 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR m 101 " --> pdb=" O LEU m 97 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR m 102 " --> pdb=" O VAL m 98 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL m 103 " --> pdb=" O PHE m 99 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS m 105 " --> pdb=" O TYR m 101 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR m 106 " --> pdb=" O TYR m 102 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS m 113 " --> pdb=" O ASP m 109 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU m 114 " --> pdb=" O ARG m 110 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN m 116 " --> pdb=" O GLU m 112 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 29 removed outlier: 3.573A pdb=" N VAL n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU n 18 " --> pdb=" O LYS n 14 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG n 24 " --> pdb=" O LYS n 20 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU n 27 " --> pdb=" O LEU n 23 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER n 28 " --> pdb=" O ARG n 24 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP n 29 " --> pdb=" O HIS n 25 " (cutoff:3.500A) Processing helix chain 'n' and resid 34 through 53 removed outlier: 3.585A pdb=" N TYR n 38 " --> pdb=" O ASP n 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS n 41 " --> pdb=" O ARG n 37 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU n 42 " --> pdb=" O TYR n 38 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG n 46 " --> pdb=" O LEU n 42 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE n 47 " --> pdb=" O LEU n 43 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU n 49 " --> pdb=" O ALA n 45 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN n 52 " --> pdb=" O ASP n 48 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLU n 53 " --> pdb=" O GLU n 49 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 72 removed outlier: 4.485A pdb=" N THR n 60 " --> pdb=" O MET n 56 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG n 64 " --> pdb=" O THR n 60 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU n 67 " --> pdb=" O LEU n 63 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU n 68 " --> pdb=" O ARG n 64 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU n 69 " --> pdb=" O GLU n 65 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N HIS n 72 " --> pdb=" O GLU n 68 " (cutoff:3.500A) Processing helix chain 'n' and resid 108 through 111 No H-bonds generated for 'chain 'n' and resid 108 through 111' Processing helix chain 'n' and resid 115 through 141 removed outlier: 3.504A pdb=" N LYS n 120 " --> pdb=" O ASP n 116 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 58 through 71 removed outlier: 5.158A pdb=" N LEU o 62 " --> pdb=" O CYS o 58 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG o 64 " --> pdb=" O HIS o 60 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE o 65 " --> pdb=" O TYR o 61 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU o 66 " --> pdb=" O LEU o 62 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP o 71 " --> pdb=" O LYS o 67 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 113 removed outlier: 3.827A pdb=" N ASP o 85 " --> pdb=" O HIS o 81 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP o 86 " --> pdb=" O GLU o 82 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP o 87 " --> pdb=" O ARG o 83 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU o 90 " --> pdb=" O TRP o 86 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS o 91 " --> pdb=" O ASP o 87 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN o 109 " --> pdb=" O ARG o 105 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG o 110 " --> pdb=" O ARG o 106 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG o 113 " --> pdb=" O GLN o 109 " (cutoff:3.500A) Processing helix chain 'p' and resid 29 through 55 removed outlier: 4.115A pdb=" N UNK p 38 " --> pdb=" O UNK p 34 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N UNK p 40 " --> pdb=" O UNK p 36 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N UNK p 41 " --> pdb=" O UNK p 37 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N UNK p 42 " --> pdb=" O UNK p 38 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N UNK p 43 " --> pdb=" O UNK p 39 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N UNK p 55 " --> pdb=" O UNK p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 116 removed outlier: 3.747A pdb=" N ALA p 87 " --> pdb=" O CYS p 83 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU p 100 " --> pdb=" O LYS p 96 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL p 102 " --> pdb=" O ASP p 98 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN p 103 " --> pdb=" O GLN p 99 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE p 104 " --> pdb=" O GLU p 100 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN p 114 " --> pdb=" O LYS p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 126 through 139 removed outlier: 3.574A pdb=" N LYS p 136 " --> pdb=" O THR p 132 " (cutoff:3.500A) Processing helix chain 'p' and resid 153 through 172 removed outlier: 3.509A pdb=" N UNK p 161 " --> pdb=" O UNK p 157 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N UNK p 164 " --> pdb=" O UNK p 160 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N UNK p 169 " --> pdb=" O UNK p 165 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N UNK p 170 " --> pdb=" O UNK p 166 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N UNK p 171 " --> pdb=" O UNK p 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N UNK p 172 " --> pdb=" O UNK p 168 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 16 removed outlier: 3.741A pdb=" N LEU q 7 " --> pdb=" O LEU q 3 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY q 10 " --> pdb=" O VAL q 6 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU q 11 " --> pdb=" O LEU q 7 " (cutoff:3.500A) Processing helix chain 'q' and resid 21 through 27 removed outlier: 3.521A pdb=" N ARG q 25 " --> pdb=" O ARG q 21 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL q 26 " --> pdb=" O GLY q 22 " (cutoff:3.500A) Processing helix chain 'r' and resid 6 through 14 removed outlier: 3.844A pdb=" N UNK r 10 " --> pdb=" O UNK r 6 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N UNK r 13 " --> pdb=" O UNK r 9 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N UNK r 14 " --> pdb=" O UNK r 10 " (cutoff:3.500A) Processing helix chain 's' and resid 11 through 20 removed outlier: 4.298A pdb=" N UNK s 17 " --> pdb=" O UNK s 13 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N UNK s 18 " --> pdb=" O UNK s 14 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 50 removed outlier: 3.918A pdb=" N ILE B 87 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE B 50 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA B 89 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B 116 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 144 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 74 through 81 removed outlier: 3.755A pdb=" N SER C 74 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 76 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 92 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER C 103 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL C 40 " --> pdb=" O CYS C 51 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLN C 39 " --> pdb=" O UNK r 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N UNK r 69 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN C 41 " --> pdb=" O UNK r 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 48 through 50 removed outlier: 3.544A pdb=" N LEU D 49 " --> pdb=" O MET D 66 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG D 63 " --> pdb=" O HIS D 79 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N HIS D 79 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS D 75 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 360 through 367 removed outlier: 4.416A pdb=" N ILE D 367 " --> pdb=" O PHE D 374 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE D 374 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS D 390 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ARG D 388 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 137 through 141 removed outlier: 3.984A pdb=" N THR E 138 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE E 140 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N MET E 153 " --> pdb=" O CYS E 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 174 through 179 removed outlier: 4.160A pdb=" N THR F 221 " --> pdb=" O TYR F 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 265 through 269 removed outlier: 4.048A pdb=" N CYS F 266 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE F 258 " --> pdb=" O CYS F 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE F 256 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL F 336 " --> pdb=" O SER F 259 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 333 through 337 current: chain 'F' and resid 306 through 308 Processing sheet with id=AA8, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.554A pdb=" N GLN G 16 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL G 18 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL G 11 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL G 20 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N TRP G 77 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE G 12 " --> pdb=" O TRP G 77 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE G 79 " --> pdb=" O PHE G 12 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 223 through 227 removed outlier: 6.166A pdb=" N UNK G 223 " --> pdb=" O UNK G 242 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N UNK G 249 " --> pdb=" O UNK G 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 421 through 423 removed outlier: 6.680A pdb=" N UNK G 422 " --> pdb=" O UNK G 406 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N UNK G 408 " --> pdb=" O UNK G 422 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N UNK G 407 " --> pdb=" O UNK G 378 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N UNK G 380 " --> pdb=" O UNK G 407 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N UNK G 450 " --> pdb=" O UNK G 377 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N UNK G 379 " --> pdb=" O UNK G 450 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N UNK G 452 " --> pdb=" O UNK G 379 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N UNK G 381 " --> pdb=" O UNK G 452 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N UNK G 451 " --> pdb=" O UNK G 489 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 571 through 574 Processing sheet with id=AB4, first strand: chain 'G' and resid 207 through 210 removed outlier: 5.018A pdb=" N ALA G 207 " --> pdb=" O ILE G 149 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR G 209 " --> pdb=" O LYS G 147 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N VAL G 146 " --> pdb=" O LYS G 140 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N LYS G 140 " --> pdb=" O VAL G 146 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 291 through 294 removed outlier: 3.781A pdb=" N UNK G 292 " --> pdb=" O UNK G 284 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N UNK G 282 " --> pdb=" O UNK G 294 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N UNK G 285 " --> pdb=" O UNK G 558 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N UNK G 558 " --> pdb=" O UNK G 285 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N UNK G 558 " --> pdb=" O UNK G 543 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N UNK G 545 " --> pdb=" O UNK G 558 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N UNK G 560 " --> pdb=" O UNK G 545 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N UNK G 547 " --> pdb=" O UNK G 560 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N UNK G 562 " --> pdb=" O UNK G 547 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 543 through 547 current: chain 'G' and resid 525 through 529 removed outlier: 4.244A pdb=" N UNK G 316 " --> pdb=" O UNK G 525 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNK G 527 " --> pdb=" O UNK G 316 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N UNK G 529 " --> pdb=" O UNK G 318 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N UNK G 342 " --> pdb=" O UNK G 315 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N UNK G 317 " --> pdb=" O UNK G 342 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N UNK G 344 " --> pdb=" O UNK G 317 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N UNK G 319 " --> pdb=" O UNK G 344 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 65 through 67 removed outlier: 4.414A pdb=" N ALA I 66 " --> pdb=" O VAL I 132 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL I 132 " --> pdb=" O ALA I 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'I' and resid 92 through 96 Processing sheet with id=AB8, first strand: chain 'L' and resid 78 through 83 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 78 through 83 current: chain 'i' and resid 95 through 98 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'O' and resid 219 through 224 removed outlier: 3.627A pdb=" N VAL O 172 " --> pdb=" O LEU O 221 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR O 223 " --> pdb=" O VAL O 172 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL O 174 " --> pdb=" O TYR O 223 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP O 173 " --> pdb=" O UNK O 28 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL O 122 " --> pdb=" O UNK O 23 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU O 125 " --> pdb=" O UNK O 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 67 through 71 removed outlier: 4.896A pdb=" N UNK P 45 " --> pdb=" O UNK P 67 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N UNK P 69 " --> pdb=" O UNK P 45 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N UNK P 21 " --> pdb=" O UNK P 44 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N UNK P 46 " --> pdb=" O UNK P 21 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N UNK P 23 " --> pdb=" O UNK P 46 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N UNK P 25 " --> pdb=" O UNK P 48 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N UNK P 90 " --> pdb=" O UNK P 20 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N UNK P 22 " --> pdb=" O UNK P 90 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N UNK P 24 " --> pdb=" O UNK P 92 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N UNK P 94 " --> pdb=" O UNK P 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 90 through 94 current: chain 'P' and resid 128 through 133 removed outlier: 3.879A pdb=" N UNK P 131 " --> pdb=" O UNK P 164 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N UNK P 165 " --> pdb=" O UNK P 226 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N UNK P 228 " --> pdb=" O UNK P 165 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Q' and resid 103 through 106 removed outlier: 3.706A pdb=" N UNK Q 37 " --> pdb=" O UNK Q 104 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N UNK Q 106 " --> pdb=" O UNK Q 37 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N UNK Q 39 " --> pdb=" O UNK Q 106 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N UNK Q 58 " --> pdb=" O UNK Q 36 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N UNK Q 56 " --> pdb=" O UNK Q 38 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N UNK Q 57 " --> pdb=" O UNK Q 84 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N UNK Q 84 " --> pdb=" O UNK Q 57 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 55 through 59 removed outlier: 6.020A pdb=" N UNK R 55 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL R 71 " --> pdb=" O CYS R 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 81 through 83 removed outlier: 3.693A pdb=" N GLY R 82 " --> pdb=" O PHE R 91 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG R 92 " --> pdb=" O UNK R 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 52 through 55 removed outlier: 5.632A pdb=" N ILE S 18 " --> pdb=" O LEU S 53 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ARG S 55 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE S 20 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG S 19 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TRP S 65 " --> pdb=" O ARG S 19 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS S 63 " --> pdb=" O HIS S 21 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS S 74 " --> pdb=" O ALA S 66 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'q' and resid 39 through 42 removed outlier: 4.212A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N TYR q 48 " --> pdb=" O GLY q 40 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP q 42 " --> pdb=" O ASN q 46 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN q 46 " --> pdb=" O ASP q 42 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLY q 45 " --> pdb=" O TYR q 64 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR q 64 " --> pdb=" O GLY q 45 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS q 47 " --> pdb=" O VAL q 62 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL q 62 " --> pdb=" O LYS q 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 1725 hydrogen bonds defined for protein. 4779 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: 13.11 Time building geometry restraints manager: 10.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 21433 1.43 - 1.65: 30058 1.65 - 1.87: 510 1.87 - 2.09: 0 2.09 - 2.30: 80 Bond restraints: 52081 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 1.504 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C10 FMN F 501 " pdb=" C4A FMN F 501 " ideal model delta sigma weight residual 1.390 1.490 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C4 FMN F 501 " pdb=" C4A FMN F 501 " ideal model delta sigma weight residual 1.390 1.488 -0.098 2.00e-02 2.50e+03 2.41e+01 ... (remaining 52076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 69261 3.28 - 6.57: 2063 6.57 - 9.85: 104 9.85 - 13.14: 46 13.14 - 16.42: 12 Bond angle restraints: 71486 Sorted by residual: angle pdb=" N ILE W 19 " pdb=" CA ILE W 19 " pdb=" C ILE W 19 " ideal model delta sigma weight residual 110.42 121.67 -11.25 9.60e-01 1.09e+00 1.37e+02 angle pdb=" CA PRO G 22 " pdb=" N PRO G 22 " pdb=" CD PRO G 22 " ideal model delta sigma weight residual 112.00 98.56 13.44 1.40e+00 5.10e-01 9.21e+01 angle pdb=" CA PRO F 53 " pdb=" N PRO F 53 " pdb=" CD PRO F 53 " ideal model delta sigma weight residual 112.00 98.71 13.29 1.40e+00 5.10e-01 9.01e+01 angle pdb=" CA PRO E 77 " pdb=" N PRO E 77 " pdb=" CD PRO E 77 " ideal model delta sigma weight residual 112.00 98.74 13.26 1.40e+00 5.10e-01 8.98e+01 angle pdb=" CA PRO E 166 " pdb=" N PRO E 166 " pdb=" CD PRO E 166 " ideal model delta sigma weight residual 112.00 98.83 13.17 1.40e+00 5.10e-01 8.85e+01 ... (remaining 71481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.87: 30402 33.87 - 67.74: 660 67.74 - 101.61: 32 101.61 - 135.48: 0 135.48 - 169.35: 1 Dihedral angle restraints: 31095 sinusoidal: 8287 harmonic: 22808 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 -133.61 -46.39 0 5.00e+00 4.00e-02 8.61e+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 93.00 171.15 -78.15 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 88.25 169.35 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 31092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.260: 8742 4.260 - 8.519: 0 8.519 - 12.779: 0 12.779 - 17.038: 0 17.038 - 21.298: 24 Chirality restraints: 8766 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 -10.74 21.30 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 G 801 " pdb=" S2 SF4 G 801 " pdb=" S3 SF4 G 801 " pdb=" S4 SF4 G 801 " both_signs ideal model delta sigma weight residual False -10.55 10.74 -21.29 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE3 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S2 SF4 G 801 " pdb=" S4 SF4 G 801 " both_signs ideal model delta sigma weight residual False -10.55 10.72 -21.28 2.00e-01 2.50e+01 1.13e+04 ... (remaining 8763 not shown) Planarity restraints: 9352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 16 " -0.117 5.00e-02 4.00e+02 1.65e-01 4.35e+01 pdb=" N PRO E 17 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO E 17 " -0.091 5.00e-02 4.00e+02 pdb=" CD PRO E 17 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN g 41 " 0.113 5.00e-02 4.00e+02 1.58e-01 3.97e+01 pdb=" N PRO g 42 " -0.272 5.00e-02 4.00e+02 pdb=" CA PRO g 42 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO g 42 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN e 24 " -0.112 5.00e-02 4.00e+02 1.56e-01 3.92e+01 pdb=" N PRO e 25 " 0.270 5.00e-02 4.00e+02 pdb=" CA PRO e 25 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO e 25 " -0.073 5.00e-02 4.00e+02 ... (remaining 9349 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 15 2.27 - 2.92: 18804 2.92 - 3.58: 69463 3.58 - 4.24: 104340 4.24 - 4.90: 177365 Nonbonded interactions: 369987 Sorted by model distance: nonbonded pdb=" CD PRO D 6 " pdb=" OG1 THR N 303 " model vdw 1.608 3.440 nonbonded pdb=" O ALA E 46 " pdb=" CD PRO E 49 " model vdw 1.765 3.440 nonbonded pdb=" CG PRO D 38 " pdb=" CB PRO N 50 " model vdw 1.779 3.840 nonbonded pdb=" CB TYR D 20 " pdb=" OD1 ASN N 171 " model vdw 1.791 3.440 nonbonded pdb=" CG PRO D 38 " pdb=" CG PRO N 50 " model vdw 1.835 3.840 ... (remaining 369982 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 'Q' selection = (chain 'l' and resid 10 through 122) } ncs_group { reference = chain 'T' selection = (chain 'U' and resid 8 through 82) } ncs_group { reference = chain 'k' selection = (chain 'r' and resid 17 through 119) } 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.390 Check model and map are aligned: 0.290 Set scattering table: 0.350 Process input model: 92.770 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.009 0.121 52081 Z= 0.563 Angle : 1.418 16.420 71486 Z= 0.894 Chirality : 1.114 21.298 8766 Planarity : 0.009 0.165 9345 Dihedral : 14.780 169.346 16145 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 3.25 % Allowed : 8.51 % Favored : 88.24 % Rotamer: Outliers : 3.32 % Allowed : 9.72 % Favored : 86.96 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.34 % 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: -4.87 (0.08), residues: 5784 helix: -3.34 (0.06), residues: 2920 sheet: -0.57 (0.42), residues: 149 loop : -3.22 (0.10), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 84 HIS 0.005 0.001 HIS R 68 PHE 0.014 0.001 PHE L 124 TYR 0.017 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) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1756 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1637 time to evaluate : 3.814 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: A 12 THR cc_start: 0.8197 (p) cc_final: 0.7897 (t) REVERT: A 65 PHE cc_start: 0.8793 (m-10) cc_final: 0.8552 (m-10) REVERT: A 67 LEU cc_start: 0.8828 (mt) cc_final: 0.8542 (mm) REVERT: B 68 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6468 (t70) REVERT: B 83 SER cc_start: 0.9029 (p) cc_final: 0.8157 (t) REVERT: B 107 MET cc_start: 0.8775 (mmm) cc_final: 0.8529 (tpt) REVERT: B 116 MET cc_start: 0.8240 (ttp) cc_final: 0.7886 (ttp) REVERT: B 121 ASN cc_start: 0.7826 (m-40) cc_final: 0.6760 (m110) REVERT: B 131 SER cc_start: 0.8822 (p) cc_final: 0.8591 (m) REVERT: B 156 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8542 (tt) REVERT: C 41 GLN cc_start: 0.8282 (tp-100) cc_final: 0.8082 (tm-30) REVERT: C 58 ILE cc_start: 0.9335 (mt) cc_final: 0.8772 (mp) REVERT: C 90 PHE cc_start: 0.8684 (m-80) cc_final: 0.8465 (m-10) REVERT: C 117 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8490 (mm) REVERT: C 198 ASP cc_start: 0.7052 (t70) cc_final: 0.6714 (t0) REVERT: D 82 LEU cc_start: 0.8844 (mt) cc_final: 0.8554 (mt) REVERT: D 106 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7867 (tp) REVERT: D 111 MET cc_start: 0.8143 (mmt) cc_final: 0.7810 (mmm) REVERT: D 114 ASN cc_start: 0.7278 (m-40) cc_final: 0.7028 (m-40) REVERT: D 135 GLN cc_start: 0.8713 (mt0) cc_final: 0.8482 (mt0) REVERT: D 136 TRP cc_start: 0.8575 (m100) cc_final: 0.8107 (m100) REVERT: D 164 MET cc_start: 0.8079 (mmm) cc_final: 0.7712 (mmt) REVERT: D 167 PHE cc_start: 0.8695 (t80) cc_final: 0.8053 (t80) REVERT: D 169 TRP cc_start: 0.8514 (m-10) cc_final: 0.7716 (m100) REVERT: D 199 VAL cc_start: 0.8149 (t) cc_final: 0.7921 (p) REVERT: D 207 LEU cc_start: 0.8199 (mt) cc_final: 0.7877 (tp) REVERT: D 271 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8392 (pttt) REVERT: D 276 ASP cc_start: 0.7935 (m-30) cc_final: 0.7034 (m-30) REVERT: D 310 ILE cc_start: 0.8990 (mp) cc_final: 0.8496 (mt) REVERT: D 330 VAL cc_start: 0.9212 (t) cc_final: 0.8807 (t) REVERT: F 367 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6587 (mp0) REVERT: F 400 GLU cc_start: 0.7740 (tt0) cc_final: 0.6746 (tp30) REVERT: F 409 ASP cc_start: 0.7408 (m-30) cc_final: 0.5316 (m-30) REVERT: G 45 ARG cc_start: 0.7176 (mtt90) cc_final: 0.6229 (ptm160) REVERT: G 105 CYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8601 (m) REVERT: G 118 ASP cc_start: 0.8549 (m-30) cc_final: 0.8082 (t0) REVERT: G 122 MET cc_start: 0.8749 (mmt) cc_final: 0.8313 (mmt) REVERT: G 160 ILE cc_start: 0.9323 (mm) cc_final: 0.8959 (mm) REVERT: H 31 MET cc_start: 0.9185 (mmm) cc_final: 0.8983 (mmt) REVERT: H 32 GLN cc_start: 0.9299 (mt0) cc_final: 0.8939 (mt0) REVERT: H 51 ASP cc_start: 0.8299 (m-30) cc_final: 0.7632 (t70) REVERT: H 86 TRP cc_start: 0.8843 (m100) cc_final: 0.8616 (m100) REVERT: H 138 GLN cc_start: 0.6971 (mt0) cc_final: 0.6717 (mt0) REVERT: H 142 TYR cc_start: 0.8499 (m-80) cc_final: 0.8291 (m-80) REVERT: H 155 LEU cc_start: 0.9103 (tp) cc_final: 0.8854 (tp) REVERT: H 166 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9081 (mm) REVERT: H 176 LEU cc_start: 0.8592 (mt) cc_final: 0.8309 (tp) REVERT: H 257 ILE cc_start: 0.8425 (mt) cc_final: 0.8170 (tp) REVERT: H 280 PHE cc_start: 0.7085 (m-80) cc_final: 0.6676 (m-80) REVERT: H 282 TYR cc_start: 0.8213 (t80) cc_final: 0.7894 (t80) REVERT: H 290 TRP cc_start: 0.8149 (OUTLIER) cc_final: 0.7778 (m-90) REVERT: H 302 MET cc_start: 0.9009 (mmm) cc_final: 0.8557 (mmp) REVERT: I 15 LYS cc_start: 0.7698 (mtmm) cc_final: 0.7302 (tptp) REVERT: I 34 LEU cc_start: 0.8353 (tt) cc_final: 0.7561 (mt) REVERT: I 40 TYR cc_start: 0.8175 (t80) cc_final: 0.7117 (t80) REVERT: I 54 LYS cc_start: 0.8318 (mmtp) cc_final: 0.7426 (tttt) REVERT: I 90 GLN cc_start: 0.8277 (mt0) cc_final: 0.7663 (mm-40) REVERT: I 110 ASP cc_start: 0.7166 (m-30) cc_final: 0.6063 (m-30) REVERT: J 7 PHE cc_start: 0.7961 (t80) cc_final: 0.7477 (t80) REVERT: J 51 PHE cc_start: 0.7999 (t80) cc_final: 0.7404 (t80) REVERT: J 52 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8647 (mp) REVERT: J 76 THR cc_start: 0.7206 (p) cc_final: 0.6717 (p) REVERT: J 100 GLU cc_start: 0.8704 (tm-30) cc_final: 0.7811 (tp30) REVERT: J 101 PHE cc_start: 0.7671 (m-80) cc_final: 0.7345 (t80) REVERT: J 102 PHE cc_start: 0.7969 (t80) cc_final: 0.6327 (t80) REVERT: J 105 TYR cc_start: 0.6730 (t80) cc_final: 0.6528 (t80) REVERT: K 34 GLU cc_start: 0.8144 (mt-10) cc_final: 0.4725 (mt-10) REVERT: K 55 LEU cc_start: 0.8068 (mt) cc_final: 0.7692 (tp) REVERT: K 59 MET cc_start: 0.8023 (mmp) cc_final: 0.7629 (mmt) REVERT: K 70 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7146 (mt-10) REVERT: L 14 LEU cc_start: 0.9053 (mt) cc_final: 0.8584 (tp) REVERT: L 20 MET cc_start: 0.8581 (mmp) cc_final: 0.7019 (tmm) REVERT: L 48 MET cc_start: 0.8285 (mmm) cc_final: 0.7997 (tpp) REVERT: L 125 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9054 (tt) REVERT: L 138 PHE cc_start: 0.8065 (t80) cc_final: 0.7863 (t80) REVERT: L 179 ASP cc_start: 0.8192 (m-30) cc_final: 0.7766 (m-30) REVERT: L 186 MET cc_start: 0.8277 (mmm) cc_final: 0.7350 (mmt) REVERT: L 223 LYS cc_start: 0.9134 (mmtp) cc_final: 0.8712 (tptt) REVERT: L 252 MET cc_start: 0.8055 (tpt) cc_final: 0.7657 (tpp) REVERT: L 291 CYS cc_start: 0.7713 (m) cc_final: 0.7392 (m) REVERT: L 389 PHE cc_start: 0.6425 (t80) cc_final: 0.5984 (t80) REVERT: L 393 ASP cc_start: 0.7754 (m-30) cc_final: 0.7350 (t0) REVERT: L 454 ILE cc_start: 0.8668 (mt) cc_final: 0.8391 (mm) REVERT: L 459 ILE cc_start: 0.8002 (mt) cc_final: 0.7724 (tt) REVERT: L 532 ILE cc_start: 0.8168 (pt) cc_final: 0.7702 (tt) REVERT: L 535 ARG cc_start: 0.5497 (tpt170) cc_final: 0.3483 (ttt-90) REVERT: L 544 MET cc_start: 0.8594 (mtp) cc_final: 0.8374 (mtt) REVERT: L 571 MET cc_start: 0.7590 (tpt) cc_final: 0.6447 (ttm) REVERT: L 576 LEU cc_start: 0.8314 (mt) cc_final: 0.8011 (mm) REVERT: L 599 MET cc_start: 0.8478 (mmm) cc_final: 0.7157 (tpt) REVERT: M 61 LEU cc_start: 0.8393 (mp) cc_final: 0.8170 (mm) REVERT: M 72 LEU cc_start: 0.9249 (mt) cc_final: 0.9033 (mt) REVERT: M 73 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7952 (tp) REVERT: M 76 MET cc_start: 0.7735 (mtm) cc_final: 0.7346 (mtm) REVERT: M 144 ASN cc_start: 0.7299 (m-40) cc_final: 0.6898 (t0) REVERT: M 200 MET cc_start: 0.8942 (mmp) cc_final: 0.8196 (mmp) REVERT: M 205 VAL cc_start: 0.9073 (t) cc_final: 0.8423 (m) REVERT: M 206 LYS cc_start: 0.7909 (mttm) cc_final: 0.7594 (mmtt) REVERT: M 269 MET cc_start: 0.8431 (mmm) cc_final: 0.7831 (mmm) REVERT: M 276 CYS cc_start: 0.8498 (t) cc_final: 0.8094 (t) REVERT: M 279 GLN cc_start: 0.6372 (mt0) cc_final: 0.5659 (mt0) REVERT: M 281 ASP cc_start: 0.8159 (m-30) cc_final: 0.7574 (m-30) REVERT: M 285 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8502 (mt) REVERT: M 293 HIS cc_start: 0.8566 (m-70) cc_final: 0.8294 (t70) REVERT: M 317 ILE cc_start: 0.9370 (mt) cc_final: 0.9085 (tt) REVERT: M 319 HIS cc_start: 0.7444 (t70) cc_final: 0.6842 (t70) REVERT: M 329 LEU cc_start: 0.9574 (mt) cc_final: 0.9243 (mp) REVERT: M 338 HIS cc_start: 0.8050 (m-70) cc_final: 0.7737 (m170) REVERT: M 401 VAL cc_start: 0.9234 (t) cc_final: 0.8945 (t) REVERT: M 439 LEU cc_start: 0.9171 (mt) cc_final: 0.8948 (tp) REVERT: M 446 LEU cc_start: 0.8395 (mt) cc_final: 0.7968 (tp) REVERT: N 35 MET cc_start: 0.8404 (mmm) cc_final: 0.8068 (ttp) REVERT: N 98 MET cc_start: 0.9107 (tpt) cc_final: 0.8877 (tpp) REVERT: N 112 HIS cc_start: 0.8582 (p-80) cc_final: 0.7847 (p-80) REVERT: N 117 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7637 (mt-10) REVERT: N 164 ILE cc_start: 0.8729 (pt) cc_final: 0.8402 (mt) REVERT: N 175 LEU cc_start: 0.9189 (tp) cc_final: 0.8571 (mt) REVERT: N 193 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8239 (t) REVERT: N 206 ILE cc_start: 0.8993 (mt) cc_final: 0.8773 (mm) REVERT: N 208 TYR cc_start: 0.8802 (t80) cc_final: 0.8102 (t80) REVERT: N 211 MET cc_start: 0.8692 (ttm) cc_final: 0.8338 (ttp) REVERT: N 294 MET cc_start: 0.8674 (mmp) cc_final: 0.8347 (tpp) REVERT: O 100 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9063 (tp) REVERT: O 110 ASP cc_start: 0.7810 (m-30) cc_final: 0.7457 (t70) REVERT: O 160 ILE cc_start: 0.9137 (mt) cc_final: 0.8851 (tt) REVERT: V 26 LEU cc_start: 0.9173 (mt) cc_final: 0.8739 (mm) REVERT: W 32 ARG cc_start: 0.7564 (tpt170) cc_final: 0.6584 (tpt90) REVERT: W 61 LYS cc_start: 0.7047 (ttmt) cc_final: 0.6436 (tptt) REVERT: W 65 MET cc_start: 0.9020 (tpt) cc_final: 0.8735 (tpt) REVERT: W 91 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6650 (tp30) REVERT: X 31 TYR cc_start: 0.8009 (t80) cc_final: 0.7374 (t80) REVERT: X 41 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7094 (tp30) REVERT: X 50 LYS cc_start: 0.6937 (tttt) cc_final: 0.5909 (tptt) REVERT: X 79 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8346 (tp30) REVERT: X 84 TYR cc_start: 0.8234 (t80) cc_final: 0.7343 (t80) REVERT: X 105 GLN cc_start: 0.8125 (mt0) cc_final: 0.7602 (tp40) REVERT: X 107 ASP cc_start: 0.7308 (t70) cc_final: 0.6889 (t0) REVERT: Y 85 ASP cc_start: 0.9080 (m-30) cc_final: 0.8812 (t0) REVERT: Y 91 ILE cc_start: 0.8326 (mt) cc_final: 0.8103 (tp) REVERT: Z 55 GLU cc_start: 0.8137 (tp30) cc_final: 0.7635 (tp30) REVERT: Z 77 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8239 (tt0) REVERT: a 18 ILE cc_start: 0.8223 (mt) cc_final: 0.8016 (mm) REVERT: a 28 ARG cc_start: 0.7874 (mtt180) cc_final: 0.6954 (ptm160) REVERT: b 42 LEU cc_start: 0.9251 (tt) cc_final: 0.9003 (tp) REVERT: d 49 ARG cc_start: 0.8137 (mtt90) cc_final: 0.7550 (tpt-90) REVERT: d 73 TYR cc_start: 0.8476 (t80) cc_final: 0.7995 (t80) REVERT: d 82 MET cc_start: 0.8305 (tpt) cc_final: 0.7885 (tpp) REVERT: d 87 ASP cc_start: 0.7676 (t70) cc_final: 0.6865 (t0) REVERT: d 94 ILE cc_start: 0.8547 (mt) cc_final: 0.8177 (mm) REVERT: e 41 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7721 (tm-30) REVERT: e 83 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7178 (tp30) REVERT: g 80 LEU cc_start: 0.7473 (mt) cc_final: 0.7199 (mt) REVERT: g 92 GLU cc_start: 0.8488 (tp30) cc_final: 0.8142 (mm-30) REVERT: g 96 LEU cc_start: 0.9262 (mt) cc_final: 0.9004 (tp) REVERT: h 43 ILE cc_start: 0.7350 (mt) cc_final: 0.7033 (pt) REVERT: i 9 LEU cc_start: 0.8736 (pp) cc_final: 0.8425 (tt) REVERT: i 20 ARG cc_start: 0.8404 (mtm110) cc_final: 0.7357 (ppt170) REVERT: m 48 LEU cc_start: 0.9468 (mt) cc_final: 0.8834 (tt) REVERT: m 67 TRP cc_start: 0.8389 (t-100) cc_final: 0.8057 (t-100) REVERT: m 80 ARG cc_start: 0.7316 (ptm160) cc_final: 0.7073 (mmt180) REVERT: n 12 GLN cc_start: 0.8520 (mt0) cc_final: 0.8311 (tp-100) REVERT: n 16 LEU cc_start: 0.9092 (mt) cc_final: 0.8455 (pp) REVERT: n 23 LEU cc_start: 0.8653 (mt) cc_final: 0.8174 (tp) REVERT: n 42 LEU cc_start: 0.8734 (tp) cc_final: 0.8519 (tt) REVERT: n 51 LYS cc_start: 0.7908 (tttm) cc_final: 0.7700 (tptt) REVERT: n 57 VAL cc_start: 0.8829 (t) cc_final: 0.8582 (p) REVERT: n 64 ARG cc_start: 0.8042 (ttt180) cc_final: 0.7518 (mmt180) REVERT: p 86 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7770 (mm-30) outliers start: 119 outliers final: 11 residues processed: 1698 average time/residue: 0.4856 time to fit residues: 1381.3896 Evaluate side-chains 986 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 960 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 570 optimal weight: 4.9990 chunk 512 optimal weight: 0.2980 chunk 284 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 345 optimal weight: 2.9990 chunk 273 optimal weight: 0.7980 chunk 529 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 322 optimal weight: 0.2980 chunk 394 optimal weight: 0.7980 chunk 613 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS D 84 HIS D 114 ASN D 116 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN D 231 ASN D 348 HIS D 398 HIS F 361 GLN ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 HIS G 100 ASN G 155 GLN H 38 ASN ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 ASN J 46 ASN L 165 ASN L 170 GLN L 199 GLN L 295 GLN L 320 ASN L 332 HIS M 26 ASN M 103 GLN M 192 ASN M 213 HIS M 293 HIS M 304 GLN M 331 ASN N 63 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN N 171 ASN N 197 ASN O 114 HIS O 151 HIS V 36 HIS ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 34 GLN f 30 ASN m 74 ASN m 78 ASN n 50 HIS ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.311 52081 Z= 0.663 Angle : 1.832 51.160 71486 Z= 1.171 Chirality : 0.335 6.680 8766 Planarity : 0.007 0.175 9345 Dihedral : 5.997 165.901 8189 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 1.63 % Allowed : 7.64 % Favored : 90.73 % Rotamer: Outliers : 0.28 % Allowed : 4.05 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 1.34 % 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: -3.41 (0.09), residues: 5784 helix: -1.76 (0.08), residues: 2998 sheet: -0.45 (0.39), residues: 175 loop : -3.01 (0.11), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F 413 HIS 0.016 0.002 HIS I 65 PHE 0.033 0.002 PHE D 167 TYR 0.029 0.002 TYR g 83 ARG 0.007 0.001 ARG n 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1179 time to evaluate : 3.891 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 61 HIS cc_start: 0.8129 (m-70) cc_final: 0.7923 (m-70) REVERT: B 62 MET cc_start: 0.8070 (tpp) cc_final: 0.7720 (tmm) REVERT: B 83 SER cc_start: 0.9012 (p) cc_final: 0.8584 (t) REVERT: B 116 MET cc_start: 0.8331 (ttp) cc_final: 0.7025 (tmm) REVERT: B 121 ASN cc_start: 0.8069 (m-40) cc_final: 0.6970 (m110) REVERT: C 48 LEU cc_start: 0.8269 (tt) cc_final: 0.7935 (mp) REVERT: C 172 VAL cc_start: 0.7966 (m) cc_final: 0.7723 (m) REVERT: D 114 ASN cc_start: 0.7726 (m110) cc_final: 0.7427 (m-40) REVERT: D 115 GLU cc_start: 0.8120 (pm20) cc_final: 0.7544 (pm20) REVERT: D 135 GLN cc_start: 0.8679 (mt0) cc_final: 0.8361 (mt0) REVERT: D 161 ILE cc_start: 0.9019 (mt) cc_final: 0.8816 (mm) REVERT: D 164 MET cc_start: 0.8237 (mmm) cc_final: 0.7869 (mmm) REVERT: D 169 TRP cc_start: 0.8549 (m100) cc_final: 0.8173 (m100) REVERT: D 276 ASP cc_start: 0.7953 (m-30) cc_final: 0.7110 (m-30) REVERT: G 45 ARG cc_start: 0.6543 (mtt90) cc_final: 0.4836 (ptt180) REVERT: G 100 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.6509 (t0) REVERT: G 160 ILE cc_start: 0.9320 (mm) cc_final: 0.9090 (mm) REVERT: H 31 MET cc_start: 0.8994 (mmm) cc_final: 0.8735 (mmm) REVERT: H 141 SER cc_start: 0.9149 (m) cc_final: 0.8944 (p) REVERT: H 176 LEU cc_start: 0.8707 (mt) cc_final: 0.8256 (tp) REVERT: H 183 MET cc_start: 0.7649 (tmm) cc_final: 0.7344 (tmm) REVERT: H 228 TYR cc_start: 0.7681 (m-10) cc_final: 0.7457 (m-80) REVERT: H 233 MET cc_start: 0.8106 (mmp) cc_final: 0.7776 (mmt) REVERT: H 248 ASN cc_start: 0.8594 (t0) cc_final: 0.8291 (t0) REVERT: H 268 MET cc_start: 0.8579 (mmp) cc_final: 0.8141 (ttp) REVERT: I 54 LYS cc_start: 0.8223 (mmtp) cc_final: 0.7516 (tttt) REVERT: I 60 ARG cc_start: 0.7606 (tpp-160) cc_final: 0.7403 (mmm160) REVERT: I 90 GLN cc_start: 0.8266 (mt0) cc_final: 0.7684 (mm-40) REVERT: I 110 ASP cc_start: 0.7074 (m-30) cc_final: 0.5868 (m-30) REVERT: I 129 ASP cc_start: 0.7148 (t70) cc_final: 0.6922 (t0) REVERT: J 52 LEU cc_start: 0.9205 (tt) cc_final: 0.8956 (mp) REVERT: J 161 LEU cc_start: 0.9576 (mt) cc_final: 0.9364 (mm) REVERT: K 62 ILE cc_start: 0.9368 (mt) cc_final: 0.9081 (tt) REVERT: K 66 PHE cc_start: 0.8449 (m-10) cc_final: 0.8218 (m-10) REVERT: K 80 MET cc_start: 0.9298 (mmm) cc_final: 0.8912 (mmt) REVERT: K 83 ASN cc_start: 0.9066 (m110) cc_final: 0.8741 (m-40) REVERT: L 14 LEU cc_start: 0.9105 (mt) cc_final: 0.8772 (tp) REVERT: L 20 MET cc_start: 0.8783 (mmp) cc_final: 0.7259 (tmm) REVERT: L 21 MET cc_start: 0.6650 (ttt) cc_final: 0.6113 (tpp) REVERT: L 45 ILE cc_start: 0.8581 (mt) cc_final: 0.8245 (tp) REVERT: L 48 MET cc_start: 0.8264 (mmm) cc_final: 0.8014 (tpp) REVERT: L 138 PHE cc_start: 0.8294 (t80) cc_final: 0.8030 (t80) REVERT: L 157 TRP cc_start: 0.9081 (t-100) cc_final: 0.8519 (t-100) REVERT: L 179 ASP cc_start: 0.7744 (m-30) cc_final: 0.7514 (m-30) REVERT: L 186 MET cc_start: 0.8093 (mmm) cc_final: 0.7535 (mmt) REVERT: L 195 THR cc_start: 0.7154 (p) cc_final: 0.6807 (t) REVERT: L 285 THR cc_start: 0.8568 (p) cc_final: 0.8359 (p) REVERT: L 291 CYS cc_start: 0.8066 (m) cc_final: 0.7641 (m) REVERT: L 373 LEU cc_start: 0.8946 (mt) cc_final: 0.8739 (mt) REVERT: L 411 MET cc_start: 0.8768 (ttm) cc_final: 0.8405 (mmt) REVERT: L 458 LEU cc_start: 0.7647 (mt) cc_final: 0.7415 (tp) REVERT: L 524 THR cc_start: 0.8679 (p) cc_final: 0.8326 (t) REVERT: L 532 ILE cc_start: 0.8118 (pt) cc_final: 0.7855 (tt) REVERT: L 535 ARG cc_start: 0.5399 (tpt170) cc_final: 0.3886 (ttt-90) REVERT: L 571 MET cc_start: 0.7817 (tpt) cc_final: 0.6781 (ttm) REVERT: L 576 LEU cc_start: 0.8285 (mt) cc_final: 0.7857 (mm) REVERT: L 581 LYS cc_start: 0.8215 (tttt) cc_final: 0.7216 (mmtt) REVERT: L 599 MET cc_start: 0.8551 (mmm) cc_final: 0.6933 (tpt) REVERT: M 56 PHE cc_start: 0.6111 (t80) cc_final: 0.5832 (t80) REVERT: M 72 LEU cc_start: 0.9261 (mt) cc_final: 0.9059 (mt) REVERT: M 147 LEU cc_start: 0.8569 (mt) cc_final: 0.8315 (tp) REVERT: M 200 MET cc_start: 0.8784 (mmp) cc_final: 0.8408 (mmp) REVERT: M 204 MET cc_start: 0.8060 (mmm) cc_final: 0.7457 (mmt) REVERT: M 205 VAL cc_start: 0.9290 (t) cc_final: 0.8775 (m) REVERT: M 206 LYS cc_start: 0.8014 (mttm) cc_final: 0.7754 (mmtt) REVERT: M 207 MET cc_start: 0.8906 (mmm) cc_final: 0.8703 (mmt) REVERT: M 249 ILE cc_start: 0.7694 (mm) cc_final: 0.7096 (mm) REVERT: M 269 MET cc_start: 0.8055 (mmm) cc_final: 0.7607 (mmm) REVERT: M 271 MET cc_start: 0.7073 (mmm) cc_final: 0.6853 (mmm) REVERT: M 276 CYS cc_start: 0.8681 (t) cc_final: 0.7733 (t) REVERT: M 279 GLN cc_start: 0.6550 (mt0) cc_final: 0.6105 (mt0) REVERT: M 281 ASP cc_start: 0.8108 (m-30) cc_final: 0.7900 (m-30) REVERT: M 316 MET cc_start: 0.8136 (mmm) cc_final: 0.7879 (mmm) REVERT: M 317 ILE cc_start: 0.9477 (mt) cc_final: 0.9206 (tt) REVERT: M 325 MET cc_start: 0.7546 (tpp) cc_final: 0.6924 (tpp) REVERT: M 338 HIS cc_start: 0.8357 (m-70) cc_final: 0.7985 (m170) REVERT: M 383 MET cc_start: 0.9054 (mmp) cc_final: 0.8609 (mmp) REVERT: M 439 LEU cc_start: 0.9141 (mt) cc_final: 0.8838 (tp) REVERT: M 446 LEU cc_start: 0.8705 (mt) cc_final: 0.8220 (tp) REVERT: N 38 LEU cc_start: 0.9297 (mt) cc_final: 0.8979 (mt) REVERT: N 58 LYS cc_start: 0.8963 (mtpp) cc_final: 0.8597 (ttmt) REVERT: N 79 MET cc_start: 0.8629 (mmm) cc_final: 0.8077 (mmm) REVERT: N 98 MET cc_start: 0.9204 (tpt) cc_final: 0.8853 (tpp) REVERT: N 112 HIS cc_start: 0.8369 (p-80) cc_final: 0.7782 (p-80) REVERT: N 117 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7931 (mt-10) REVERT: N 208 TYR cc_start: 0.8971 (t80) cc_final: 0.8219 (t80) REVERT: N 251 MET cc_start: 0.8091 (mmm) cc_final: 0.7357 (mmm) REVERT: N 294 MET cc_start: 0.8808 (mmp) cc_final: 0.8488 (tpp) REVERT: N 302 LEU cc_start: 0.8481 (mt) cc_final: 0.8217 (mt) REVERT: O 110 ASP cc_start: 0.7827 (m-30) cc_final: 0.7615 (t70) REVERT: O 147 GLN cc_start: 0.8295 (mp10) cc_final: 0.7909 (mp10) REVERT: O 162 GLU cc_start: 0.8248 (tm-30) cc_final: 0.8013 (tm-30) REVERT: V 54 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8240 (tptt) REVERT: W 36 ARG cc_start: 0.8550 (tpt170) cc_final: 0.8204 (ttm-80) REVERT: W 38 TRP cc_start: 0.7753 (t-100) cc_final: 0.7195 (t-100) REVERT: W 41 GLU cc_start: 0.8319 (tp30) cc_final: 0.8053 (tp30) REVERT: W 61 LYS cc_start: 0.6726 (ttmt) cc_final: 0.6398 (tptm) REVERT: W 77 VAL cc_start: 0.9542 (t) cc_final: 0.9005 (t) REVERT: X 31 TYR cc_start: 0.8045 (t80) cc_final: 0.7788 (t80) REVERT: X 50 LYS cc_start: 0.7145 (tttt) cc_final: 0.6552 (mmtp) REVERT: X 51 ASP cc_start: 0.8496 (m-30) cc_final: 0.8078 (t70) REVERT: X 58 GLU cc_start: 0.8522 (mp0) cc_final: 0.7797 (mp0) REVERT: X 60 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8701 (mtpt) REVERT: Y 39 SER cc_start: 0.8905 (t) cc_final: 0.8484 (t) REVERT: Y 91 ILE cc_start: 0.8704 (mt) cc_final: 0.8488 (tp) REVERT: Z 55 GLU cc_start: 0.8214 (tp30) cc_final: 0.7892 (tp30) REVERT: Z 77 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8194 (mt-10) REVERT: Z 91 GLU cc_start: 0.9059 (tp30) cc_final: 0.8643 (tp30) REVERT: a 28 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7017 (ptm160) REVERT: d 33 PHE cc_start: 0.8765 (t80) cc_final: 0.8455 (t80) REVERT: d 49 ARG cc_start: 0.8244 (mtt90) cc_final: 0.7595 (tpt-90) REVERT: d 90 MET cc_start: 0.8561 (ptp) cc_final: 0.8338 (ptm) REVERT: g 67 SER cc_start: 0.7725 (p) cc_final: 0.7521 (p) REVERT: g 92 GLU cc_start: 0.8692 (tp30) cc_final: 0.8263 (mm-30) REVERT: i 9 LEU cc_start: 0.8761 (pp) cc_final: 0.8532 (tt) REVERT: i 19 ARG cc_start: 0.8393 (tpt90) cc_final: 0.7234 (tpm170) REVERT: i 20 ARG cc_start: 0.8908 (mtm110) cc_final: 0.7710 (ppt170) REVERT: m 48 LEU cc_start: 0.9525 (mt) cc_final: 0.8940 (tt) REVERT: m 84 LYS cc_start: 0.7362 (mptt) cc_final: 0.6075 (pttp) REVERT: n 16 LEU cc_start: 0.9130 (mt) cc_final: 0.8620 (pp) REVERT: n 20 LYS cc_start: 0.8851 (ttpt) cc_final: 0.8498 (ttpt) REVERT: n 23 LEU cc_start: 0.8701 (mt) cc_final: 0.8085 (tp) REVERT: n 51 LYS cc_start: 0.8107 (tttm) cc_final: 0.7866 (tptt) REVERT: n 64 ARG cc_start: 0.8131 (ttt180) cc_final: 0.7759 (mmt-90) REVERT: n 69 GLU cc_start: 0.8118 (pt0) cc_final: 0.7897 (tm-30) REVERT: p 86 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7792 (mm-30) outliers start: 10 outliers final: 2 residues processed: 1187 average time/residue: 0.4809 time to fit residues: 975.6137 Evaluate side-chains 856 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 853 time to evaluate : 3.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 341 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 510 optimal weight: 5.9990 chunk 418 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 614 optimal weight: 10.0000 chunk 664 optimal weight: 10.0000 chunk 547 optimal weight: 20.0000 chunk 609 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 493 optimal weight: 9.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN B 127 HIS C 69 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN H 169 GLN H 287 HIS H 304 HIS ** I 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN L 135 ASN L 274 GLN L 296 ASN M 81 GLN ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN M 374 ASN N 36 ASN N 49 ASN N 112 HIS N 144 GLN O 92 ASN V 20 HIS V 49 GLN ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 103 GLN Z 53 ASN a 44 GLN ** d 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 106 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.271 52081 Z= 0.774 Angle : 1.980 51.605 71486 Z= 1.231 Chirality : 0.334 6.726 8766 Planarity : 0.007 0.163 9345 Dihedral : 7.052 160.378 8189 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 1.45 % Allowed : 10.27 % Favored : 88.28 % Rotamer: Outliers : 0.70 % Allowed : 6.42 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.10), residues: 5784 helix: -1.10 (0.08), residues: 3056 sheet: -0.60 (0.40), residues: 163 loop : -2.93 (0.11), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP M 71 HIS 0.023 0.003 HIS I 65 PHE 0.047 0.004 PHE M 57 TYR 0.063 0.003 TYR G 42 ARG 0.014 0.001 ARG D 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 939 time to evaluate : 3.885 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: A 77 TRP cc_start: 0.8977 (t60) cc_final: 0.8452 (t-100) REVERT: B 83 SER cc_start: 0.9069 (p) cc_final: 0.8051 (p) REVERT: B 96 MET cc_start: 0.8172 (mmm) cc_final: 0.7845 (mmm) REVERT: B 107 MET cc_start: 0.8925 (mmm) cc_final: 0.8494 (mmm) REVERT: B 116 MET cc_start: 0.8189 (ttp) cc_final: 0.7455 (tmm) REVERT: B 121 ASN cc_start: 0.8436 (m-40) cc_final: 0.7851 (m-40) REVERT: C 58 ILE cc_start: 0.9725 (mm) cc_final: 0.9492 (mm) REVERT: C 124 TYR cc_start: 0.6456 (t80) cc_final: 0.5814 (t80) REVERT: C 131 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7352 (mt-10) REVERT: D 72 MET cc_start: 0.7415 (ppp) cc_final: 0.6854 (ppp) REVERT: D 82 LEU cc_start: 0.8943 (mt) cc_final: 0.8730 (mt) REVERT: D 104 ASP cc_start: 0.7528 (t0) cc_final: 0.7062 (t0) REVERT: D 115 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7486 (pt0) REVERT: D 169 TRP cc_start: 0.8834 (m100) cc_final: 0.7795 (m100) REVERT: D 189 MET cc_start: 0.7821 (ttm) cc_final: 0.7491 (ttm) REVERT: D 259 MET cc_start: 0.8238 (mmt) cc_final: 0.7812 (mmt) REVERT: D 302 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6907 (mm-30) REVERT: D 338 MET cc_start: 0.9177 (ppp) cc_final: 0.8757 (tmm) REVERT: F 367 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7519 (tp30) REVERT: F 388 GLU cc_start: 0.8551 (tp30) cc_final: 0.8285 (tp30) REVERT: G 113 GLU cc_start: 0.7357 (tt0) cc_final: 0.7008 (mt-10) REVERT: H 248 ASN cc_start: 0.8702 (t0) cc_final: 0.8181 (t0) REVERT: H 268 MET cc_start: 0.8913 (mmp) cc_final: 0.8398 (ttp) REVERT: H 302 MET cc_start: 0.9281 (mmm) cc_final: 0.9066 (mmm) REVERT: I 90 GLN cc_start: 0.8402 (mt0) cc_final: 0.7652 (mm-40) REVERT: I 117 ILE cc_start: 0.9426 (pt) cc_final: 0.8856 (mt) REVERT: I 138 GLU cc_start: 0.6996 (tt0) cc_final: 0.5906 (tm-30) REVERT: J 100 GLU cc_start: 0.9301 (tm-30) cc_final: 0.8950 (tm-30) REVERT: J 141 MET cc_start: 0.7290 (ttm) cc_final: 0.5812 (ttm) REVERT: J 170 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8424 (tm-30) REVERT: K 6 MET cc_start: 0.7814 (mmt) cc_final: 0.7570 (mmt) REVERT: K 7 ASN cc_start: 0.9176 (p0) cc_final: 0.8916 (p0) REVERT: K 55 LEU cc_start: 0.8727 (tp) cc_final: 0.8199 (mp) REVERT: K 59 MET cc_start: 0.8037 (mtt) cc_final: 0.6930 (mtp) REVERT: L 14 LEU cc_start: 0.9357 (mt) cc_final: 0.9002 (tp) REVERT: L 16 THR cc_start: 0.9337 (p) cc_final: 0.9012 (t) REVERT: L 17 MET cc_start: 0.8339 (ttp) cc_final: 0.7859 (tmm) REVERT: L 20 MET cc_start: 0.8886 (mmp) cc_final: 0.8652 (mmp) REVERT: L 21 MET cc_start: 0.7458 (mtp) cc_final: 0.7210 (mmp) REVERT: L 60 GLU cc_start: 0.7250 (tt0) cc_final: 0.6681 (pt0) REVERT: L 88 MET cc_start: 0.8491 (tpp) cc_final: 0.8071 (mpp) REVERT: L 186 MET cc_start: 0.8554 (mmm) cc_final: 0.8079 (mmt) REVERT: L 291 CYS cc_start: 0.8997 (m) cc_final: 0.8718 (m) REVERT: L 352 ASP cc_start: 0.8483 (t70) cc_final: 0.7862 (t0) REVERT: L 353 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6863 (mm-30) REVERT: L 411 MET cc_start: 0.9042 (ttm) cc_final: 0.8663 (ttm) REVERT: L 571 MET cc_start: 0.7890 (tpt) cc_final: 0.6537 (ttm) REVERT: L 599 MET cc_start: 0.8672 (mmm) cc_final: 0.7612 (tpt) REVERT: M 61 LEU cc_start: 0.8433 (mm) cc_final: 0.8200 (mt) REVERT: M 76 MET cc_start: 0.8149 (mtm) cc_final: 0.7775 (mtm) REVERT: M 106 LEU cc_start: 0.9390 (mm) cc_final: 0.9187 (mm) REVERT: M 162 VAL cc_start: 0.9362 (m) cc_final: 0.9053 (t) REVERT: M 178 MET cc_start: 0.8855 (mmm) cc_final: 0.8597 (mmm) REVERT: M 200 MET cc_start: 0.8896 (mmp) cc_final: 0.8682 (mmp) REVERT: M 204 MET cc_start: 0.8306 (mmm) cc_final: 0.7872 (mmm) REVERT: M 263 MET cc_start: 0.8838 (mtp) cc_final: 0.8482 (mmm) REVERT: M 276 CYS cc_start: 0.8684 (t) cc_final: 0.8363 (t) REVERT: M 279 GLN cc_start: 0.7061 (mt0) cc_final: 0.6838 (mt0) REVERT: M 317 ILE cc_start: 0.9492 (mt) cc_final: 0.9184 (tt) REVERT: M 325 MET cc_start: 0.7978 (tpp) cc_final: 0.7645 (tpp) REVERT: M 338 HIS cc_start: 0.8500 (m-70) cc_final: 0.8252 (m170) REVERT: M 383 MET cc_start: 0.9122 (mmp) cc_final: 0.8621 (mmp) REVERT: M 437 MET cc_start: 0.9206 (mmt) cc_final: 0.8984 (mmt) REVERT: N 35 MET cc_start: 0.8478 (mmm) cc_final: 0.8132 (mmt) REVERT: N 36 ASN cc_start: 0.9231 (OUTLIER) cc_final: 0.8764 (m-40) REVERT: N 38 LEU cc_start: 0.9293 (mt) cc_final: 0.9021 (mt) REVERT: N 98 MET cc_start: 0.9392 (tpt) cc_final: 0.9078 (tpp) REVERT: N 218 MET cc_start: 0.8499 (tpp) cc_final: 0.7984 (tpp) REVERT: O 101 TYR cc_start: 0.9414 (t80) cc_final: 0.9118 (t80) REVERT: O 147 GLN cc_start: 0.8532 (mp10) cc_final: 0.8138 (mp10) REVERT: W 36 ARG cc_start: 0.8532 (tpt170) cc_final: 0.8032 (ttm-80) REVERT: W 57 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8532 (tm-30) REVERT: X 50 LYS cc_start: 0.7075 (tttt) cc_final: 0.6298 (mptt) REVERT: X 51 ASP cc_start: 0.8510 (m-30) cc_final: 0.8097 (t70) REVERT: X 108 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8573 (mm-30) REVERT: Y 48 PHE cc_start: 0.6617 (m-10) cc_final: 0.6105 (m-80) REVERT: Y 91 ILE cc_start: 0.8912 (mt) cc_final: 0.8709 (tp) REVERT: Z 49 MET cc_start: 0.8690 (tpt) cc_final: 0.8455 (tpt) REVERT: Z 55 GLU cc_start: 0.8643 (tp30) cc_final: 0.8175 (tp30) REVERT: Z 77 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8449 (mt-10) REVERT: Z 91 GLU cc_start: 0.9196 (tp30) cc_final: 0.8868 (tp30) REVERT: Z 93 GLU cc_start: 0.8693 (tp30) cc_final: 0.8417 (tp30) REVERT: a 12 MET cc_start: 0.8337 (mmt) cc_final: 0.7924 (mmp) REVERT: d 33 PHE cc_start: 0.9044 (t80) cc_final: 0.8649 (t80) REVERT: d 49 ARG cc_start: 0.8529 (mtt90) cc_final: 0.7910 (tpt170) REVERT: d 64 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7573 (m-10) REVERT: d 87 ASP cc_start: 0.8120 (t0) cc_final: 0.7208 (t0) REVERT: e 83 GLU cc_start: 0.8050 (pt0) cc_final: 0.7711 (pt0) REVERT: f 34 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7970 (pp) REVERT: g 58 MET cc_start: 0.6531 (tpp) cc_final: 0.5175 (mmm) REVERT: i 9 LEU cc_start: 0.8686 (pp) cc_final: 0.8333 (tt) REVERT: i 16 GLU cc_start: 0.9147 (pm20) cc_final: 0.8779 (pm20) REVERT: i 20 ARG cc_start: 0.9172 (mtm110) cc_final: 0.7926 (ppt170) REVERT: m 48 LEU cc_start: 0.9638 (mt) cc_final: 0.9114 (tt) REVERT: m 84 LYS cc_start: 0.7857 (mptt) cc_final: 0.6690 (pttp) REVERT: n 20 LYS cc_start: 0.9052 (ttpt) cc_final: 0.8694 (ttpt) REVERT: n 24 ARG cc_start: 0.8471 (tpp-160) cc_final: 0.8178 (tpp-160) REVERT: n 27 GLU cc_start: 0.8712 (tt0) cc_final: 0.8205 (tm-30) REVERT: n 64 ARG cc_start: 0.8116 (ttt180) cc_final: 0.7609 (mmt-90) REVERT: n 69 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: p 86 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8075 (mm-30) REVERT: p 128 LEU cc_start: 0.8999 (tp) cc_final: 0.8659 (tt) outliers start: 25 outliers final: 4 residues processed: 957 average time/residue: 0.4716 time to fit residues: 778.3187 Evaluate side-chains 753 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 744 time to evaluate : 3.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 607 optimal weight: 20.0000 chunk 462 optimal weight: 8.9990 chunk 319 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 293 optimal weight: 0.1980 chunk 412 optimal weight: 0.7980 chunk 617 optimal weight: 7.9990 chunk 653 optimal weight: 8.9990 chunk 322 optimal weight: 0.0670 chunk 584 optimal weight: 7.9990 chunk 176 optimal weight: 20.0000 overall best weight: 1.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 HIS G 117 GLN I 144 HIS I 168 ASN L 194 ASN ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 HIS M 81 GLN ** M 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 HIS N 36 ASN N 120 GLN ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN d 46 ASN m 47 GLN p 133 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.274 52081 Z= 0.633 Angle : 1.828 51.011 71486 Z= 1.168 Chirality : 0.332 6.456 8766 Planarity : 0.005 0.148 9345 Dihedral : 6.258 163.359 8189 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 1.28 % Allowed : 7.94 % Favored : 90.78 % Rotamer: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.04 % 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: -2.30 (0.10), residues: 5784 helix: -0.57 (0.09), residues: 3067 sheet: -0.49 (0.39), residues: 171 loop : -2.85 (0.11), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 264 HIS 0.010 0.001 HIS I 65 PHE 0.034 0.002 PHE L 522 TYR 0.038 0.002 TYR M 406 ARG 0.018 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 986 time to evaluate : 3.870 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: A 12 THR cc_start: 0.9104 (p) cc_final: 0.8873 (t) REVERT: A 77 TRP cc_start: 0.8594 (t60) cc_final: 0.8182 (t-100) REVERT: B 83 SER cc_start: 0.9014 (p) cc_final: 0.7558 (p) REVERT: B 84 ASP cc_start: 0.8226 (p0) cc_final: 0.7896 (p0) REVERT: B 96 MET cc_start: 0.8366 (mmm) cc_final: 0.7951 (mmm) REVERT: B 107 MET cc_start: 0.8953 (mmm) cc_final: 0.8413 (mmm) REVERT: B 116 MET cc_start: 0.8127 (ttp) cc_final: 0.7855 (ttp) REVERT: C 125 LYS cc_start: 0.8990 (mmmt) cc_final: 0.8694 (tppt) REVERT: D 72 MET cc_start: 0.7266 (ppp) cc_final: 0.6888 (ppp) REVERT: D 82 LEU cc_start: 0.9083 (mt) cc_final: 0.8681 (mt) REVERT: D 98 GLN cc_start: 0.9105 (tt0) cc_final: 0.8632 (mt0) REVERT: D 104 ASP cc_start: 0.6936 (t0) cc_final: 0.6255 (t0) REVERT: D 135 GLN cc_start: 0.8868 (mt0) cc_final: 0.8021 (mt0) REVERT: D 143 GLU cc_start: 0.7995 (tp30) cc_final: 0.7770 (tp30) REVERT: D 156 THR cc_start: 0.9540 (p) cc_final: 0.9265 (t) REVERT: D 169 TRP cc_start: 0.8974 (m-10) cc_final: 0.7824 (m100) REVERT: D 189 MET cc_start: 0.7865 (ttm) cc_final: 0.7425 (ttm) REVERT: D 239 THR cc_start: 0.8371 (p) cc_final: 0.7714 (t) REVERT: D 259 MET cc_start: 0.8265 (mmt) cc_final: 0.7841 (mmt) REVERT: D 267 TRP cc_start: 0.8683 (t60) cc_final: 0.8386 (t60) REVERT: D 338 MET cc_start: 0.9151 (ppp) cc_final: 0.8700 (tmm) REVERT: G 116 LEU cc_start: 0.9180 (tp) cc_final: 0.8905 (tp) REVERT: G 121 MET cc_start: 0.9003 (mmp) cc_final: 0.8792 (mmp) REVERT: H 10 ILE cc_start: 0.9400 (mm) cc_final: 0.9015 (mm) REVERT: H 31 MET cc_start: 0.9035 (mmm) cc_final: 0.8800 (mmm) REVERT: H 141 SER cc_start: 0.8746 (p) cc_final: 0.8489 (t) REVERT: H 156 MET cc_start: 0.8871 (ttm) cc_final: 0.8643 (ttm) REVERT: H 248 ASN cc_start: 0.8611 (t0) cc_final: 0.8157 (t0) REVERT: H 268 MET cc_start: 0.8907 (mmp) cc_final: 0.8377 (ttp) REVERT: I 34 LEU cc_start: 0.8446 (tt) cc_final: 0.7956 (mt) REVERT: I 48 ILE cc_start: 0.8771 (mp) cc_final: 0.8534 (mp) REVERT: I 90 GLN cc_start: 0.8343 (mt0) cc_final: 0.7768 (mm-40) REVERT: I 117 ILE cc_start: 0.9105 (pt) cc_final: 0.8599 (mt) REVERT: I 138 GLU cc_start: 0.7133 (tt0) cc_final: 0.5817 (tm-30) REVERT: I 150 ASN cc_start: 0.8408 (p0) cc_final: 0.8151 (p0) REVERT: J 74 MET cc_start: 0.8634 (mmp) cc_final: 0.7886 (tpt) REVERT: J 100 GLU cc_start: 0.9225 (tm-30) cc_final: 0.8461 (tm-30) REVERT: K 7 ASN cc_start: 0.9153 (p0) cc_final: 0.8770 (p0) REVERT: K 37 MET cc_start: 0.8390 (mmp) cc_final: 0.7688 (tpp) REVERT: K 59 MET cc_start: 0.8165 (mtt) cc_final: 0.7581 (mtp) REVERT: L 14 LEU cc_start: 0.9335 (mt) cc_final: 0.9008 (tp) REVERT: L 16 THR cc_start: 0.9320 (p) cc_final: 0.9083 (t) REVERT: L 17 MET cc_start: 0.8385 (ttp) cc_final: 0.7854 (tmm) REVERT: L 60 GLU cc_start: 0.6934 (tt0) cc_final: 0.6582 (pt0) REVERT: L 88 MET cc_start: 0.8538 (tpp) cc_final: 0.8163 (mpp) REVERT: L 291 CYS cc_start: 0.8867 (m) cc_final: 0.8596 (m) REVERT: L 352 ASP cc_start: 0.8247 (t70) cc_final: 0.7434 (t0) REVERT: L 524 THR cc_start: 0.8797 (p) cc_final: 0.8515 (t) REVERT: L 533 MET cc_start: 0.6611 (tpp) cc_final: 0.6306 (tpt) REVERT: L 571 MET cc_start: 0.7592 (tpt) cc_final: 0.6300 (ttm) REVERT: L 599 MET cc_start: 0.8634 (mmm) cc_final: 0.7740 (tpt) REVERT: M 106 LEU cc_start: 0.9087 (mm) cc_final: 0.8738 (mm) REVERT: M 162 VAL cc_start: 0.9176 (m) cc_final: 0.8891 (t) REVERT: M 178 MET cc_start: 0.8815 (mmm) cc_final: 0.8449 (mmm) REVERT: M 200 MET cc_start: 0.8891 (mmp) cc_final: 0.8190 (mmp) REVERT: M 204 MET cc_start: 0.8172 (mmm) cc_final: 0.7458 (mmt) REVERT: M 250 LEU cc_start: 0.9016 (mm) cc_final: 0.8738 (mm) REVERT: M 317 ILE cc_start: 0.9504 (mt) cc_final: 0.9140 (tt) REVERT: M 325 MET cc_start: 0.7844 (tpp) cc_final: 0.7559 (tpp) REVERT: M 338 HIS cc_start: 0.8512 (m-70) cc_final: 0.8209 (m170) REVERT: N 14 MET cc_start: 0.8318 (mmt) cc_final: 0.8009 (mmp) REVERT: N 35 MET cc_start: 0.8211 (mmm) cc_final: 0.7847 (tpt) REVERT: N 36 ASN cc_start: 0.9167 (m-40) cc_final: 0.8537 (m-40) REVERT: N 38 LEU cc_start: 0.9407 (mt) cc_final: 0.9099 (mt) REVERT: N 98 MET cc_start: 0.9285 (tpt) cc_final: 0.9070 (tpp) REVERT: N 179 MET cc_start: 0.8994 (mmm) cc_final: 0.8737 (mmm) REVERT: N 218 MET cc_start: 0.8466 (tpp) cc_final: 0.7962 (tpp) REVERT: N 269 GLU cc_start: 0.8586 (mt-10) cc_final: 0.7474 (tt0) REVERT: N 281 PHE cc_start: 0.8688 (t80) cc_final: 0.8414 (t80) REVERT: N 282 MET cc_start: 0.8586 (ttm) cc_final: 0.8299 (ttm) REVERT: O 101 TYR cc_start: 0.9290 (t80) cc_final: 0.8357 (t80) REVERT: W 36 ARG cc_start: 0.8438 (tpt170) cc_final: 0.8061 (ttm-80) REVERT: W 57 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8341 (tm-30) REVERT: W 61 LYS cc_start: 0.7375 (ttmt) cc_final: 0.6944 (tptm) REVERT: X 31 TYR cc_start: 0.8284 (t80) cc_final: 0.8067 (t80) REVERT: X 50 LYS cc_start: 0.7075 (tttt) cc_final: 0.6259 (mptt) REVERT: X 54 ARG cc_start: 0.9054 (mmt-90) cc_final: 0.8694 (mmp80) REVERT: X 108 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8576 (mm-30) REVERT: Y 48 PHE cc_start: 0.6571 (m-10) cc_final: 0.6007 (m-80) REVERT: Z 49 MET cc_start: 0.8483 (tpt) cc_final: 0.8109 (tpt) REVERT: Z 55 GLU cc_start: 0.8534 (tp30) cc_final: 0.8095 (tp30) REVERT: Z 77 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8113 (mt-10) REVERT: Z 91 GLU cc_start: 0.9069 (tp30) cc_final: 0.8651 (tp30) REVERT: Z 97 MET cc_start: 0.7651 (mmp) cc_final: 0.7123 (mmp) REVERT: a 12 MET cc_start: 0.8251 (mmt) cc_final: 0.7932 (mmp) REVERT: a 28 ARG cc_start: 0.8633 (mtt180) cc_final: 0.7400 (ttt180) REVERT: d 33 PHE cc_start: 0.8953 (t80) cc_final: 0.8455 (t80) REVERT: d 49 ARG cc_start: 0.8469 (mtt90) cc_final: 0.8008 (tpt170) REVERT: d 87 ASP cc_start: 0.7925 (t0) cc_final: 0.7082 (t0) REVERT: e 67 LEU cc_start: 0.8991 (mt) cc_final: 0.8639 (mp) REVERT: e 83 GLU cc_start: 0.7975 (pt0) cc_final: 0.7570 (pt0) REVERT: f 22 PHE cc_start: 0.8861 (t80) cc_final: 0.8082 (t80) REVERT: g 58 MET cc_start: 0.6063 (tpp) cc_final: 0.5254 (tpp) REVERT: g 101 GLU cc_start: 0.8417 (pt0) cc_final: 0.8206 (pt0) REVERT: h 38 ILE cc_start: 0.8351 (mm) cc_final: 0.7660 (tt) REVERT: i 16 GLU cc_start: 0.8970 (pm20) cc_final: 0.8604 (pm20) REVERT: i 20 ARG cc_start: 0.9022 (mtm110) cc_final: 0.7792 (ppt170) REVERT: m 48 LEU cc_start: 0.9592 (mt) cc_final: 0.9064 (tt) REVERT: m 84 LYS cc_start: 0.7569 (mptt) cc_final: 0.6537 (pttp) REVERT: n 20 LYS cc_start: 0.8960 (ttpt) cc_final: 0.8680 (tppt) REVERT: n 24 ARG cc_start: 0.8378 (tpp-160) cc_final: 0.8132 (tpp-160) REVERT: n 27 GLU cc_start: 0.8592 (tt0) cc_final: 0.8106 (tm-30) REVERT: n 64 ARG cc_start: 0.7894 (ttt180) cc_final: 0.7406 (mmt-90) outliers start: 2 outliers final: 0 residues processed: 988 average time/residue: 0.4615 time to fit residues: 784.0618 Evaluate side-chains 770 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 770 time to evaluate : 3.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 544 optimal weight: 3.9990 chunk 370 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 486 optimal weight: 9.9990 chunk 269 optimal weight: 0.0870 chunk 557 optimal weight: 8.9990 chunk 451 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 333 optimal weight: 30.0000 chunk 586 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 GLN F 421 HIS ** G 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 HIS ** I 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN ** M 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 HIS ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN N 120 GLN N 197 ASN N 232 HIS ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 12 GLN p 133 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.275 52081 Z= 0.656 Angle : 1.843 51.078 71486 Z= 1.175 Chirality : 0.332 6.531 8766 Planarity : 0.006 0.146 9345 Dihedral : 6.189 161.155 8189 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 1.24 % Allowed : 9.58 % Favored : 89.18 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.11), residues: 5784 helix: -0.39 (0.09), residues: 3073 sheet: -0.71 (0.39), residues: 165 loop : -2.78 (0.12), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP N 264 HIS 0.012 0.002 HIS I 65 PHE 0.038 0.002 PHE L 85 TYR 0.051 0.002 TYR D 108 ARG 0.022 0.001 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 912 time to evaluate : 3.890 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: A 12 THR cc_start: 0.9102 (p) cc_final: 0.8899 (t) REVERT: B 72 PHE cc_start: 0.6883 (m-80) cc_final: 0.6597 (m-80) REVERT: B 83 SER cc_start: 0.9082 (p) cc_final: 0.7714 (p) REVERT: B 84 ASP cc_start: 0.8294 (p0) cc_final: 0.7967 (p0) REVERT: B 96 MET cc_start: 0.8315 (mmm) cc_final: 0.7888 (mmm) REVERT: B 107 MET cc_start: 0.8913 (mmm) cc_final: 0.8411 (mmm) REVERT: B 116 MET cc_start: 0.8030 (ttp) cc_final: 0.7513 (tmm) REVERT: B 121 ASN cc_start: 0.8593 (m-40) cc_final: 0.8143 (m-40) REVERT: B 125 TYR cc_start: 0.7078 (m-80) cc_final: 0.6837 (m-80) REVERT: C 125 LYS cc_start: 0.9083 (mmmt) cc_final: 0.8744 (tppt) REVERT: C 131 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7292 (mt-10) REVERT: D 72 MET cc_start: 0.7401 (ppp) cc_final: 0.7019 (ppp) REVERT: D 82 LEU cc_start: 0.8924 (mt) cc_final: 0.8530 (mt) REVERT: D 98 GLN cc_start: 0.9281 (tt0) cc_final: 0.8638 (mt0) REVERT: D 135 GLN cc_start: 0.8906 (mt0) cc_final: 0.8262 (mt0) REVERT: D 167 PHE cc_start: 0.8683 (t80) cc_final: 0.8391 (t80) REVERT: D 239 THR cc_start: 0.8340 (p) cc_final: 0.7689 (t) REVERT: D 267 TRP cc_start: 0.8847 (t60) cc_final: 0.8505 (t60) REVERT: D 338 MET cc_start: 0.9117 (ppp) cc_final: 0.8674 (tmm) REVERT: F 389 ILE cc_start: 0.9018 (pt) cc_final: 0.8767 (tp) REVERT: G 116 LEU cc_start: 0.9218 (tp) cc_final: 0.8887 (tp) REVERT: G 117 GLN cc_start: 0.8862 (mt0) cc_final: 0.8558 (mp10) REVERT: H 10 ILE cc_start: 0.9345 (mm) cc_final: 0.8955 (mm) REVERT: H 31 MET cc_start: 0.9075 (mmm) cc_final: 0.8818 (mmm) REVERT: H 105 MET cc_start: 0.8497 (mmp) cc_final: 0.8183 (mmp) REVERT: H 141 SER cc_start: 0.8802 (p) cc_final: 0.8588 (t) REVERT: H 183 MET cc_start: 0.8156 (tmm) cc_final: 0.7458 (tmm) REVERT: H 184 MET cc_start: 0.9311 (mmm) cc_final: 0.8365 (mmm) REVERT: H 248 ASN cc_start: 0.8681 (t0) cc_final: 0.8189 (t0) REVERT: H 268 MET cc_start: 0.8936 (mmp) cc_final: 0.8355 (ttp) REVERT: H 284 GLN cc_start: 0.8477 (pt0) cc_final: 0.8248 (pp30) REVERT: I 34 LEU cc_start: 0.8629 (tt) cc_final: 0.8013 (mt) REVERT: I 90 GLN cc_start: 0.8326 (mt0) cc_final: 0.7767 (mm-40) REVERT: I 117 ILE cc_start: 0.9231 (pt) cc_final: 0.8464 (mt) REVERT: J 51 PHE cc_start: 0.8951 (t80) cc_final: 0.8605 (t80) REVERT: J 74 MET cc_start: 0.8764 (mmp) cc_final: 0.8149 (tpt) REVERT: J 100 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8800 (tm-30) REVERT: J 160 SER cc_start: 0.9003 (m) cc_final: 0.8189 (m) REVERT: K 7 ASN cc_start: 0.9219 (p0) cc_final: 0.8632 (p0) REVERT: K 55 LEU cc_start: 0.7971 (mp) cc_final: 0.7707 (pt) REVERT: K 59 MET cc_start: 0.8499 (mtt) cc_final: 0.7682 (mtp) REVERT: L 14 LEU cc_start: 0.9325 (mt) cc_final: 0.8985 (tp) REVERT: L 17 MET cc_start: 0.8369 (ttp) cc_final: 0.7921 (tmm) REVERT: L 20 MET cc_start: 0.9132 (mmp) cc_final: 0.8839 (mmm) REVERT: L 60 GLU cc_start: 0.7008 (tt0) cc_final: 0.6702 (pt0) REVERT: L 279 CYS cc_start: 0.8049 (t) cc_final: 0.7784 (t) REVERT: L 291 CYS cc_start: 0.8786 (m) cc_final: 0.8497 (m) REVERT: L 352 ASP cc_start: 0.8466 (t70) cc_final: 0.7860 (t0) REVERT: L 366 MET cc_start: 0.8472 (tpp) cc_final: 0.8260 (tpp) REVERT: L 533 MET cc_start: 0.6698 (tpp) cc_final: 0.6418 (tpt) REVERT: L 571 MET cc_start: 0.7685 (tpt) cc_final: 0.6270 (ttm) REVERT: L 599 MET cc_start: 0.8582 (mmm) cc_final: 0.7647 (tpt) REVERT: M 76 MET cc_start: 0.7915 (mtm) cc_final: 0.7652 (mtt) REVERT: M 162 VAL cc_start: 0.9234 (m) cc_final: 0.8900 (t) REVERT: M 178 MET cc_start: 0.8864 (mmm) cc_final: 0.8462 (mmm) REVERT: M 200 MET cc_start: 0.8875 (mmp) cc_final: 0.8060 (mmp) REVERT: M 204 MET cc_start: 0.8177 (mmm) cc_final: 0.7643 (mmm) REVERT: M 207 MET cc_start: 0.8715 (mtt) cc_final: 0.7915 (mtt) REVERT: M 222 GLU cc_start: 0.9147 (tp30) cc_final: 0.8853 (tp30) REVERT: M 285 LEU cc_start: 0.9095 (mt) cc_final: 0.8877 (mt) REVERT: M 317 ILE cc_start: 0.9529 (mt) cc_final: 0.9130 (tt) REVERT: M 325 MET cc_start: 0.7918 (tpp) cc_final: 0.7681 (tpp) REVERT: M 338 HIS cc_start: 0.8482 (m-70) cc_final: 0.8214 (m170) REVERT: M 369 LEU cc_start: 0.8614 (mt) cc_final: 0.8368 (mt) REVERT: M 383 MET cc_start: 0.9118 (mmp) cc_final: 0.8588 (mmp) REVERT: M 437 MET cc_start: 0.9100 (mmt) cc_final: 0.8784 (mmt) REVERT: N 35 MET cc_start: 0.8337 (mmm) cc_final: 0.7891 (tpt) REVERT: N 36 ASN cc_start: 0.9221 (m-40) cc_final: 0.8897 (m-40) REVERT: N 54 GLU cc_start: 0.8053 (tt0) cc_final: 0.7701 (tt0) REVERT: N 98 MET cc_start: 0.9359 (tpt) cc_final: 0.9095 (tpp) REVERT: N 218 MET cc_start: 0.8524 (tpp) cc_final: 0.8017 (tpp) REVERT: N 281 PHE cc_start: 0.8927 (t80) cc_final: 0.8574 (t80) REVERT: O 107 GLN cc_start: 0.8875 (pt0) cc_final: 0.7705 (mm-40) REVERT: O 110 ASP cc_start: 0.8375 (t70) cc_final: 0.8134 (t70) REVERT: V 49 GLN cc_start: 0.7861 (pp30) cc_final: 0.7596 (pp30) REVERT: W 57 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8391 (tm-30) REVERT: W 61 LYS cc_start: 0.7498 (ttmt) cc_final: 0.7054 (tptm) REVERT: X 31 TYR cc_start: 0.8399 (t80) cc_final: 0.8054 (t80) REVERT: X 50 LYS cc_start: 0.6849 (tttt) cc_final: 0.5863 (mptt) REVERT: X 54 ARG cc_start: 0.9132 (mmt-90) cc_final: 0.8844 (mmp80) REVERT: X 108 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8531 (mm-30) REVERT: Y 48 PHE cc_start: 0.6994 (m-10) cc_final: 0.6554 (m-80) REVERT: Y 73 SER cc_start: 0.8070 (p) cc_final: 0.7659 (p) REVERT: Z 55 GLU cc_start: 0.8825 (tp30) cc_final: 0.8362 (tp30) REVERT: Z 77 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8281 (mt-10) REVERT: Z 85 MET cc_start: 0.8598 (mmp) cc_final: 0.8279 (mmm) REVERT: Z 91 GLU cc_start: 0.8920 (tp30) cc_final: 0.8521 (tp30) REVERT: a 12 MET cc_start: 0.8331 (mmt) cc_final: 0.7978 (mmp) REVERT: a 28 ARG cc_start: 0.8698 (mtt180) cc_final: 0.7588 (ttt180) REVERT: d 33 PHE cc_start: 0.8971 (t80) cc_final: 0.8555 (t80) REVERT: d 49 ARG cc_start: 0.8697 (mtt90) cc_final: 0.8013 (tpt170) REVERT: d 87 ASP cc_start: 0.7804 (t0) cc_final: 0.7121 (t0) REVERT: e 67 LEU cc_start: 0.8961 (mt) cc_final: 0.8659 (mp) REVERT: e 83 GLU cc_start: 0.7733 (pt0) cc_final: 0.7421 (pt0) REVERT: f 22 PHE cc_start: 0.8711 (t80) cc_final: 0.8450 (t80) REVERT: g 58 MET cc_start: 0.6261 (tpp) cc_final: 0.5410 (tpp) REVERT: g 99 TYR cc_start: 0.8620 (t80) cc_final: 0.8283 (t80) REVERT: h 38 ILE cc_start: 0.8422 (mm) cc_final: 0.7710 (tt) REVERT: i 16 GLU cc_start: 0.8958 (pm20) cc_final: 0.8684 (pm20) REVERT: i 20 ARG cc_start: 0.9132 (mtm110) cc_final: 0.7912 (ppt170) REVERT: m 48 LEU cc_start: 0.9606 (mt) cc_final: 0.9077 (tt) REVERT: m 84 LYS cc_start: 0.7704 (mptt) cc_final: 0.6657 (pttp) REVERT: n 20 LYS cc_start: 0.9038 (ttpt) cc_final: 0.8683 (ttpt) REVERT: n 24 ARG cc_start: 0.8391 (tpp-160) cc_final: 0.8127 (tpp-160) REVERT: n 27 GLU cc_start: 0.8664 (tt0) cc_final: 0.8220 (tm-30) REVERT: n 64 ARG cc_start: 0.7902 (ttt180) cc_final: 0.7478 (mmt-90) REVERT: p 107 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8575 (mm-30) outliers start: 0 outliers final: 0 residues processed: 912 average time/residue: 0.4669 time to fit residues: 735.1974 Evaluate side-chains 730 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 730 time to evaluate : 3.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 219 optimal weight: 5.9990 chunk 588 optimal weight: 10.0000 chunk 129 optimal weight: 0.0050 chunk 383 optimal weight: 4.9990 chunk 161 optimal weight: 0.0060 chunk 654 optimal weight: 0.8980 chunk 542 optimal weight: 0.9990 chunk 302 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 chunk 343 optimal weight: 3.9990 overall best weight: 0.4410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 HIS ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 HIS ** G 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN M 83 HIS M 213 HIS ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN N 232 HIS ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 34 GLN n 25 HIS p 133 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.267 52081 Z= 0.625 Angle : 1.810 50.916 71486 Z= 1.160 Chirality : 0.332 6.477 8766 Planarity : 0.005 0.137 9345 Dihedral : 5.751 162.436 8189 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 1.14 % Allowed : 7.92 % Favored : 90.94 % Rotamer: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -1.91 (0.11), residues: 5784 helix: -0.22 (0.09), residues: 3076 sheet: -0.78 (0.37), residues: 188 loop : -2.68 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP N 264 HIS 0.014 0.001 HIS M 319 PHE 0.027 0.002 PHE J 93 TYR 0.046 0.002 TYR D 108 ARG 0.008 0.000 ARG D 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 979 time to evaluate : 3.909 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: A 12 THR cc_start: 0.9059 (p) cc_final: 0.8818 (t) REVERT: A 77 TRP cc_start: 0.8569 (t60) cc_final: 0.8306 (t60) REVERT: B 83 SER cc_start: 0.9050 (p) cc_final: 0.7654 (p) REVERT: B 84 ASP cc_start: 0.8192 (p0) cc_final: 0.7911 (p0) REVERT: B 107 MET cc_start: 0.8859 (mmm) cc_final: 0.8385 (mmm) REVERT: B 121 ASN cc_start: 0.8355 (m-40) cc_final: 0.7904 (m-40) REVERT: C 48 LEU cc_start: 0.8072 (tt) cc_final: 0.7780 (mp) REVERT: D 98 GLN cc_start: 0.8947 (tt0) cc_final: 0.8423 (mt0) REVERT: D 104 ASP cc_start: 0.7071 (t0) cc_final: 0.6462 (t0) REVERT: D 115 GLU cc_start: 0.7876 (pm20) cc_final: 0.7102 (pt0) REVERT: D 135 GLN cc_start: 0.8879 (mt0) cc_final: 0.8261 (mt0) REVERT: D 156 THR cc_start: 0.9516 (p) cc_final: 0.9224 (t) REVERT: D 189 MET cc_start: 0.8080 (ttm) cc_final: 0.7736 (ttm) REVERT: D 239 THR cc_start: 0.8264 (p) cc_final: 0.7637 (t) REVERT: D 267 TRP cc_start: 0.8742 (t60) cc_final: 0.8525 (t60) REVERT: D 338 MET cc_start: 0.9021 (ppp) cc_final: 0.8746 (tmm) REVERT: F 388 GLU cc_start: 0.8313 (tp30) cc_final: 0.7804 (tp30) REVERT: F 389 ILE cc_start: 0.8957 (pt) cc_final: 0.8657 (tp) REVERT: H 10 ILE cc_start: 0.9257 (mm) cc_final: 0.8885 (mm) REVERT: H 24 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8125 (tm-30) REVERT: H 31 MET cc_start: 0.8970 (mmm) cc_final: 0.8724 (mmm) REVERT: H 105 MET cc_start: 0.8591 (mmp) cc_final: 0.8229 (mmp) REVERT: H 121 TRP cc_start: 0.8234 (m100) cc_final: 0.7950 (m100) REVERT: H 141 SER cc_start: 0.8716 (p) cc_final: 0.8496 (t) REVERT: H 183 MET cc_start: 0.8057 (tmm) cc_final: 0.7724 (tmm) REVERT: H 248 ASN cc_start: 0.8588 (t0) cc_final: 0.8112 (t0) REVERT: H 268 MET cc_start: 0.8850 (mmp) cc_final: 0.8326 (ttp) REVERT: H 284 GLN cc_start: 0.8613 (pt0) cc_final: 0.8116 (pp30) REVERT: I 34 LEU cc_start: 0.8546 (tt) cc_final: 0.7979 (mt) REVERT: I 90 GLN cc_start: 0.8176 (mt0) cc_final: 0.7630 (mm-40) REVERT: I 138 GLU cc_start: 0.6503 (tt0) cc_final: 0.5852 (tt0) REVERT: I 150 ASN cc_start: 0.8231 (p0) cc_final: 0.7981 (p0) REVERT: I 161 TRP cc_start: 0.7249 (m100) cc_final: 0.7022 (m100) REVERT: J 74 MET cc_start: 0.8569 (mmp) cc_final: 0.8057 (tpt) REVERT: J 100 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8727 (tm-30) REVERT: K 7 ASN cc_start: 0.9157 (p0) cc_final: 0.8505 (p0) REVERT: K 59 MET cc_start: 0.8325 (mtt) cc_final: 0.7555 (mtp) REVERT: L 14 LEU cc_start: 0.9288 (mt) cc_final: 0.8956 (tp) REVERT: L 17 MET cc_start: 0.8383 (ttp) cc_final: 0.7821 (tmm) REVERT: L 21 MET cc_start: 0.7656 (mmp) cc_final: 0.7365 (ttt) REVERT: L 136 ASN cc_start: 0.7788 (m110) cc_final: 0.7446 (m-40) REVERT: L 291 CYS cc_start: 0.8559 (m) cc_final: 0.8279 (m) REVERT: L 297 ASP cc_start: 0.8349 (m-30) cc_final: 0.7836 (m-30) REVERT: L 352 ASP cc_start: 0.8240 (t70) cc_final: 0.7656 (t0) REVERT: L 366 MET cc_start: 0.8346 (tpp) cc_final: 0.8073 (tpp) REVERT: L 571 MET cc_start: 0.7544 (tpt) cc_final: 0.6059 (ttm) REVERT: L 599 MET cc_start: 0.8584 (mmm) cc_final: 0.7707 (tpt) REVERT: M 61 LEU cc_start: 0.8177 (mm) cc_final: 0.7846 (mt) REVERT: M 76 MET cc_start: 0.7724 (mtm) cc_final: 0.7431 (mtt) REVERT: M 200 MET cc_start: 0.8975 (mmp) cc_final: 0.8549 (mmp) REVERT: M 204 MET cc_start: 0.8296 (mmm) cc_final: 0.8082 (mmt) REVERT: M 222 GLU cc_start: 0.8762 (tp30) cc_final: 0.8529 (tt0) REVERT: M 279 GLN cc_start: 0.7256 (mt0) cc_final: 0.6993 (mt0) REVERT: M 285 LEU cc_start: 0.9022 (mt) cc_final: 0.8765 (mt) REVERT: M 317 ILE cc_start: 0.9495 (mt) cc_final: 0.9083 (tt) REVERT: M 338 HIS cc_start: 0.8413 (m-70) cc_final: 0.8163 (m170) REVERT: M 383 MET cc_start: 0.9059 (mmp) cc_final: 0.8611 (mmp) REVERT: N 36 ASN cc_start: 0.9066 (m-40) cc_final: 0.8320 (m-40) REVERT: N 37 MET cc_start: 0.8343 (tpp) cc_final: 0.8002 (tpp) REVERT: N 43 ILE cc_start: 0.9550 (tt) cc_final: 0.9335 (tp) REVERT: N 71 MET cc_start: 0.9093 (mmm) cc_final: 0.8730 (tpp) REVERT: N 240 MET cc_start: 0.8498 (ttm) cc_final: 0.8169 (ttm) REVERT: O 107 GLN cc_start: 0.8884 (pt0) cc_final: 0.7698 (mm-40) REVERT: O 110 ASP cc_start: 0.8298 (t70) cc_final: 0.8064 (t0) REVERT: O 136 GLU cc_start: 0.9077 (tp30) cc_final: 0.8850 (tp30) REVERT: W 57 GLN cc_start: 0.8347 (tm-30) cc_final: 0.8018 (tm-30) REVERT: X 31 TYR cc_start: 0.8403 (t80) cc_final: 0.7965 (t80) REVERT: X 37 LYS cc_start: 0.9227 (mtpt) cc_final: 0.9001 (mtmm) REVERT: X 50 LYS cc_start: 0.6980 (tttt) cc_final: 0.5876 (mptt) REVERT: X 54 ARG cc_start: 0.9163 (mmt-90) cc_final: 0.8672 (mmp80) REVERT: X 95 LEU cc_start: 0.7313 (tt) cc_final: 0.7079 (mt) REVERT: X 108 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8478 (mm-30) REVERT: Y 48 PHE cc_start: 0.7028 (m-10) cc_final: 0.6613 (m-80) REVERT: Y 73 SER cc_start: 0.8172 (p) cc_final: 0.7263 (p) REVERT: Z 50 MET cc_start: 0.7250 (ptt) cc_final: 0.6945 (ptt) REVERT: Z 55 GLU cc_start: 0.8772 (tp30) cc_final: 0.8311 (tp30) REVERT: Z 65 GLU cc_start: 0.7880 (tp30) cc_final: 0.7647 (tp30) REVERT: Z 91 GLU cc_start: 0.8899 (tp30) cc_final: 0.8502 (tp30) REVERT: Z 97 MET cc_start: 0.7450 (mmp) cc_final: 0.6985 (mmp) REVERT: d 33 PHE cc_start: 0.8911 (t80) cc_final: 0.8511 (t80) REVERT: d 49 ARG cc_start: 0.8568 (mtt90) cc_final: 0.8001 (tpt170) REVERT: d 87 ASP cc_start: 0.7723 (t0) cc_final: 0.6935 (t0) REVERT: e 67 LEU cc_start: 0.8913 (mt) cc_final: 0.8648 (mp) REVERT: e 83 GLU cc_start: 0.7777 (pt0) cc_final: 0.7498 (pt0) REVERT: g 58 MET cc_start: 0.6041 (tpp) cc_final: 0.5356 (tpp) REVERT: g 99 TYR cc_start: 0.8514 (t80) cc_final: 0.8176 (t80) REVERT: h 38 ILE cc_start: 0.8384 (mm) cc_final: 0.7714 (tt) REVERT: i 16 GLU cc_start: 0.8946 (pm20) cc_final: 0.8559 (pm20) REVERT: i 20 ARG cc_start: 0.9027 (mtm110) cc_final: 0.7747 (ppt170) REVERT: m 48 LEU cc_start: 0.9584 (mt) cc_final: 0.9215 (tt) REVERT: m 84 LYS cc_start: 0.7694 (mptt) cc_final: 0.6585 (pttp) REVERT: n 20 LYS cc_start: 0.9027 (ttpt) cc_final: 0.8674 (ttpt) REVERT: n 24 ARG cc_start: 0.8407 (tpp-160) cc_final: 0.8181 (tpp-160) REVERT: n 27 GLU cc_start: 0.8652 (tt0) cc_final: 0.8333 (tm-30) REVERT: n 64 ARG cc_start: 0.7876 (ttt180) cc_final: 0.7357 (mmt-90) outliers start: 1 outliers final: 1 residues processed: 980 average time/residue: 0.4609 time to fit residues: 781.1635 Evaluate side-chains 768 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 767 time to evaluate : 3.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 630 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 372 optimal weight: 0.8980 chunk 477 optimal weight: 10.0000 chunk 370 optimal weight: 4.9990 chunk 550 optimal weight: 0.5980 chunk 365 optimal weight: 2.9990 chunk 651 optimal weight: 5.9990 chunk 407 optimal weight: 0.1980 chunk 397 optimal weight: 2.9990 chunk 300 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 114 ASN D 357 GLN F 421 HIS ** G 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN I 168 ASN L 248 HIS ** M 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 366 ASN N 232 HIS X 64 GLN Z 53 ASN p 106 GLN p 133 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.277 52081 Z= 0.625 Angle : 1.804 50.866 71486 Z= 1.158 Chirality : 0.332 6.472 8766 Planarity : 0.005 0.141 9345 Dihedral : 5.494 161.685 8189 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.28 % Favored : 90.72 % Rotamer: Outliers : 0.06 % Allowed : 1.68 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.11), residues: 5784 helix: -0.10 (0.09), residues: 3087 sheet: -0.82 (0.37), residues: 188 loop : -2.64 (0.12), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP L 407 HIS 0.019 0.001 HIS D 190 PHE 0.034 0.002 PHE d 91 TYR 0.040 0.001 TYR D 108 ARG 0.007 0.000 ARG D 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 964 time to evaluate : 3.861 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: A 12 THR cc_start: 0.9043 (p) cc_final: 0.8752 (t) REVERT: A 77 TRP cc_start: 0.8563 (t60) cc_final: 0.8309 (t60) REVERT: A 104 TYR cc_start: 0.8953 (t80) cc_final: 0.8642 (t80) REVERT: B 83 SER cc_start: 0.9049 (p) cc_final: 0.7585 (p) REVERT: B 84 ASP cc_start: 0.8179 (p0) cc_final: 0.7905 (p0) REVERT: B 107 MET cc_start: 0.8797 (mmm) cc_final: 0.8322 (mmm) REVERT: B 116 MET cc_start: 0.7848 (ttp) cc_final: 0.7642 (ttp) REVERT: B 121 ASN cc_start: 0.8322 (m-40) cc_final: 0.7928 (m-40) REVERT: C 162 PHE cc_start: 0.7714 (t80) cc_final: 0.7466 (t80) REVERT: D 82 LEU cc_start: 0.9040 (mt) cc_final: 0.8731 (mt) REVERT: D 104 ASP cc_start: 0.6893 (t0) cc_final: 0.6156 (t0) REVERT: D 135 GLN cc_start: 0.8882 (mt0) cc_final: 0.8239 (mt0) REVERT: D 143 GLU cc_start: 0.7920 (tp30) cc_final: 0.7719 (tp30) REVERT: D 169 TRP cc_start: 0.8983 (m-10) cc_final: 0.7574 (m100) REVERT: D 239 THR cc_start: 0.8347 (p) cc_final: 0.7677 (t) REVERT: D 338 MET cc_start: 0.8968 (ppp) cc_final: 0.8721 (tmm) REVERT: F 388 GLU cc_start: 0.8301 (tp30) cc_final: 0.7820 (tp30) REVERT: F 389 ILE cc_start: 0.8928 (pt) cc_final: 0.8653 (tp) REVERT: H 24 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8053 (tm-30) REVERT: H 31 MET cc_start: 0.9072 (mmm) cc_final: 0.8805 (mmm) REVERT: H 98 MET cc_start: 0.4525 (tpt) cc_final: 0.4230 (tpt) REVERT: H 105 MET cc_start: 0.8593 (mmp) cc_final: 0.8273 (mmp) REVERT: H 141 SER cc_start: 0.8696 (p) cc_final: 0.8484 (t) REVERT: H 248 ASN cc_start: 0.8567 (t0) cc_final: 0.8090 (t0) REVERT: H 268 MET cc_start: 0.8801 (mmp) cc_final: 0.8323 (ttp) REVERT: H 280 PHE cc_start: 0.7013 (m-80) cc_final: 0.6737 (m-80) REVERT: H 282 TYR cc_start: 0.8888 (t80) cc_final: 0.8434 (t80) REVERT: H 284 GLN cc_start: 0.8589 (pt0) cc_final: 0.7961 (pp30) REVERT: H 303 TRP cc_start: 0.8805 (t-100) cc_final: 0.8365 (t60) REVERT: I 18 THR cc_start: 0.8932 (t) cc_final: 0.8704 (t) REVERT: I 90 GLN cc_start: 0.8190 (mt0) cc_final: 0.7591 (mm-40) REVERT: I 138 GLU cc_start: 0.6532 (tt0) cc_final: 0.6259 (tt0) REVERT: I 150 ASN cc_start: 0.8200 (p0) cc_final: 0.7945 (p0) REVERT: J 74 MET cc_start: 0.8567 (mmp) cc_final: 0.7993 (tpt) REVERT: J 100 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8824 (tm-30) REVERT: J 160 SER cc_start: 0.8919 (m) cc_final: 0.8262 (m) REVERT: K 7 ASN cc_start: 0.9182 (p0) cc_final: 0.8734 (p0) REVERT: K 59 MET cc_start: 0.8040 (mtt) cc_final: 0.7450 (mtp) REVERT: L 14 LEU cc_start: 0.9310 (mt) cc_final: 0.8969 (tp) REVERT: L 17 MET cc_start: 0.8373 (ttp) cc_final: 0.7816 (tmm) REVERT: L 20 MET cc_start: 0.9006 (mmt) cc_final: 0.8748 (mmm) REVERT: L 21 MET cc_start: 0.7640 (mmp) cc_final: 0.7326 (ttt) REVERT: L 101 MET cc_start: 0.8574 (mmt) cc_final: 0.8374 (mmm) REVERT: L 179 ASP cc_start: 0.6995 (m-30) cc_final: 0.6714 (m-30) REVERT: L 291 CYS cc_start: 0.8428 (m) cc_final: 0.8157 (m) REVERT: L 297 ASP cc_start: 0.8215 (m-30) cc_final: 0.7555 (m-30) REVERT: L 300 LYS cc_start: 0.8139 (mttt) cc_final: 0.7930 (ttmt) REVERT: L 352 ASP cc_start: 0.8166 (t70) cc_final: 0.7671 (t0) REVERT: L 366 MET cc_start: 0.8443 (tpp) cc_final: 0.8003 (tpp) REVERT: L 389 PHE cc_start: 0.5829 (t80) cc_final: 0.5539 (t80) REVERT: L 524 THR cc_start: 0.9015 (p) cc_final: 0.8791 (p) REVERT: L 533 MET cc_start: 0.5992 (tpt) cc_final: 0.5620 (tpt) REVERT: L 571 MET cc_start: 0.7553 (tpt) cc_final: 0.6010 (ttm) REVERT: L 599 MET cc_start: 0.8542 (mmm) cc_final: 0.7696 (tpt) REVERT: M 61 LEU cc_start: 0.8093 (mm) cc_final: 0.7717 (mt) REVERT: M 76 MET cc_start: 0.7774 (mtm) cc_final: 0.7418 (mtt) REVERT: M 95 PHE cc_start: 0.5771 (m-80) cc_final: 0.5405 (m-10) REVERT: M 98 MET cc_start: 0.8607 (tpp) cc_final: 0.8343 (tpp) REVERT: M 204 MET cc_start: 0.8329 (mmm) cc_final: 0.8042 (mtm) REVERT: M 243 MET cc_start: 0.8423 (mmp) cc_final: 0.8173 (mmp) REVERT: M 279 GLN cc_start: 0.7234 (mt0) cc_final: 0.6956 (mt0) REVERT: M 285 LEU cc_start: 0.9023 (mt) cc_final: 0.8797 (mt) REVERT: M 317 ILE cc_start: 0.9366 (mt) cc_final: 0.9053 (tt) REVERT: M 338 HIS cc_start: 0.8349 (m-70) cc_final: 0.8101 (m170) REVERT: M 383 MET cc_start: 0.9094 (mmp) cc_final: 0.8640 (mmp) REVERT: M 415 GLN cc_start: 0.6265 (tt0) cc_final: 0.6050 (tm-30) REVERT: M 437 MET cc_start: 0.9035 (mmt) cc_final: 0.8809 (mmt) REVERT: N 35 MET cc_start: 0.8205 (mmm) cc_final: 0.7806 (tpt) REVERT: N 36 ASN cc_start: 0.9083 (m-40) cc_final: 0.8492 (p0) REVERT: N 43 ILE cc_start: 0.9536 (tt) cc_final: 0.9318 (tp) REVERT: N 54 GLU cc_start: 0.7974 (tt0) cc_final: 0.7417 (tt0) REVERT: N 58 LYS cc_start: 0.9394 (ttmt) cc_final: 0.9112 (ttpt) REVERT: N 74 VAL cc_start: 0.9445 (t) cc_final: 0.9199 (p) REVERT: N 139 MET cc_start: 0.8440 (mmm) cc_final: 0.8196 (mmm) REVERT: N 209 ILE cc_start: 0.9195 (mm) cc_final: 0.8961 (tp) REVERT: N 232 HIS cc_start: 0.7238 (t-90) cc_final: 0.6877 (t70) REVERT: N 260 PHE cc_start: 0.8709 (t80) cc_final: 0.8490 (t80) REVERT: O 107 GLN cc_start: 0.8860 (pt0) cc_final: 0.7633 (mm-40) REVERT: O 110 ASP cc_start: 0.8314 (t70) cc_final: 0.8084 (t0) REVERT: O 136 GLU cc_start: 0.9104 (tp30) cc_final: 0.8866 (tp30) REVERT: V 49 GLN cc_start: 0.7493 (pp30) cc_final: 0.7290 (pp30) REVERT: W 34 LEU cc_start: 0.9409 (tt) cc_final: 0.8957 (tt) REVERT: W 57 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7989 (tm-30) REVERT: X 31 TYR cc_start: 0.8329 (t80) cc_final: 0.7862 (t80) REVERT: X 37 LYS cc_start: 0.9187 (mtpt) cc_final: 0.8978 (mtmm) REVERT: X 50 LYS cc_start: 0.6896 (tttt) cc_final: 0.5786 (mptt) REVERT: X 54 ARG cc_start: 0.9074 (mmt-90) cc_final: 0.8737 (mmp80) REVERT: X 95 LEU cc_start: 0.7107 (tt) cc_final: 0.6832 (mt) REVERT: X 108 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8537 (mm-30) REVERT: Y 48 PHE cc_start: 0.7072 (m-10) cc_final: 0.6636 (m-80) REVERT: Y 73 SER cc_start: 0.8144 (p) cc_final: 0.7352 (p) REVERT: Z 55 GLU cc_start: 0.8696 (tp30) cc_final: 0.8215 (tp30) REVERT: Z 65 GLU cc_start: 0.7698 (tp30) cc_final: 0.7491 (tp30) REVERT: Z 91 GLU cc_start: 0.8904 (tp30) cc_final: 0.8499 (tp30) REVERT: d 33 PHE cc_start: 0.8998 (t80) cc_final: 0.8513 (t80) REVERT: d 49 ARG cc_start: 0.8386 (mtt90) cc_final: 0.7924 (tpt170) REVERT: d 87 ASP cc_start: 0.7564 (t0) cc_final: 0.6937 (t0) REVERT: e 83 GLU cc_start: 0.7879 (pt0) cc_final: 0.7602 (pt0) REVERT: g 58 MET cc_start: 0.6133 (tpp) cc_final: 0.5342 (tpp) REVERT: g 99 TYR cc_start: 0.8569 (t80) cc_final: 0.8226 (t80) REVERT: h 38 ILE cc_start: 0.8349 (mm) cc_final: 0.7699 (tt) REVERT: i 20 ARG cc_start: 0.9023 (mtm110) cc_final: 0.7717 (ppt170) REVERT: m 48 LEU cc_start: 0.9540 (mt) cc_final: 0.9166 (tt) REVERT: m 76 TYR cc_start: 0.7259 (m-10) cc_final: 0.7010 (m-80) REVERT: m 84 LYS cc_start: 0.7654 (mptt) cc_final: 0.6517 (pttp) REVERT: n 20 LYS cc_start: 0.9019 (ttpt) cc_final: 0.8681 (ttpt) REVERT: n 24 ARG cc_start: 0.8422 (tpp-160) cc_final: 0.8186 (tpp-160) REVERT: n 27 GLU cc_start: 0.8661 (tt0) cc_final: 0.8330 (tm-30) REVERT: n 64 ARG cc_start: 0.7951 (ttt180) cc_final: 0.7401 (mmt-90) outliers start: 2 outliers final: 0 residues processed: 965 average time/residue: 0.4615 time to fit residues: 771.4504 Evaluate side-chains 774 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 774 time to evaluate : 3.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 403 optimal weight: 0.0270 chunk 260 optimal weight: 5.9990 chunk 389 optimal weight: 0.7980 chunk 196 optimal weight: 20.0000 chunk 128 optimal weight: 0.0000 chunk 126 optimal weight: 0.7980 chunk 414 optimal weight: 0.9990 chunk 443 optimal weight: 30.0000 chunk 322 optimal weight: 0.9980 chunk 60 optimal weight: 0.1980 chunk 512 optimal weight: 6.9990 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN D 398 HIS F 421 HIS ** G 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN H 284 GLN I 168 ASN ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 ASN ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN N 204 ASN X 64 GLN Z 53 ASN ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.274 52081 Z= 0.629 Angle : 1.807 50.888 71486 Z= 1.159 Chirality : 0.332 6.467 8766 Planarity : 0.005 0.141 9345 Dihedral : 5.380 161.594 8189 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.95 % Allowed : 8.02 % Favored : 91.03 % Rotamer: Outliers : 0.03 % Allowed : 0.98 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -1.70 (0.11), residues: 5784 helix: -0.05 (0.09), residues: 3064 sheet: -0.82 (0.37), residues: 190 loop : -2.56 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP L 407 HIS 0.012 0.001 HIS M 319 PHE 0.026 0.001 PHE D 167 TYR 0.043 0.002 TYR D 275 ARG 0.008 0.000 ARG I 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 973 time to evaluate : 3.906 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: A 12 THR cc_start: 0.8995 (p) cc_final: 0.8714 (t) REVERT: A 77 TRP cc_start: 0.8440 (t60) cc_final: 0.8164 (t60) REVERT: B 83 SER cc_start: 0.9005 (p) cc_final: 0.7553 (p) REVERT: B 84 ASP cc_start: 0.8228 (p0) cc_final: 0.7911 (p0) REVERT: B 96 MET cc_start: 0.8265 (mmm) cc_final: 0.7885 (mmm) REVERT: B 107 MET cc_start: 0.8787 (mmm) cc_final: 0.8268 (mmm) REVERT: B 121 ASN cc_start: 0.8306 (m-40) cc_final: 0.7806 (m-40) REVERT: B 164 GLN cc_start: 0.8482 (mt0) cc_final: 0.7673 (mp10) REVERT: C 58 ILE cc_start: 0.9370 (mm) cc_final: 0.9076 (mm) REVERT: C 83 ILE cc_start: 0.9333 (tp) cc_final: 0.9109 (mm) REVERT: C 162 PHE cc_start: 0.7689 (t80) cc_final: 0.7436 (t80) REVERT: D 82 LEU cc_start: 0.9069 (mt) cc_final: 0.8490 (mt) REVERT: D 98 GLN cc_start: 0.8816 (tt0) cc_final: 0.8382 (mt0) REVERT: D 165 THR cc_start: 0.9310 (p) cc_final: 0.9110 (p) REVERT: D 169 TRP cc_start: 0.8856 (m-10) cc_final: 0.7447 (m100) REVERT: D 190 HIS cc_start: 0.6747 (m170) cc_final: 0.6080 (m170) REVERT: D 239 THR cc_start: 0.8274 (p) cc_final: 0.7656 (t) REVERT: D 338 MET cc_start: 0.8951 (ppp) cc_final: 0.8713 (tmm) REVERT: F 388 GLU cc_start: 0.8311 (tp30) cc_final: 0.7809 (tp30) REVERT: F 389 ILE cc_start: 0.8912 (pt) cc_final: 0.8661 (tp) REVERT: G 122 MET cc_start: 0.8687 (mmp) cc_final: 0.8166 (mmt) REVERT: H 24 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8035 (tm-30) REVERT: H 31 MET cc_start: 0.8925 (mmm) cc_final: 0.8651 (mmm) REVERT: H 98 MET cc_start: 0.4537 (tpt) cc_final: 0.4268 (tpt) REVERT: H 105 MET cc_start: 0.8596 (mmp) cc_final: 0.8287 (mmp) REVERT: H 138 GLN cc_start: 0.7764 (mt0) cc_final: 0.7382 (mt0) REVERT: H 141 SER cc_start: 0.8742 (p) cc_final: 0.8308 (t) REVERT: H 183 MET cc_start: 0.8294 (tmm) cc_final: 0.7749 (tmm) REVERT: H 248 ASN cc_start: 0.8543 (t0) cc_final: 0.8072 (t0) REVERT: H 268 MET cc_start: 0.8698 (mmp) cc_final: 0.8278 (ttp) REVERT: H 280 PHE cc_start: 0.6873 (m-80) cc_final: 0.6511 (m-10) REVERT: H 282 TYR cc_start: 0.8825 (t80) cc_final: 0.8316 (t80) REVERT: H 284 GLN cc_start: 0.8495 (pt0) cc_final: 0.7562 (pt0) REVERT: H 302 MET cc_start: 0.8431 (mmp) cc_final: 0.8205 (mmm) REVERT: H 303 TRP cc_start: 0.8748 (t-100) cc_final: 0.8340 (t60) REVERT: I 18 THR cc_start: 0.8953 (t) cc_final: 0.8703 (t) REVERT: I 90 GLN cc_start: 0.7976 (mt0) cc_final: 0.7529 (mm-40) REVERT: I 150 ASN cc_start: 0.8000 (p0) cc_final: 0.7714 (p0) REVERT: J 74 MET cc_start: 0.8520 (mmp) cc_final: 0.8014 (tpt) REVERT: J 100 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8553 (tm-30) REVERT: K 3 MET cc_start: 0.7374 (tpt) cc_final: 0.7020 (mmm) REVERT: K 7 ASN cc_start: 0.9157 (p0) cc_final: 0.8666 (p0) REVERT: K 36 MET cc_start: 0.8768 (ttp) cc_final: 0.8462 (ttm) REVERT: K 59 MET cc_start: 0.8027 (mtt) cc_final: 0.7421 (mtp) REVERT: L 14 LEU cc_start: 0.9301 (mt) cc_final: 0.8929 (tp) REVERT: L 17 MET cc_start: 0.8403 (ttp) cc_final: 0.7935 (tmm) REVERT: L 20 MET cc_start: 0.9015 (mmt) cc_final: 0.8761 (mmm) REVERT: L 179 ASP cc_start: 0.7195 (m-30) cc_final: 0.6875 (m-30) REVERT: L 251 THR cc_start: 0.8271 (m) cc_final: 0.8027 (p) REVERT: L 291 CYS cc_start: 0.8395 (m) cc_final: 0.8139 (m) REVERT: L 366 MET cc_start: 0.8367 (tpp) cc_final: 0.7968 (tpp) REVERT: L 524 THR cc_start: 0.8968 (p) cc_final: 0.8733 (p) REVERT: L 533 MET cc_start: 0.6205 (tpt) cc_final: 0.5623 (tpt) REVERT: L 571 MET cc_start: 0.7506 (tpt) cc_final: 0.6038 (ttm) REVERT: L 599 MET cc_start: 0.8636 (mmm) cc_final: 0.7806 (tpt) REVERT: M 61 LEU cc_start: 0.8034 (mm) cc_final: 0.7715 (mt) REVERT: M 76 MET cc_start: 0.7711 (mtm) cc_final: 0.7483 (mtt) REVERT: M 113 MET cc_start: 0.5574 (mpp) cc_final: 0.5204 (mpp) REVERT: M 200 MET cc_start: 0.9092 (mmp) cc_final: 0.8722 (mmp) REVERT: M 207 MET cc_start: 0.8652 (mtt) cc_final: 0.8359 (mtm) REVERT: M 269 MET cc_start: 0.7924 (tpp) cc_final: 0.7544 (tpp) REVERT: M 279 GLN cc_start: 0.7237 (mt0) cc_final: 0.6979 (mt0) REVERT: M 317 ILE cc_start: 0.9428 (mt) cc_final: 0.8908 (tt) REVERT: M 338 HIS cc_start: 0.8346 (m-70) cc_final: 0.8115 (m170) REVERT: M 383 MET cc_start: 0.9111 (mmp) cc_final: 0.8652 (mmp) REVERT: M 406 TYR cc_start: 0.8099 (m-80) cc_final: 0.7888 (m-80) REVERT: N 35 MET cc_start: 0.8182 (mmm) cc_final: 0.7794 (mmt) REVERT: N 36 ASN cc_start: 0.9095 (m-40) cc_final: 0.8033 (m-40) REVERT: N 43 ILE cc_start: 0.9518 (tt) cc_final: 0.9302 (tp) REVERT: N 58 LYS cc_start: 0.9431 (ttmt) cc_final: 0.9008 (ttpt) REVERT: N 117 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7911 (mt-10) REVERT: N 302 LEU cc_start: 0.8462 (mm) cc_final: 0.8175 (mm) REVERT: O 107 GLN cc_start: 0.8850 (pt0) cc_final: 0.7609 (mm-40) REVERT: O 113 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7091 (tp30) REVERT: O 136 GLU cc_start: 0.9083 (tp30) cc_final: 0.8836 (tp30) REVERT: V 49 GLN cc_start: 0.7472 (pp30) cc_final: 0.7170 (pp30) REVERT: W 34 LEU cc_start: 0.9395 (tt) cc_final: 0.8950 (tt) REVERT: W 57 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7940 (tm-30) REVERT: X 31 TYR cc_start: 0.8313 (t80) cc_final: 0.7996 (t80) REVERT: X 50 LYS cc_start: 0.6935 (tttt) cc_final: 0.5768 (mptt) REVERT: X 54 ARG cc_start: 0.9059 (mmt-90) cc_final: 0.8831 (mmp80) REVERT: X 95 LEU cc_start: 0.7190 (tt) cc_final: 0.6959 (mt) REVERT: X 108 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8529 (mm-30) REVERT: Y 48 PHE cc_start: 0.7027 (m-10) cc_final: 0.6661 (m-80) REVERT: Y 73 SER cc_start: 0.8147 (p) cc_final: 0.7624 (p) REVERT: Z 55 GLU cc_start: 0.8714 (tp30) cc_final: 0.8212 (tp30) REVERT: Z 91 GLU cc_start: 0.8900 (tp30) cc_final: 0.8489 (tp30) REVERT: Z 97 MET cc_start: 0.7153 (mmp) cc_final: 0.6591 (mmp) REVERT: d 33 PHE cc_start: 0.9035 (t80) cc_final: 0.8483 (t80) REVERT: d 49 ARG cc_start: 0.8356 (mtt90) cc_final: 0.7912 (tpt170) REVERT: d 87 ASP cc_start: 0.7692 (t0) cc_final: 0.7068 (t0) REVERT: e 63 ARG cc_start: 0.9181 (tpp80) cc_final: 0.8929 (tpp80) REVERT: e 83 GLU cc_start: 0.8005 (pt0) cc_final: 0.7641 (pt0) REVERT: g 58 MET cc_start: 0.6139 (tpp) cc_final: 0.5359 (tpp) REVERT: g 99 TYR cc_start: 0.8631 (t80) cc_final: 0.8286 (t80) REVERT: h 38 ILE cc_start: 0.8247 (mm) cc_final: 0.7558 (tt) REVERT: i 20 ARG cc_start: 0.8998 (mtm110) cc_final: 0.7698 (ppt170) REVERT: m 48 LEU cc_start: 0.9524 (mt) cc_final: 0.9160 (tt) REVERT: m 84 LYS cc_start: 0.7597 (mptt) cc_final: 0.6291 (pttp) REVERT: n 20 LYS cc_start: 0.9039 (ttpt) cc_final: 0.8661 (ttpt) REVERT: n 27 GLU cc_start: 0.8593 (tt0) cc_final: 0.8325 (tm-30) REVERT: n 64 ARG cc_start: 0.7934 (ttt180) cc_final: 0.7339 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 973 average time/residue: 0.4531 time to fit residues: 766.2402 Evaluate side-chains 759 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 759 time to evaluate : 3.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 592 optimal weight: 40.0000 chunk 624 optimal weight: 10.0000 chunk 569 optimal weight: 2.9990 chunk 607 optimal weight: 20.0000 chunk 365 optimal weight: 0.0870 chunk 264 optimal weight: 10.0000 chunk 476 optimal weight: 5.9990 chunk 186 optimal weight: 20.0000 chunk 548 optimal weight: 30.0000 chunk 574 optimal weight: 0.9990 chunk 605 optimal weight: 20.0000 overall best weight: 4.0168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS D 114 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 HIS F 421 HIS ** G 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 HIS M 169 ASN ** M 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 HIS ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 133 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.265 52081 Z= 0.653 Angle : 1.841 51.287 71486 Z= 1.174 Chirality : 0.333 6.478 8766 Planarity : 0.005 0.144 9345 Dihedral : 5.668 160.169 8189 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.49 % Favored : 89.59 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.04 % 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: -1.66 (0.11), residues: 5784 helix: -0.01 (0.09), residues: 3085 sheet: -1.02 (0.38), residues: 181 loop : -2.56 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP M 136 HIS 0.014 0.002 HIS M 319 PHE 0.032 0.002 PHE K 12 TYR 0.040 0.002 TYR D 108 ARG 0.012 0.001 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 897 time to evaluate : 3.904 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: A 12 THR cc_start: 0.9072 (p) cc_final: 0.8827 (t) REVERT: A 77 TRP cc_start: 0.8699 (t60) cc_final: 0.8304 (t60) REVERT: B 61 HIS cc_start: 0.7883 (m-70) cc_final: 0.7649 (m-70) REVERT: B 83 SER cc_start: 0.9042 (p) cc_final: 0.7683 (p) REVERT: B 84 ASP cc_start: 0.8358 (p0) cc_final: 0.8022 (p0) REVERT: B 107 MET cc_start: 0.8823 (mmm) cc_final: 0.8333 (mmm) REVERT: B 121 ASN cc_start: 0.8345 (m-40) cc_final: 0.7869 (m-40) REVERT: C 58 ILE cc_start: 0.9550 (mm) cc_final: 0.9246 (mm) REVERT: C 125 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8570 (tppt) REVERT: C 131 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7435 (mt-10) REVERT: C 162 PHE cc_start: 0.7858 (t80) cc_final: 0.7480 (t80) REVERT: D 98 GLN cc_start: 0.9203 (tt0) cc_final: 0.8481 (mt0) REVERT: D 167 PHE cc_start: 0.8522 (t80) cc_final: 0.8180 (t80) REVERT: D 169 TRP cc_start: 0.9095 (m-10) cc_final: 0.7576 (m100) REVERT: D 173 GLU cc_start: 0.8446 (pp20) cc_final: 0.8107 (pp20) REVERT: D 189 MET cc_start: 0.8007 (ttp) cc_final: 0.7674 (ttp) REVERT: D 190 HIS cc_start: 0.7097 (m170) cc_final: 0.5139 (m170) REVERT: D 239 THR cc_start: 0.8447 (p) cc_final: 0.7794 (t) REVERT: D 338 MET cc_start: 0.9093 (ppp) cc_final: 0.8793 (tmm) REVERT: F 388 GLU cc_start: 0.8584 (tp30) cc_final: 0.7990 (tp30) REVERT: F 389 ILE cc_start: 0.8960 (pt) cc_final: 0.8700 (tp) REVERT: G 118 ASP cc_start: 0.7888 (p0) cc_final: 0.7601 (p0) REVERT: G 122 MET cc_start: 0.8823 (mmp) cc_final: 0.8524 (mmm) REVERT: H 10 ILE cc_start: 0.9107 (mm) cc_final: 0.8749 (mm) REVERT: H 24 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8198 (tm-30) REVERT: H 77 MET cc_start: 0.8140 (tpp) cc_final: 0.7922 (tpp) REVERT: H 105 MET cc_start: 0.8684 (mmp) cc_final: 0.8448 (mmp) REVERT: H 108 MET cc_start: 0.8785 (mmm) cc_final: 0.8483 (mmm) REVERT: H 127 TYR cc_start: 0.8024 (t80) cc_final: 0.7796 (t80) REVERT: H 138 GLN cc_start: 0.7664 (mt0) cc_final: 0.7283 (mt0) REVERT: H 172 MET cc_start: 0.7199 (ppp) cc_final: 0.6973 (ppp) REVERT: H 183 MET cc_start: 0.8080 (tmm) cc_final: 0.7089 (tmm) REVERT: H 248 ASN cc_start: 0.8655 (t0) cc_final: 0.8141 (t0) REVERT: H 268 MET cc_start: 0.8814 (mmp) cc_final: 0.8253 (ttp) REVERT: H 280 PHE cc_start: 0.7217 (m-80) cc_final: 0.6985 (m-80) REVERT: H 282 TYR cc_start: 0.8905 (t80) cc_final: 0.8589 (t80) REVERT: I 18 THR cc_start: 0.8942 (t) cc_final: 0.8721 (t) REVERT: I 40 TYR cc_start: 0.8752 (t80) cc_final: 0.8338 (t80) REVERT: I 90 GLN cc_start: 0.8091 (mt0) cc_final: 0.7565 (mm-40) REVERT: I 117 ILE cc_start: 0.8935 (pt) cc_final: 0.8648 (mp) REVERT: I 138 GLU cc_start: 0.6738 (tt0) cc_final: 0.6388 (tt0) REVERT: I 164 GLU cc_start: 0.7289 (mp0) cc_final: 0.6918 (mp0) REVERT: J 41 CYS cc_start: 0.7871 (m) cc_final: 0.7565 (m) REVERT: J 74 MET cc_start: 0.8687 (mmp) cc_final: 0.8105 (tpt) REVERT: J 100 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8572 (tm-30) REVERT: J 102 PHE cc_start: 0.7266 (t80) cc_final: 0.6920 (t80) REVERT: K 7 ASN cc_start: 0.9105 (p0) cc_final: 0.8683 (p0) REVERT: K 59 MET cc_start: 0.8128 (mtt) cc_final: 0.7795 (mtt) REVERT: L 14 LEU cc_start: 0.9305 (mt) cc_final: 0.8979 (tp) REVERT: L 17 MET cc_start: 0.8300 (ttp) cc_final: 0.7932 (tmm) REVERT: L 20 MET cc_start: 0.9013 (mmt) cc_final: 0.8793 (mmm) REVERT: L 179 ASP cc_start: 0.7225 (m-30) cc_final: 0.6884 (m-30) REVERT: L 366 MET cc_start: 0.8537 (tpp) cc_final: 0.8108 (tpp) REVERT: L 533 MET cc_start: 0.6079 (tpt) cc_final: 0.5826 (tpt) REVERT: L 571 MET cc_start: 0.7651 (tpt) cc_final: 0.6243 (ttm) REVERT: L 580 GLN cc_start: 0.6570 (mt0) cc_final: 0.5933 (mm-40) REVERT: L 599 MET cc_start: 0.8747 (mmm) cc_final: 0.7946 (tpt) REVERT: M 76 MET cc_start: 0.7796 (mtm) cc_final: 0.7535 (mtt) REVERT: M 200 MET cc_start: 0.9237 (mmp) cc_final: 0.8571 (mmp) REVERT: M 201 MET cc_start: 0.7968 (mmp) cc_final: 0.7601 (mtm) REVERT: M 207 MET cc_start: 0.8785 (mtt) cc_final: 0.8440 (mtm) REVERT: M 269 MET cc_start: 0.8283 (tpp) cc_final: 0.7817 (tpp) REVERT: M 317 ILE cc_start: 0.9511 (mt) cc_final: 0.9084 (tt) REVERT: M 325 MET cc_start: 0.7557 (tpp) cc_final: 0.6403 (tpp) REVERT: M 338 HIS cc_start: 0.8398 (m-70) cc_final: 0.8147 (m170) REVERT: M 383 MET cc_start: 0.9091 (mmp) cc_final: 0.8612 (mmp) REVERT: M 406 TYR cc_start: 0.8269 (m-80) cc_final: 0.7955 (m-80) REVERT: N 35 MET cc_start: 0.8318 (mmm) cc_final: 0.7911 (tpt) REVERT: N 36 ASN cc_start: 0.9099 (m-40) cc_final: 0.8880 (m110) REVERT: N 54 GLU cc_start: 0.7989 (tt0) cc_final: 0.7614 (tt0) REVERT: N 58 LYS cc_start: 0.9452 (ttmt) cc_final: 0.9026 (ttpt) REVERT: N 117 GLU cc_start: 0.8657 (mt-10) cc_final: 0.7938 (mt-10) REVERT: N 240 MET cc_start: 0.8397 (ttp) cc_final: 0.7535 (ttp) REVERT: O 107 GLN cc_start: 0.8952 (pt0) cc_final: 0.7755 (mm-40) REVERT: O 136 GLU cc_start: 0.9162 (tp30) cc_final: 0.8911 (tp30) REVERT: W 34 LEU cc_start: 0.9425 (tt) cc_final: 0.8915 (tt) REVERT: W 57 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8266 (tm-30) REVERT: X 31 TYR cc_start: 0.8444 (t80) cc_final: 0.8210 (t80) REVERT: X 50 LYS cc_start: 0.6989 (tttt) cc_final: 0.6009 (mptt) REVERT: X 54 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8820 (mmp80) REVERT: X 108 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8563 (mm-30) REVERT: Y 48 PHE cc_start: 0.7419 (m-10) cc_final: 0.7046 (m-80) REVERT: Z 55 GLU cc_start: 0.8847 (tp30) cc_final: 0.8388 (tp30) REVERT: Z 91 GLU cc_start: 0.8929 (tp30) cc_final: 0.8518 (tp30) REVERT: Z 97 MET cc_start: 0.7160 (mmp) cc_final: 0.6939 (mmp) REVERT: d 33 PHE cc_start: 0.9025 (t80) cc_final: 0.8544 (t80) REVERT: d 49 ARG cc_start: 0.8569 (mtt90) cc_final: 0.7974 (tpt170) REVERT: d 87 ASP cc_start: 0.7718 (t0) cc_final: 0.7051 (t0) REVERT: e 63 ARG cc_start: 0.9236 (tpp80) cc_final: 0.8976 (tpp80) REVERT: e 83 GLU cc_start: 0.7871 (pt0) cc_final: 0.7575 (pt0) REVERT: f 22 PHE cc_start: 0.8638 (t80) cc_final: 0.8001 (t80) REVERT: g 58 MET cc_start: 0.6284 (tpp) cc_final: 0.5434 (tpp) REVERT: g 99 TYR cc_start: 0.8692 (t80) cc_final: 0.8409 (t80) REVERT: h 38 ILE cc_start: 0.8347 (mm) cc_final: 0.7658 (tt) REVERT: i 20 ARG cc_start: 0.9131 (mtm110) cc_final: 0.7704 (ppt170) REVERT: m 48 LEU cc_start: 0.9563 (mt) cc_final: 0.9174 (tt) REVERT: m 76 TYR cc_start: 0.7244 (m-10) cc_final: 0.6890 (m-80) REVERT: m 84 LYS cc_start: 0.7714 (mptt) cc_final: 0.6615 (pttp) REVERT: n 20 LYS cc_start: 0.9136 (ttpt) cc_final: 0.8731 (ttpt) REVERT: n 27 GLU cc_start: 0.8707 (tt0) cc_final: 0.8248 (tm-30) REVERT: n 64 ARG cc_start: 0.7994 (ttt180) cc_final: 0.7460 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 897 average time/residue: 0.4751 time to fit residues: 739.6919 Evaluate side-chains 731 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 731 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 398 optimal weight: 0.8980 chunk 642 optimal weight: 10.0000 chunk 391 optimal weight: 2.9990 chunk 304 optimal weight: 7.9990 chunk 446 optimal weight: 20.0000 chunk 673 optimal weight: 20.0000 chunk 619 optimal weight: 10.0000 chunk 536 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 414 optimal weight: 0.0870 chunk 328 optimal weight: 6.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 HIS ** G 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 53 ASN a 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.6297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.267 52081 Z= 0.633 Angle : 1.830 51.023 71486 Z= 1.168 Chirality : 0.333 6.424 8766 Planarity : 0.005 0.146 9345 Dihedral : 5.671 161.218 8189 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.86 % Allowed : 9.16 % Favored : 89.97 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -1.63 (0.11), residues: 5784 helix: 0.03 (0.09), residues: 3072 sheet: -0.95 (0.38), residues: 182 loop : -2.56 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP X 47 HIS 0.012 0.001 HIS F 402 PHE 0.034 0.002 PHE D 171 TYR 0.034 0.002 TYR D 108 ARG 0.013 0.001 ARG D 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 895 time to evaluate : 3.952 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: A 12 THR cc_start: 0.9045 (p) cc_final: 0.8816 (t) REVERT: A 77 TRP cc_start: 0.8606 (t60) cc_final: 0.8189 (t60) REVERT: B 83 SER cc_start: 0.9038 (p) cc_final: 0.7705 (p) REVERT: B 84 ASP cc_start: 0.8350 (p0) cc_final: 0.8025 (p0) REVERT: B 107 MET cc_start: 0.8874 (mmm) cc_final: 0.8394 (mmm) REVERT: C 28 TYR cc_start: 0.8505 (t80) cc_final: 0.8283 (t80) REVERT: C 58 ILE cc_start: 0.9523 (mm) cc_final: 0.9233 (mm) REVERT: C 162 PHE cc_start: 0.7713 (t80) cc_final: 0.7342 (t80) REVERT: D 165 THR cc_start: 0.9502 (p) cc_final: 0.9297 (p) REVERT: D 167 PHE cc_start: 0.8406 (t80) cc_final: 0.8091 (t80) REVERT: D 169 TRP cc_start: 0.9072 (m-10) cc_final: 0.7698 (m100) REVERT: D 170 MET cc_start: 0.8932 (mmm) cc_final: 0.8693 (mmm) REVERT: D 173 GLU cc_start: 0.8361 (pp20) cc_final: 0.7847 (pp20) REVERT: D 189 MET cc_start: 0.7627 (ttp) cc_final: 0.6787 (ttm) REVERT: D 190 HIS cc_start: 0.7349 (m170) cc_final: 0.7123 (m170) REVERT: D 239 THR cc_start: 0.8378 (p) cc_final: 0.7784 (t) REVERT: D 338 MET cc_start: 0.9065 (ppp) cc_final: 0.8738 (tmm) REVERT: F 388 GLU cc_start: 0.8486 (tp30) cc_final: 0.7931 (tp30) REVERT: F 389 ILE cc_start: 0.8947 (pt) cc_final: 0.8674 (tp) REVERT: G 122 MET cc_start: 0.8825 (mmp) cc_final: 0.8497 (mmm) REVERT: H 24 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8141 (tm-30) REVERT: H 31 MET cc_start: 0.9138 (mmm) cc_final: 0.8702 (mmm) REVERT: H 85 MET cc_start: 0.9159 (tpp) cc_final: 0.8956 (tpp) REVERT: H 183 MET cc_start: 0.8022 (tmm) cc_final: 0.7614 (tmm) REVERT: H 248 ASN cc_start: 0.8670 (t0) cc_final: 0.8242 (t0) REVERT: H 268 MET cc_start: 0.8800 (mmp) cc_final: 0.8321 (ttp) REVERT: H 280 PHE cc_start: 0.7384 (m-80) cc_final: 0.7103 (m-80) REVERT: H 282 TYR cc_start: 0.8953 (t80) cc_final: 0.8741 (t80) REVERT: I 40 TYR cc_start: 0.8688 (t80) cc_final: 0.8358 (t80) REVERT: I 90 GLN cc_start: 0.8232 (mt0) cc_final: 0.7520 (mm-40) REVERT: I 150 ASN cc_start: 0.8308 (p0) cc_final: 0.8089 (p0) REVERT: J 46 ASN cc_start: 0.8757 (m110) cc_final: 0.8275 (m-40) REVERT: J 74 MET cc_start: 0.8642 (mmp) cc_final: 0.8111 (tpt) REVERT: J 100 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8639 (tm-30) REVERT: J 102 PHE cc_start: 0.7350 (t80) cc_final: 0.7044 (t80) REVERT: K 3 MET cc_start: 0.7324 (tpt) cc_final: 0.7042 (mmm) REVERT: K 6 MET cc_start: 0.7184 (mmt) cc_final: 0.6686 (mtt) REVERT: K 7 ASN cc_start: 0.9139 (p0) cc_final: 0.8660 (p0) REVERT: K 59 MET cc_start: 0.7885 (mtt) cc_final: 0.7240 (mtp) REVERT: L 14 LEU cc_start: 0.9287 (mt) cc_final: 0.8965 (tp) REVERT: L 17 MET cc_start: 0.8281 (ttp) cc_final: 0.7912 (tmm) REVERT: L 366 MET cc_start: 0.8529 (tpp) cc_final: 0.8127 (tpp) REVERT: L 533 MET cc_start: 0.6414 (tpt) cc_final: 0.5940 (tpt) REVERT: L 571 MET cc_start: 0.7594 (tpt) cc_final: 0.6105 (ttm) REVERT: L 599 MET cc_start: 0.8719 (mmm) cc_final: 0.7921 (tpt) REVERT: M 76 MET cc_start: 0.7867 (mtm) cc_final: 0.7573 (mtt) REVERT: M 200 MET cc_start: 0.9254 (mmp) cc_final: 0.8442 (mmp) REVERT: M 201 MET cc_start: 0.7862 (mmp) cc_final: 0.7584 (mtm) REVERT: M 243 MET cc_start: 0.8473 (mmp) cc_final: 0.8208 (mmp) REVERT: M 259 TYR cc_start: 0.7983 (t80) cc_final: 0.7629 (t80) REVERT: M 269 MET cc_start: 0.8300 (tpp) cc_final: 0.7945 (tpp) REVERT: M 281 ASP cc_start: 0.8723 (m-30) cc_final: 0.8242 (m-30) REVERT: M 317 ILE cc_start: 0.9474 (mt) cc_final: 0.9136 (tt) REVERT: M 325 MET cc_start: 0.7492 (tpp) cc_final: 0.6588 (tpp) REVERT: M 338 HIS cc_start: 0.8400 (m-70) cc_final: 0.8154 (m170) REVERT: M 383 MET cc_start: 0.9015 (mmp) cc_final: 0.8526 (mmp) REVERT: M 406 TYR cc_start: 0.8236 (m-80) cc_final: 0.7952 (m-80) REVERT: M 437 MET cc_start: 0.8920 (mmp) cc_final: 0.8717 (mmm) REVERT: N 35 MET cc_start: 0.8212 (mmm) cc_final: 0.7835 (tpt) REVERT: N 36 ASN cc_start: 0.9238 (m-40) cc_final: 0.8227 (m-40) REVERT: N 54 GLU cc_start: 0.8007 (tt0) cc_final: 0.7595 (tt0) REVERT: N 58 LYS cc_start: 0.9437 (ttmt) cc_final: 0.9130 (ttpt) REVERT: N 117 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8032 (mt-10) REVERT: N 232 HIS cc_start: 0.7738 (t70) cc_final: 0.7331 (t70) REVERT: O 107 GLN cc_start: 0.8935 (pt0) cc_final: 0.7719 (mm-40) REVERT: O 136 GLU cc_start: 0.9174 (tp30) cc_final: 0.8946 (tp30) REVERT: W 34 LEU cc_start: 0.9414 (tt) cc_final: 0.8895 (tt) REVERT: W 57 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8233 (tm-30) REVERT: X 54 ARG cc_start: 0.9043 (mmt-90) cc_final: 0.8829 (mmp80) REVERT: Y 48 PHE cc_start: 0.7399 (m-10) cc_final: 0.7044 (m-80) REVERT: Z 55 GLU cc_start: 0.8916 (tp30) cc_final: 0.8489 (tp30) REVERT: Z 91 GLU cc_start: 0.8934 (tp30) cc_final: 0.8489 (tp30) REVERT: Z 97 MET cc_start: 0.6896 (mmp) cc_final: 0.6591 (mmp) REVERT: d 33 PHE cc_start: 0.9082 (t80) cc_final: 0.8532 (t80) REVERT: d 49 ARG cc_start: 0.8424 (mtt90) cc_final: 0.7850 (tpt170) REVERT: d 87 ASP cc_start: 0.7690 (t0) cc_final: 0.7015 (t0) REVERT: e 83 GLU cc_start: 0.7920 (pt0) cc_final: 0.7633 (pt0) REVERT: f 22 PHE cc_start: 0.8616 (t80) cc_final: 0.7962 (t80) REVERT: g 58 MET cc_start: 0.6353 (tpp) cc_final: 0.5914 (tpp) REVERT: g 99 TYR cc_start: 0.8703 (t80) cc_final: 0.8431 (t80) REVERT: h 38 ILE cc_start: 0.8366 (mm) cc_final: 0.7675 (tt) REVERT: i 20 ARG cc_start: 0.9112 (mtm110) cc_final: 0.7686 (ppt170) REVERT: m 48 LEU cc_start: 0.9555 (mt) cc_final: 0.9175 (tt) REVERT: m 76 TYR cc_start: 0.7117 (m-10) cc_final: 0.6759 (m-80) REVERT: m 84 LYS cc_start: 0.7717 (mptt) cc_final: 0.6623 (pttp) REVERT: n 20 LYS cc_start: 0.9106 (ttpt) cc_final: 0.8716 (ttpt) REVERT: n 27 GLU cc_start: 0.8678 (tt0) cc_final: 0.8227 (tm-30) REVERT: n 64 ARG cc_start: 0.7979 (ttt180) cc_final: 0.7442 (mmt-90) REVERT: p 133 GLN cc_start: 0.8943 (pt0) cc_final: 0.8704 (pt0) outliers start: 0 outliers final: 0 residues processed: 895 average time/residue: 0.4560 time to fit residues: 710.7890 Evaluate side-chains 726 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 726 time to evaluate : 4.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 425 optimal weight: 20.0000 chunk 571 optimal weight: 6.9990 chunk 164 optimal weight: 20.0000 chunk 494 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 149 optimal weight: 0.0000 chunk 537 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 551 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 114 ASN F 421 HIS ** G 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN ** L 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 ASN M 319 HIS ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.075428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.067595 restraints weight = 247875.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.068818 restraints weight = 153000.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.069672 restraints weight = 104083.002| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.6314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.272 52081 Z= 0.628 Angle : 1.819 50.982 71486 Z= 1.163 Chirality : 0.332 6.471 8766 Planarity : 0.005 0.145 9345 Dihedral : 5.498 161.534 8189 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.90 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -1.57 (0.11), residues: 5784 helix: 0.09 (0.09), residues: 3062 sheet: -0.98 (0.39), residues: 181 loop : -2.52 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 136 HIS 0.015 0.001 HIS C 160 PHE 0.030 0.002 PHE D 167 TYR 0.031 0.002 TYR D 108 ARG 0.009 0.000 ARG D 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12332.48 seconds wall clock time: 212 minutes 8.24 seconds (12728.24 seconds total)