Starting phenix.real_space_refine on Tue Sep 24 18:16:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lc5_4032/09_2024/5lc5_4032.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lc5_4032/09_2024/5lc5_4032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lc5_4032/09_2024/5lc5_4032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lc5_4032/09_2024/5lc5_4032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lc5_4032/09_2024/5lc5_4032.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lc5_4032/09_2024/5lc5_4032.cif" } resolution = 4.35 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= 0.026 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 32754 2.51 5 N 9185 2.21 5 O 9421 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: 51718 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 806 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 6, 'TRANS': 104} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 49 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: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3301 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 28, 'TRANS': 397} 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: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2389 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 21, 'TRANS': 291} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 59 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: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1854 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 207} Link IDs: {'PTRANS': 10, 'TRANS': 303} Unresolved non-hydrogen bonds: 654 Unresolved non-hydrogen angles: 878 Unresolved non-hydrogen dihedrals: 496 Unresolved non-hydrogen chiralities: 34 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: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 1675 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 335} Link IDs: {'TRANS': 334} Unresolved non-hydrogen bonds: 670 Unresolved non-hydrogen angles: 1005 Unresolved non-hydrogen dihedrals: 335 Planarities with less than four sites: {'UNK:plan-1': 335} Unresolved non-hydrogen planarities: 335 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': 1, 'PTRANS': 4, '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 1538 SG CYS B 119 95.637 89.752 203.824 1.00 57.50 S ATOM 1040 SG CYS B 55 89.959 92.248 205.638 1.00 59.15 S ATOM 1034 SG CYS B 54 90.163 86.462 202.850 1.00 57.95 S ATOM 1768 SG CYS B 149 92.660 87.213 208.877 1.00 57.36 S ATOM 7448 SG CYS E 103 113.001 41.062 258.943 1.00 95.94 S ATOM 7476 SG CYS E 108 111.341 38.006 260.139 1.00 96.80 S ATOM 7657 SG CYS E 144 116.147 38.582 255.787 1.00 96.49 S ATOM 7677 SG CYS E 148 114.959 35.237 256.730 1.00 97.95 S ATOM 9705 SG CYS F 362 119.328 47.060 234.692 1.00 77.88 S ATOM 9725 SG CYS F 365 115.431 47.207 239.624 1.00 75.60 S ATOM 10049 SG CYS F 405 119.772 42.263 239.069 1.00 78.31 S ATOM 9686 SG CYS F 359 121.911 48.209 240.429 1.00 79.38 S ATOM 10931 SG CYS G 114 115.268 66.143 226.383 1.00 64.90 S ATOM 10870 SG CYS G 105 109.440 68.865 227.314 1.00 60.54 S ATOM 10891 SG CYS G 108 114.452 70.843 230.826 1.00 63.01 S ATOM 11179 SG CYS G 156 123.008 58.981 231.500 1.00 62.59 S ATOM 11156 SG CYS G 153 120.414 62.565 236.404 1.00 61.82 S ATOM 11203 SG CYS G 159 126.703 62.997 234.740 1.00 64.98 S ATOM 11433 SG CYS G 203 122.142 65.370 230.809 1.00 60.43 S ATOM 10449 SG CYS G 41 123.125 53.961 228.276 1.00 75.29 S ATOM 10526 SG CYS G 52 119.542 52.786 228.160 1.00 74.23 S ATOM 10551 SG CYS G 55 120.990 49.486 224.042 1.00 75.63 S ATOM 10624 SG CYS G 69 124.385 50.711 224.346 1.00 77.25 S ATOM 17174 SG CYS I 119 96.660 81.741 213.818 1.00 54.10 S ATOM 17148 SG CYS I 116 97.154 87.932 215.388 1.00 52.88 S ATOM 17195 SG CYS I 122 98.285 83.463 220.006 1.00 52.87 S ATOM 16922 SG CYS I 87 102.364 84.308 214.874 1.00 51.52 S ATOM 17224 SG CYS I 126 100.911 80.127 227.349 1.00 55.77 S ATOM 16895 SG CYS I 83 104.436 82.420 222.324 1.00 54.68 S ATOM 16853 SG CYS I 77 105.615 84.586 228.236 1.00 58.19 S ATOM 16872 SG CYS I 80 107.081 78.494 226.979 1.00 56.50 S ATOM 34601 SG CYS R 59 103.227 75.643 242.730 1.00 83.32 S ATOM 34752 SG CYS R 84 106.049 76.705 240.253 1.00 81.75 S ATOM 34774 SG CYS R 87 103.086 78.980 240.861 1.00 81.65 S Time building chain proxies: 22.97, per 1000 atoms: 0.44 Number of scatterers: 51718 At special positions: 0 Unit cell: (186.2, 183.54, 289.94, 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 9421 8.00 N 9185 7.00 C 32754 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: 9.40 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " 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="FE4 SF4 B 201 " - pdb=" SG CYS B 149 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 55 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " 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="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " 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="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " 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="FE1 SF4 I 201 " - pdb=" SG CYS I 119 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 122 " 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="FE2 SF4 I 202 " - pdb=" SG CYS I 83 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 80 " 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 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15088 Finding SS restraints... Secondary structure from input PDB file: 248 helices and 23 sheets defined 62.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 removed outlier: 3.540A pdb=" N THR A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 77 removed outlier: 3.568A pdb=" N PHE A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 4.612A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 106 removed outlier: 4.111A pdb=" N THR A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.070A 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: 3.766A pdb=" N PHE A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.770A pdb=" N ASP B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 94 through 105 Proline residue: B 98 - end of helix removed outlier: 3.619A pdb=" N ARG B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS B 102 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 3.719A 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: 4.338A pdb=" N TYR B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 29 removed outlier: 3.574A pdb=" N SER C 23 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL C 29 " --> pdb=" O GLY C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.767A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 138 removed outlier: 3.504A pdb=" N ARG C 132 " --> pdb=" O TRP C 129 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP C 135 " --> pdb=" O ARG C 132 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP C 136 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET C 137 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE C 138 " --> pdb=" O TRP C 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 14 removed outlier: 4.264A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.947A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 Proline residue: D 101 - end of helix removed outlier: 4.245A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.074A pdb=" N GLN D 116 " --> pdb=" O MET D 112 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA D 117 " --> pdb=" O CYS D 113 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 161 removed outlier: 3.642A pdb=" N TRP D 136 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 139 " --> pdb=" O GLN D 135 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N HIS D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 182 removed outlier: 3.554A pdb=" N MET D 170 " --> pdb=" O PRO D 166 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE D 171 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 229 removed outlier: 4.945A pdb=" N ASP D 210 " --> pdb=" O GLY D 206 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR D 212 " --> pdb=" O MET D 208 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU D 225 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 249 through 253 Processing helix chain 'D' and resid 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: 4.492A pdb=" N ARG D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE D 308 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG D 309 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 5.511A 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: 4.190A pdb=" N TYR D 352 " --> pdb=" O HIS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.869A pdb=" N HIS D 398 " --> pdb=" O GLY D 395 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 399 " --> pdb=" O PHE D 396 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 400 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP D 403 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET D 405 " --> pdb=" O LEU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.894A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 37 removed outlier: 4.566A pdb=" N LYS E 29 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU E 32 " --> pdb=" O LYS E 29 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE E 34 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL E 35 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN E 37 " --> pdb=" O ILE E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 4.199A pdb=" N ASP E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 removed outlier: 3.505A pdb=" N ILE E 72 " --> pdb=" O LYS E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 86 removed outlier: 3.829A pdb=" N ALA E 84 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR E 85 " --> pdb=" O TYR E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 111 removed outlier: 4.542A pdb=" N ARG E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 123 Processing helix chain 'E' and resid 166 through 178 removed outlier: 4.442A pdb=" N GLU E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS E 177 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ALA E 178 " --> pdb=" O ASP E 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 39 removed outlier: 3.622A pdb=" N GLN F 37 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 3.750A 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: 3.974A pdb=" N VAL F 60 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER F 63 " --> pdb=" O GLU F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 81 Processing helix chain 'F' and resid 105 through 112 removed outlier: 3.710A pdb=" N ILE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG F 112 " --> pdb=" O ARG F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 129 removed outlier: 3.544A pdb=" N LEU F 118 " --> pdb=" O PRO F 115 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL F 119 " --> pdb=" O HIS F 116 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU F 120 " --> pdb=" O LYS F 117 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N CYS F 122 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY F 125 " --> pdb=" O CYS F 122 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY F 126 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG F 127 " --> pdb=" O VAL F 124 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ALA F 128 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET F 129 " --> pdb=" O GLY F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 159 removed outlier: 3.647A pdb=" N ASN F 148 " --> pdb=" O ASN F 144 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU F 149 " --> pdb=" O GLU F 145 " (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: 4.149A pdb=" N ILE F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 236 removed outlier: 3.648A pdb=" N ALA F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL F 230 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 3.714A 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: 3.794A pdb=" N PHE F 242 " --> pdb=" O GLY F 239 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 243 " --> pdb=" O ALA F 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 239 through 243' Processing helix chain 'F' and resid 276 through 283 removed outlier: 3.576A pdb=" N GLU F 281 " --> pdb=" O LYS F 277 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS F 283 " --> pdb=" O LEU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 324 removed outlier: 3.588A pdb=" N ILE F 323 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLN F 324 " --> pdb=" O ASP F 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 319 through 324' Processing helix chain 'F' and resid 343 through 356 removed outlier: 3.610A pdb=" N ARG F 349 " --> pdb=" O LYS F 345 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 350 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 381 removed outlier: 3.556A pdb=" N GLU F 367 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY F 368 " --> pdb=" O PRO F 364 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TRP F 371 " --> pdb=" O GLU F 367 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL F 375 " --> pdb=" O TRP F 371 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG F 378 " --> pdb=" O LYS F 374 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE F 379 " --> pdb=" O VAL F 375 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL F 380 " --> pdb=" O MET F 376 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 401 removed outlier: 3.951A pdb=" N ILE F 389 " --> pdb=" O PRO F 386 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER F 391 " --> pdb=" O GLU F 388 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 395 " --> pdb=" O LEU F 392 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER F 396 " --> pdb=" O TRP F 393 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS F 397 " --> pdb=" O GLU F 394 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE F 399 " --> pdb=" O SER F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 419 Proline residue: F 414 - end of helix removed outlier: 3.807A pdb=" N LEU F 418 " --> pdb=" O PRO F 414 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE F 419 " --> pdb=" O VAL F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 438 removed outlier: 3.919A pdb=" N ARG F 429 " --> pdb=" O GLU F 425 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET F 430 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE F 433 " --> pdb=" O ARG F 429 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 32 removed outlier: 3.713A pdb=" N GLU G 31 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 99 removed outlier: 3.561A pdb=" N ALA G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY G 92 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET G 94 " --> pdb=" O ARG G 90 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 122 removed outlier: 3.507A pdb=" N SER G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET G 121 " --> pdb=" O GLN G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 166 removed outlier: 3.901A pdb=" N SER G 164 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 202 removed outlier: 3.837A pdb=" N ILE G 200 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 275 removed outlier: 4.384A pdb=" N UNK G 271 " --> pdb=" O UNK G 268 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N UNK G 272 " --> pdb=" O UNK G 269 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N UNK G 274 " --> pdb=" O UNK G 271 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N UNK G 275 " --> pdb=" O UNK G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 removed outlier: 3.832A pdb=" N UNK G 301 " --> pdb=" O UNK G 297 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N UNK G 302 " --> pdb=" O UNK G 298 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N UNK G 306 " --> pdb=" O UNK G 302 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N UNK G 307 " --> pdb=" O UNK G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 337 Processing helix chain 'G' and resid 390 through 400 removed outlier: 3.520A pdb=" N UNK G 395 " --> pdb=" O UNK G 391 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N UNK G 399 " --> pdb=" O UNK G 395 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N UNK G 400 " --> pdb=" O UNK G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 433 removed outlier: 4.183A pdb=" N UNK G 430 " --> pdb=" O UNK G 426 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N UNK G 431 " --> pdb=" O UNK G 427 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N UNK G 433 " --> pdb=" O UNK G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 445 removed outlier: 4.753A pdb=" N UNK G 442 " --> pdb=" O UNK G 438 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N UNK G 444 " --> pdb=" O UNK G 440 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N UNK G 445 " --> pdb=" O UNK G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 473 removed outlier: 3.674A pdb=" N UNK G 465 " --> pdb=" O UNK G 461 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N UNK G 468 " --> pdb=" O UNK G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 504 removed outlier: 3.621A pdb=" N UNK G 503 " --> pdb=" O UNK G 500 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N UNK G 504 " --> pdb=" O UNK G 501 " (cutoff:3.500A) Processing helix chain 'G' and resid 552 through 556 removed outlier: 3.733A pdb=" N UNK G 555 " --> pdb=" O UNK G 552 " (cutoff:3.500A) removed outlier: 3.854A 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: 3.614A pdb=" N UNK G 600 " --> pdb=" O UNK G 596 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N UNK G 601 " --> pdb=" O UNK G 597 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N UNK G 604 " --> pdb=" O UNK G 600 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N UNK G 605 " --> pdb=" O UNK G 601 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N UNK G 606 " --> pdb=" O UNK G 602 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N UNK G 607 " --> pdb=" O UNK G 603 " (cutoff:3.500A) Processing helix chain 'G' and resid 616 through 626 removed outlier: 3.594A pdb=" N UNK G 620 " --> pdb=" O UNK G 616 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N UNK G 621 " --> pdb=" O UNK G 617 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N UNK G 624 " --> pdb=" O UNK G 620 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N UNK G 625 " --> pdb=" O UNK G 621 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N UNK G 626 " --> pdb=" O UNK G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 642 through 653 removed outlier: 3.515A pdb=" N UNK G 646 " --> pdb=" O UNK G 642 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N UNK G 647 " --> pdb=" O UNK G 643 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N UNK G 648 " --> pdb=" O UNK G 644 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N UNK G 652 " --> pdb=" O UNK G 648 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N UNK G 653 " --> pdb=" O UNK G 649 " (cutoff:3.500A) Processing helix chain 'G' and resid 683 through 691 removed outlier: 4.426A pdb=" N UNK G 687 " --> pdb=" O UNK G 683 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N UNK G 688 " --> pdb=" O UNK G 684 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 31 removed outlier: 3.842A pdb=" N ILE H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) Proline residue: H 12 - end of helix removed outlier: 3.997A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL H 23 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG H 25 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU H 28 " --> pdb=" O GLU H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 57 removed outlier: 3.812A pdb=" N ILE H 49 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP H 51 " --> pdb=" O PRO H 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA H 52 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU H 55 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE H 56 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 4.659A 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: 3.735A pdb=" N LEU H 81 " --> pdb=" O MET H 77 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.592A pdb=" N SER H 109 " --> pdb=" O MET H 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY H 120 " --> pdb=" O ILE H 116 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TRP H 121 " --> pdb=" O LEU H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 156 removed outlier: 3.539A pdb=" N ALA H 135 " --> pdb=" O GLY H 131 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA H 137 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TYR H 142 " --> pdb=" O GLN H 138 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 169 removed outlier: 4.001A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) removed outlier: 4.388A 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: 3.846A pdb=" N MET H 183 " --> pdb=" O TRP H 179 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE H 186 " --> pdb=" O ALA H 182 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE H 187 " --> pdb=" O MET H 183 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR H 189 " --> pdb=" O TRP H 185 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU H 190 " --> pdb=" O PHE H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 241 removed outlier: 3.563A pdb=" N ALA H 226 " --> pdb=" O LEU H 222 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA H 229 " --> pdb=" O MET H 225 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE H 231 " --> pdb=" O GLU H 227 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 274 removed outlier: 3.665A pdb=" N THR H 256 " --> pdb=" O GLU H 253 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE H 257 " --> pdb=" O LEU H 254 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE H 259 " --> pdb=" O THR H 256 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE H 261 " --> pdb=" O ASN H 258 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS H 262 " --> pdb=" O PHE H 259 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU H 265 " --> pdb=" O LYS H 262 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET H 268 " --> pdb=" O LEU H 265 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE H 270 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP H 272 " --> pdb=" O SER H 269 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG H 274 " --> pdb=" O LEU H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.681A pdb=" N LEU H 289 " --> pdb=" O LEU H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 311 removed outlier: 3.637A 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: 3.853A pdb=" N ASP I 19 " --> pdb=" O LYS I 15 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG I 20 " --> pdb=" O SER I 16 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 42 removed outlier: 3.712A pdb=" N THR I 37 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 3.986A 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: 5.206A pdb=" N ALA I 163 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA I 166 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE I 169 " --> pdb=" O ALA I 166 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN I 170 " --> pdb=" O ALA I 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 22 removed outlier: 3.916A pdb=" N LEU J 9 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL J 11 " --> pdb=" O PHE J 7 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE J 12 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE J 17 " --> pdb=" O PHE J 13 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY J 19 " --> pdb=" O MET J 15 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N PHE J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER J 21 " --> pdb=" O PHE J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 45 removed outlier: 3.893A pdb=" N GLY J 32 " --> pdb=" O TYR J 28 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU J 33 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY J 37 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL J 44 " --> pdb=" O GLY J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 59 removed outlier: 3.970A pdb=" N VAL J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE J 57 " --> pdb=" O GLY J 53 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE J 59 " --> pdb=" O MET J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 74 removed outlier: 3.660A pdb=" N THR J 72 " --> pdb=" O PHE J 68 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA J 73 " --> pdb=" O GLY J 69 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N MET J 74 " --> pdb=" O TYR J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 108 removed outlier: 4.252A pdb=" N GLY J 91 " --> pdb=" O ALA J 88 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL J 94 " --> pdb=" O GLY J 91 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR J 95 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU J 97 " --> pdb=" O VAL J 94 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE J 101 " --> pdb=" O LEU J 98 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N PHE J 102 " --> pdb=" O MET J 99 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL J 104 " --> pdb=" O PHE J 101 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR J 105 " --> pdb=" O PHE J 102 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU J 108 " --> pdb=" O TYR J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 170 removed outlier: 3.556A pdb=" N GLY J 164 " --> pdb=" O SER J 160 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL J 165 " --> pdb=" O LEU J 161 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL J 166 " --> pdb=" O LEU J 162 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET J 169 " --> pdb=" O VAL J 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 20 removed outlier: 4.298A pdb=" N ASN K 7 " --> pdb=" O MET K 3 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE K 8 " --> pdb=" O VAL K 4 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL K 14 " --> pdb=" O MET K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 50 removed outlier: 4.118A pdb=" N LEU K 30 " --> pdb=" O LEU K 26 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU K 34 " --> pdb=" O LEU K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 83 Proline residue: K 60 - end of helix removed outlier: 3.501A pdb=" N LEU K 64 " --> pdb=" O ILE K 61 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA K 68 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU K 70 " --> pdb=" O ALA K 67 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA K 72 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY K 74 " --> pdb=" O ALA K 71 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU K 75 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU K 78 " --> pdb=" O LEU K 75 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL K 81 " --> pdb=" O LEU K 78 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN K 83 " --> pdb=" O MET K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 23 removed outlier: 4.022A pdb=" N LEU L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL L 10 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU L 15 " --> pdb=" O THR L 11 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Proline residue: L 18 - end of helix removed outlier: 3.856A pdb=" N SER L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 56 removed outlier: 3.617A pdb=" N VAL L 36 " --> pdb=" O TYR L 32 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS L 37 " --> pdb=" O PRO L 33 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR L 42 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE L 45 " --> pdb=" O SER L 41 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.523A pdb=" N HIS L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 106 removed outlier: 3.668A pdb=" N ILE L 90 " --> pdb=" O SER L 86 " (cutoff:3.500A) Proline residue: L 91 - end of helix removed outlier: 3.725A pdb=" N SER L 99 " --> pdb=" O PHE L 95 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU L 102 " --> pdb=" O TRP L 98 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N MET L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 removed outlier: 3.989A pdb=" N PHE L 118 " --> pdb=" O ILE L 114 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR L 120 " --> pdb=" O LYS L 116 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU L 121 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU L 123 " --> pdb=" O LYS L 119 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 156 removed outlier: 3.676A pdb=" N ILE L 142 " --> pdb=" O PHE L 138 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY L 143 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE L 152 " --> pdb=" O GLY L 148 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU L 153 " --> pdb=" O ILE L 149 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU L 154 " --> pdb=" O MET L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 190 removed outlier: 3.586A pdb=" N ALA L 168 " --> pdb=" O ALA L 164 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA L 171 " --> pdb=" O ALA L 167 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE L 172 " --> pdb=" O ALA L 168 " (cutoff:3.500A) removed outlier: 3.903A 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: 4.487A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 202 removed outlier: 4.709A 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: 3.759A pdb=" N LEU L 213 " --> pdb=" O SER L 209 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE L 214 " --> pdb=" O ASN L 210 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY L 215 " --> pdb=" O MET L 211 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA L 217 " --> pdb=" O LEU L 213 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU L 218 " --> pdb=" O ILE L 214 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR L 221 " --> pdb=" O ALA L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 237 Proline residue: L 234 - end of helix removed outlier: 4.009A 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: 4.610A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU L 259 " --> pdb=" O ALA L 255 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU L 260 " --> pdb=" O GLY L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 268 Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.548A pdb=" N SER L 275 " --> pdb=" O LYS L 271 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE L 276 " --> pdb=" O TYR L 272 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU L 278 " --> pdb=" O GLN L 274 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE L 283 " --> pdb=" O CYS L 279 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR L 284 " --> pdb=" O LEU L 280 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR L 285 " --> pdb=" O GLY L 281 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU L 286 " --> pdb=" O ALA L 282 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR L 288 " --> pdb=" O THR L 284 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS L 291 " --> pdb=" O PHE L 287 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA L 292 " --> pdb=" O THR L 288 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 319 removed outlier: 4.058A pdb=" N ILE L 302 " --> pdb=" O ILE L 298 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER L 307 " --> pdb=" O ALA L 303 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU L 312 " --> pdb=" O SER L 308 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET L 313 " --> pdb=" O GLN L 309 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE L 317 " --> pdb=" O MET L 313 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY L 318 " --> pdb=" O MET L 314 " (cutoff:3.500A) Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.764A pdb=" N PHE L 326 " --> pdb=" O PRO L 322 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU L 327 " --> pdb=" O TYR L 323 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS L 328 " --> pdb=" O LEU L 324 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE L 329 " --> pdb=" O ALA L 325 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR L 331 " --> pdb=" O LEU L 327 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA L 337 " --> pdb=" O ALA L 333 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET L 338 " --> pdb=" O PHE L 334 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU L 339 " --> pdb=" O PHE L 335 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET L 341 " --> pdb=" O ALA L 337 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER L 343 " --> pdb=" O LEU L 339 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE L 346 " --> pdb=" O CYS L 342 " (cutoff:3.500A) Processing helix chain 'L' and resid 367 through 380 removed outlier: 3.988A pdb=" N ALA L 372 " --> pdb=" O PHE L 368 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU L 380 " --> pdb=" O GLY L 376 " (cutoff:3.500A) Processing helix chain 'L' and resid 388 through 401 removed outlier: 3.971A pdb=" N ASP L 393 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE L 395 " --> pdb=" O SER L 391 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE L 396 " --> pdb=" O LYS L 392 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN L 400 " --> pdb=" O ILE L 396 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.588A pdb=" N ILE L 414 " --> pdb=" O LEU L 410 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER L 417 " --> pdb=" O LEU L 413 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE L 421 " --> pdb=" O SER L 417 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR L 422 " --> pdb=" O PHE L 418 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER L 423 " --> pdb=" O THR L 419 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE L 426 " --> pdb=" O TYR L 422 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE L 427 " --> pdb=" O SER L 423 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE L 429 " --> pdb=" O ARG L 425 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA L 430 " --> pdb=" O ILE L 426 " (cutoff:3.500A) Processing helix chain 'L' and resid 449 through 463 removed outlier: 4.058A pdb=" N SER L 453 " --> pdb=" O LEU L 449 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS L 455 " --> pdb=" O ILE L 451 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ARG L 456 " --> pdb=" O ASN L 452 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE L 459 " --> pdb=" O LYS L 455 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY L 460 " --> pdb=" O ARG L 456 " (cutoff:3.500A) Processing helix chain 'L' and resid 464 through 471 removed outlier: 4.568A pdb=" N SER L 469 " --> pdb=" O GLY L 465 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN L 470 " --> pdb=" O TYR L 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 487 through 510 removed outlier: 4.673A pdb=" N LEU L 491 " --> pdb=" O LYS L 487 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR L 494 " --> pdb=" O ALA L 490 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET L 507 " --> pdb=" O GLU L 503 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 531 through 563 removed outlier: 4.436A pdb=" N ARG L 535 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU L 536 " --> pdb=" O ILE L 532 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA L 537 " --> pdb=" O MET L 533 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.718A pdb=" N SER L 545 " --> pdb=" O ASN L 541 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER L 548 " --> pdb=" O MET L 544 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA L 549 " --> pdb=" O SER L 545 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER L 550 " --> pdb=" O GLN L 546 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER L 551 " --> pdb=" O LYS L 547 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU L 552 " --> pdb=" O SER L 548 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP L 554 " --> pdb=" O SER L 550 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU L 555 " --> pdb=" O SER L 551 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP L 557 " --> pdb=" O LEU L 553 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU L 558 " --> pdb=" O ASP L 554 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLU L 559 " --> pdb=" O LEU L 555 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE L 561 " --> pdb=" O TRP L 557 " (cutoff:3.500A) removed outlier: 5.379A 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: 4.839A pdb=" N LEU L 568 " --> pdb=" O LYS L 564 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA L 569 " --> pdb=" O THR L 565 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR L 575 " --> pdb=" O MET L 571 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU L 576 " --> pdb=" O LYS L 572 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 599 removed outlier: 3.667A pdb=" N LEU L 592 " --> pdb=" O PHE L 588 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE L 593 " --> pdb=" O LEU L 589 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE L 595 " --> pdb=" O PHE L 591 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 17 removed outlier: 3.582A pdb=" N THR M 8 " --> pdb=" O TYR M 4 " (cutoff:3.500A) removed outlier: 6.360A 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: 4.422A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix removed outlier: 4.103A pdb=" N TRP M 16 " --> pdb=" O MET M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 41 removed outlier: 3.842A pdb=" N SER M 31 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE M 34 " --> pdb=" O HIS M 30 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER M 38 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU M 40 " --> pdb=" O PHE M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 80 removed outlier: 3.511A pdb=" N LEU M 72 " --> pdb=" O THR M 69 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU M 73 " --> pdb=" O MET M 70 " (cutoff:3.500A) Proline residue: M 74 - end of helix removed outlier: 4.355A pdb=" N ALA M 79 " --> pdb=" O MET M 76 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER M 80 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 111 removed outlier: 3.865A pdb=" N LEU M 94 " --> pdb=" O ARG M 91 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE M 96 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 4.403A 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: 3.521A pdb=" N LEU M 106 " --> pdb=" O GLN M 103 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE M 107 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE M 110 " --> pdb=" O ILE M 107 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR M 111 " --> pdb=" O MET M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 136 removed outlier: 3.845A pdb=" N ILE M 120 " --> pdb=" O ILE M 116 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU M 121 " --> pdb=" O LEU M 117 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA M 124 " --> pdb=" O ILE M 120 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix removed outlier: 3.543A pdb=" N ILE M 131 " --> pdb=" O VAL M 127 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TRP M 136 " --> pdb=" O ILE M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 171 removed outlier: 5.182A pdb=" N TYR M 148 " --> pdb=" O ASN M 144 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU M 150 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR M 152 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA M 155 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY M 156 " --> pdb=" O TYR M 152 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 4.230A pdb=" N VAL M 162 " --> pdb=" O LEU M 158 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE M 165 " --> pdb=" O LEU M 161 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR M 166 " --> pdb=" O VAL M 162 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR M 170 " --> pdb=" O TYR M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.350A pdb=" N PHE M 194 " --> pdb=" O TRP M 190 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N MET M 195 " --> pdb=" O SER M 191 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL M 205 " --> pdb=" O MET M 201 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS M 206 " --> pdb=" O ALA M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 220 removed outlier: 3.902A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA M 219 " --> pdb=" O TRP M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 230 through 250 removed outlier: 3.515A pdb=" N LEU M 238 " --> pdb=" O VAL M 234 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TYR M 241 " --> pdb=" O LYS M 237 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY M 242 " --> pdb=" O LEU M 238 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N MET M 243 " --> pdb=" O GLY M 239 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU M 244 " --> pdb=" O GLY M 240 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG M 245 " --> pdb=" O TYR M 241 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR M 247 " --> pdb=" O MET M 243 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 277 removed outlier: 3.717A pdb=" N TYR M 259 " --> pdb=" O PHE M 256 " (cutoff:3.500A) Proline residue: M 260 - end of helix removed outlier: 3.816A pdb=" N LEU M 264 " --> pdb=" O PHE M 261 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TRP M 267 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET M 269 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE M 270 " --> pdb=" O TRP M 267 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N MET M 271 " --> pdb=" O GLY M 268 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR M 272 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER M 274 " --> pdb=" O MET M 271 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE M 275 " --> pdb=" O THR M 272 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS M 276 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU M 277 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.276A pdb=" N TYR M 288 " --> pdb=" O LEU M 285 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER M 290 " --> pdb=" O ALA M 287 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER M 292 " --> pdb=" O SER M 289 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS M 293 " --> pdb=" O SER M 290 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET M 294 " --> pdb=" O VAL M 291 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU M 296 " --> pdb=" O HIS M 293 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL M 299 " --> pdb=" O LEU M 296 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE M 301 " --> pdb=" O ILE M 298 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 337 removed outlier: 3.731A pdb=" N ALA M 314 " --> pdb=" O MET M 310 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE M 317 " --> pdb=" O THR M 313 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY M 320 " --> pdb=" O MET M 316 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU M 321 " --> pdb=" O ILE M 317 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER M 324 " --> pdb=" O GLY M 320 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET M 325 " --> pdb=" O LEU M 321 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN M 333 " --> pdb=" O LEU M 329 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 355 through 366 removed outlier: 3.871A pdb=" N ASN M 366 " --> pdb=" O ALA M 362 " (cutoff:3.500A) Processing helix chain 'M' and resid 373 through 388 removed outlier: 3.875A pdb=" N PHE M 380 " --> pdb=" O ILE M 376 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL M 381 " --> pdb=" O GLY M 377 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER M 387 " --> pdb=" O MET M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 392 through 415 removed outlier: 4.081A pdb=" N VAL M 398 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA M 404 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU M 405 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER M 407 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR M 409 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N MET M 410 " --> pdb=" O TYR M 406 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR M 414 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 449 removed outlier: 4.063A pdb=" N MET M 437 " --> pdb=" O GLU M 433 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 3.517A pdb=" N THR M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU M 449 " --> pdb=" O LEU M 445 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 21 removed outlier: 3.611A pdb=" N ILE N 9 " --> pdb=" O PHE N 6 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU N 10 " --> pdb=" O ILE N 7 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE N 13 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU N 15 " --> pdb=" O THR N 12 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR N 17 " --> pdb=" O MET N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 45 removed outlier: 3.668A pdb=" N TRP N 30 " --> pdb=" O TRP N 26 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN N 36 " --> pdb=" O GLY N 32 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA N 39 " --> pdb=" O MET N 35 " (cutoff:3.500A) removed outlier: 4.124A 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: 3.758A pdb=" N GLU N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN N 63 " --> pdb=" O TYR N 59 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR N 65 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ALA N 66 " --> pdb=" O THR N 62 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 105 removed outlier: 3.577A pdb=" N ALA N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET N 104 " --> pdb=" O MET N 100 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS N 105 " --> pdb=" O ALA N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 121 removed outlier: 5.178A pdb=" N HIS N 112 " --> pdb=" O ALA N 109 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE N 113 " --> pdb=" O PRO N 110 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP N 114 " --> pdb=" O PHE N 111 " (cutoff:3.500A) Proline residue: N 116 - end of helix removed outlier: 4.024A pdb=" N THR N 119 " --> pdb=" O PRO N 116 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN N 120 " --> pdb=" O GLU N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 144 removed outlier: 4.068A pdb=" N ILE N 129 " --> pdb=" O SER N 125 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU N 130 " --> pdb=" O SER N 126 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU N 131 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR N 132 " --> pdb=" O LEU N 128 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.840A pdb=" N VAL N 141 " --> pdb=" O ALA N 137 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 170 removed outlier: 4.042A pdb=" N THR N 156 " --> pdb=" O ASN N 152 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU N 157 " --> pdb=" O LEU N 153 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER N 161 " --> pdb=" O LEU N 157 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE N 162 " --> pdb=" O SER N 158 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 194 removed outlier: 3.620A pdb=" N ILE N 184 " --> pdb=" O ALA N 180 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET N 190 " --> pdb=" O HIS N 186 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA N 192 " --> pdb=" O GLY N 188 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 219 removed outlier: 3.558A pdb=" N ASN N 204 " --> pdb=" O THR N 201 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE N 207 " --> pdb=" O ASN N 204 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE N 209 " --> pdb=" O ILE N 206 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE N 210 " --> pdb=" O ILE N 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER N 213 " --> pdb=" O ILE N 210 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR N 214 " --> pdb=" O MET N 211 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE N 216 " --> pdb=" O SER N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.822A pdb=" N SER N 231 " --> pdb=" O THR N 227 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.450A 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: 4.451A pdb=" N VAL N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU N 243 " --> pdb=" O ILE N 239 " (cutoff:3.500A) removed outlier: 3.609A 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: 3.501A pdb=" N MET N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE N 266 " --> pdb=" O LYS N 263 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE N 267 " --> pdb=" O TRP N 264 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU N 269 " --> pdb=" O ILE N 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR N 271 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS N 272 " --> pdb=" O GLU N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 297 removed outlier: 3.752A pdb=" N PHE N 281 " --> pdb=" O ILE N 277 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR N 293 " --> pdb=" O ASN N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 323 through 332 removed outlier: 5.741A pdb=" N LEU N 326 " --> pdb=" O MET N 323 " (cutoff:3.500A) Proline residue: N 327 - end of helix removed outlier: 3.670A pdb=" N VAL N 331 " --> pdb=" O THR N 328 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU N 332 " --> pdb=" O MET N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 340 through 345 removed outlier: 4.115A pdb=" N VAL N 345 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 44 removed outlier: 4.583A pdb=" N UNK O 38 " --> pdb=" O UNK O 34 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N UNK O 39 " --> pdb=" O UNK O 35 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N UNK O 41 " --> pdb=" O UNK O 37 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N UNK O 42 " --> pdb=" O UNK O 38 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N UNK O 44 " --> pdb=" O UNK O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 116 removed outlier: 4.448A pdb=" N GLN O 97 " --> pdb=" O SER O 93 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP O 99 " --> pdb=" O ARG O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 62 removed outlier: 4.114A pdb=" N UNK O 61 " --> pdb=" O UNK O 57 " (cutoff:3.500A) removed outlier: 3.963A 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: 3.814A pdb=" N PHE O 134 " --> pdb=" O SER O 130 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET O 138 " --> pdb=" O PHE O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 162 removed outlier: 3.538A pdb=" N ASP O 150 " --> pdb=" O LYS O 146 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS O 151 " --> pdb=" O GLN O 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN O 154 " --> pdb=" O ASP O 150 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL O 158 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE O 160 " --> pdb=" O LYS O 156 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU O 162 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 178 through 185 removed outlier: 3.908A pdb=" N ARG O 182 " --> pdb=" O GLU O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 215 removed outlier: 3.680A pdb=" N LYS O 207 " --> pdb=" O GLU O 203 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY O 208 " --> pdb=" O ASN O 204 " (cutoff:3.500A) removed outlier: 3.792A 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 removed outlier: 3.504A pdb=" N ASP O 237 " --> pdb=" O LYS O 233 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE O 238 " --> pdb=" O VAL O 234 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU O 239 " --> pdb=" O VAL O 235 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 264 removed outlier: 4.090A pdb=" N HIS O 257 " --> pdb=" O ASP O 253 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS O 258 " --> pdb=" O ARG O 254 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU O 259 " --> pdb=" O ASN O 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET O 261 " --> pdb=" O HIS O 257 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 271 Processing helix chain 'O' and resid 286 through 298 removed outlier: 3.748A pdb=" N GLN O 291 " --> pdb=" O HIS O 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 40 removed outlier: 5.178A pdb=" N UNK P 33 " --> pdb=" O UNK P 29 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNK P 40 " --> pdb=" O UNK P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 61 removed outlier: 4.306A pdb=" N UNK P 60 " --> pdb=" O UNK P 56 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N UNK P 61 " --> pdb=" O UNK P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 85 removed outlier: 3.696A pdb=" N UNK P 85 " --> pdb=" O UNK P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 123 removed outlier: 3.896A pdb=" N UNK P 112 " --> pdb=" O UNK P 108 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N UNK P 113 " --> pdb=" O UNK P 109 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N UNK P 114 " --> pdb=" O UNK P 110 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N UNK P 115 " --> pdb=" O UNK P 111 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N UNK P 118 " --> pdb=" O UNK P 114 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N UNK P 123 " --> pdb=" O UNK P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 157 removed outlier: 5.551A pdb=" N UNK P 151 " --> pdb=" O UNK P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 219 removed outlier: 3.582A pdb=" N UNK P 211 " --> pdb=" O UNK P 207 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N UNK P 212 " --> pdb=" O UNK P 208 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 249 removed outlier: 3.566A pdb=" N UNK P 248 " --> pdb=" O UNK P 244 " (cutoff:3.500A) removed outlier: 3.543A 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: 5.186A pdb=" N UNK P 182 " --> pdb=" O UNK P 178 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N UNK P 183 " --> pdb=" O UNK P 179 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N UNK P 185 " --> pdb=" O UNK P 181 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N UNK P 186 " --> pdb=" O UNK P 182 " (cutoff:3.500A) Processing helix chain 'P' and resid 280 through 289 removed outlier: 3.808A pdb=" N UNK P 285 " --> pdb=" O UNK P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 312 through 319 removed outlier: 6.399A pdb=" N UNK P 316 " --> pdb=" O UNK P 312 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N UNK P 317 " --> pdb=" O UNK P 313 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 98 removed outlier: 3.751A pdb=" N UNK Q 93 " --> pdb=" O UNK Q 89 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N UNK Q 94 " --> pdb=" O UNK Q 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 removed outlier: 4.131A pdb=" N UNK R 45 " --> pdb=" O UNK R 41 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N UNK R 46 " --> pdb=" O UNK R 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 41 through 46' Processing helix chain 'S' and resid 30 through 45 removed outlier: 4.443A pdb=" N ASP S 34 " --> pdb=" O GLN S 30 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR S 40 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU S 42 " --> pdb=" O LYS S 38 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS S 45 " --> pdb=" O VAL S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 94 removed outlier: 3.525A pdb=" N GLU S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 21 removed outlier: 3.568A pdb=" N TYR T 17 " --> pdb=" O ASP T 13 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL T 18 " --> pdb=" O ARG T 14 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU T 21 " --> pdb=" O TYR T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 58 removed outlier: 4.815A pdb=" N VAL T 48 " --> pdb=" O SER T 44 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE T 50 " --> pdb=" O ASP T 46 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE T 51 " --> pdb=" O GLN T 47 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP T 56 " --> pdb=" O MET T 52 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU T 57 " --> pdb=" O ALA T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.022A pdb=" N GLU T 68 " --> pdb=" O ASP T 64 " (cutoff:3.500A) removed outlier: 4.527A 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: 3.882A pdb=" N ASP T 78 " --> pdb=" O GLN T 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 21 removed outlier: 3.630A pdb=" N LEU U 21 " --> pdb=" O TYR U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 57 removed outlier: 4.570A pdb=" N VAL U 48 " --> pdb=" O SER U 44 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU U 49 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE U 51 " --> pdb=" O GLN U 47 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP U 56 " --> pdb=" O MET U 52 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU U 57 " --> pdb=" O ALA U 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.567A pdb=" N GLU U 68 " --> pdb=" O ASP U 64 " (cutoff:3.500A) removed outlier: 4.820A 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 Processing helix chain 'V' and resid 21 through 35 removed outlier: 3.823A pdb=" N LEU V 26 " --> pdb=" O ARG V 22 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR V 27 " --> pdb=" O LEU V 23 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU V 31 " --> pdb=" O TYR V 27 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP V 32 " --> pdb=" O THR V 28 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY V 35 " --> pdb=" O LEU V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 removed outlier: 3.505A pdb=" N THR V 47 " --> pdb=" O TYR V 43 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN V 49 " --> pdb=" O LYS V 45 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE V 50 " --> pdb=" O TYR V 46 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU V 53 " --> pdb=" O GLN V 49 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET V 57 " --> pdb=" O GLU V 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 70 removed outlier: 3.988A pdb=" N GLU V 68 " --> pdb=" O VAL V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 95 removed outlier: 3.797A pdb=" N GLN V 82 " --> pdb=" O GLU V 78 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU V 87 " --> pdb=" O ALA V 83 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER V 88 " --> pdb=" O GLU V 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 46 removed outlier: 4.223A pdb=" N ARG W 29 " --> pdb=" O ASN W 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL W 31 " --> pdb=" O ALA W 27 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG W 32 " --> pdb=" O LYS W 28 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA W 37 " --> pdb=" O GLU W 33 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU W 41 " --> pdb=" O ALA W 37 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL W 42 " --> pdb=" O TRP W 38 " (cutoff:3.500A) Proline residue: W 43 - end of helix removed outlier: 4.222A pdb=" N VAL W 46 " --> pdb=" O VAL W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 69 removed outlier: 3.661A pdb=" N ASP W 60 " --> pdb=" O LYS W 56 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET W 65 " --> pdb=" O LYS W 61 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE W 66 " --> pdb=" O VAL W 62 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN W 69 " --> pdb=" O MET W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 93 removed outlier: 3.791A pdb=" N MET W 87 " --> pdb=" O ILE W 83 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU W 89 " --> pdb=" O GLY W 85 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLU W 90 " --> pdb=" O LYS W 86 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR W 92 " --> pdb=" O GLU W 88 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 100 through 103 removed outlier: 6.503A 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: 3.800A pdb=" N TYR W 122 " --> pdb=" O LEU W 118 " (cutoff:3.500A) Processing helix chain 'X' and resid 22 through 26 removed outlier: 4.885A pdb=" N LYS X 25 " --> pdb=" O SER X 22 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 47 removed outlier: 3.519A pdb=" N GLU X 41 " --> pdb=" O LYS X 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 76 removed outlier: 5.913A pdb=" N GLU X 57 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLU X 58 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU X 61 " --> pdb=" O GLU X 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL X 62 " --> pdb=" O GLU X 58 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU X 68 " --> pdb=" O GLN X 64 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE X 70 " --> pdb=" O ALA X 66 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN X 72 " --> pdb=" O GLU X 68 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE X 73 " --> pdb=" O PHE X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 91 removed outlier: 3.589A pdb=" N ASP X 89 " --> pdb=" O TRP X 85 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER X 91 " --> pdb=" O CYS X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 99 through 113 removed outlier: 3.513A pdb=" N ALA X 104 " --> pdb=" O ARG X 100 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN X 105 " --> pdb=" O LYS X 101 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE X 106 " --> pdb=" O GLN X 102 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP X 107 " --> pdb=" O GLN X 103 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU X 108 " --> pdb=" O ALA X 104 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N CYS X 109 " --> pdb=" O GLN X 105 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL X 110 " --> pdb=" O PHE X 106 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP X 112 " --> pdb=" O GLU X 108 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS X 113 " --> pdb=" O CYS X 109 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 12 removed outlier: 3.616A pdb=" N GLN Y 7 " --> pdb=" O THR Y 3 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR Y 8 " --> pdb=" O VAL Y 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP Y 9 " --> pdb=" O LEU Y 5 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP Y 10 " --> pdb=" O ARG Y 6 " (cutoff:3.500A) removed outlier: 4.006A 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: 4.279A pdb=" N TYR Y 22 " --> pdb=" O HIS Y 18 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR Y 25 " --> pdb=" O THR Y 21 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER Y 26 " --> pdb=" O TYR Y 22 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE Y 27 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL Y 35 " --> pdb=" O ALA Y 31 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL Y 40 " --> pdb=" O SER Y 36 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA Y 41 " --> pdb=" O ALA Y 37 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU Y 42 " --> pdb=" O TYR Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 78 removed outlier: 3.835A pdb=" N THR Y 55 " --> pdb=" O GLY Y 51 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG Y 57 " --> pdb=" O ALA Y 53 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR Y 58 " --> pdb=" O ARG Y 54 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR Y 61 " --> pdb=" O ARG Y 57 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY Y 66 " --> pdb=" O ALA Y 62 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N CYS Y 74 " --> pdb=" O GLY Y 70 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA Y 77 " --> pdb=" O SER Y 73 " (cutoff:3.500A) Processing helix chain 'Y' and resid 87 through 102 removed outlier: 3.644A pdb=" N ILE Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY Y 92 " --> pdb=" O ASN Y 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA Y 95 " --> pdb=" O ILE Y 91 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY Y 96 " --> pdb=" O GLY Y 92 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY Y 97 " --> pdb=" O GLY Y 93 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE Y 99 " --> pdb=" O ALA Y 95 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU Y 100 " --> pdb=" O GLY Y 96 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY Y 101 " --> pdb=" O GLY Y 97 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA Y 102 " --> pdb=" O LEU Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 110 through 125 removed outlier: 5.487A pdb=" N ALA Y 115 " --> pdb=" O ALA Y 111 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TYR Y 116 " --> pdb=" O ALA Y 112 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR Y 120 " --> pdb=" O TYR Y 116 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL Y 124 " --> pdb=" O THR Y 120 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS Y 125 " --> pdb=" O ALA Y 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 95 removed outlier: 3.807A pdb=" N PHE Z 35 " --> pdb=" O GLY Z 31 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA Z 36 " --> pdb=" O TYR Z 32 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL Z 37 " --> pdb=" O SER Z 33 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP Z 47 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS Z 51 " --> pdb=" O TRP Z 47 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TRP Z 52 " --> pdb=" O SER Z 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG Z 58 " --> pdb=" O ARG Z 54 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU Z 59 " --> pdb=" O GLU Z 55 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU Z 62 " --> pdb=" O ARG Z 58 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA Z 66 " --> pdb=" O GLU Z 62 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG Z 67 " --> pdb=" O ASP Z 63 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE Z 68 " --> pdb=" O PHE Z 64 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N MET Z 71 " --> pdb=" O ARG Z 67 " (cutoff:3.500A) Proline residue: Z 72 - end of helix removed outlier: 3.688A pdb=" N GLU Z 77 " --> pdb=" O LEU Z 73 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS Z 78 " --> pdb=" O LEU Z 74 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU Z 83 " --> pdb=" O ASP Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 135 Processing helix chain 'a' and resid 42 through 53 removed outlier: 3.580A pdb=" N LEU a 47 " --> pdb=" O TYR a 43 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET a 48 " --> pdb=" O GLN a 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 1 through 29 removed outlier: 4.334A pdb=" N VAL a 5 " --> pdb=" O MET a 1 " (cutoff:3.500A) Proline residue: a 7 - end of helix removed outlier: 3.935A pdb=" N MET a 12 " --> pdb=" O GLY a 8 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL a 14 " --> pdb=" O ALA a 10 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS a 15 " --> pdb=" O VAL a 11 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE a 17 " --> pdb=" O GLY a 13 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.669A pdb=" N THR a 23 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA a 24 " --> pdb=" O GLY a 20 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE a 26 " --> pdb=" O ALA a 22 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS a 27 " --> pdb=" O THR a 23 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N PHE a 29 " --> pdb=" O ARG a 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 13 removed outlier: 4.972A pdb=" N ALA b 6 " --> pdb=" O GLU b 2 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE b 7 " --> pdb=" O ARG b 3 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU b 8 " --> pdb=" O VAL b 4 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS b 9 " --> pdb=" O ALA b 5 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN b 10 " --> pdb=" O ALA b 6 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL b 11 " --> pdb=" O PHE b 7 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP b 12 " --> pdb=" O LEU b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 32 removed outlier: 4.307A pdb=" N ALA b 20 " --> pdb=" O PRO b 16 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE b 22 " --> pdb=" O LEU b 18 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL b 29 " --> pdb=" O ALA b 25 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE b 30 " --> pdb=" O GLY b 26 " (cutoff:3.500A) Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 46 removed outlier: 3.529A pdb=" N SER b 41 " --> pdb=" O THR b 38 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU b 42 " --> pdb=" O LYS b 39 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE b 44 " --> pdb=" O SER b 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 44 removed outlier: 3.867A pdb=" N LEU c 19 " --> pdb=" O LEU c 15 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER c 24 " --> pdb=" O THR c 20 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL c 25 " --> pdb=" O LEU c 21 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR c 30 " --> pdb=" O PHE c 26 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN c 34 " --> pdb=" O TYR c 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 48 removed outlier: 3.767A pdb=" N PHE d 33 " --> pdb=" O PRO d 29 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY d 42 " --> pdb=" O GLY d 38 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASN d 46 " --> pdb=" O GLY d 42 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA d 47 " --> pdb=" O LEU d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 60 through 97 removed outlier: 3.597A pdb=" N ILE d 65 " --> pdb=" O LEU d 62 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR d 66 " --> pdb=" O LEU d 63 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER d 67 " --> pdb=" O TYR d 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE d 68 " --> pdb=" O ILE d 65 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE d 70 " --> pdb=" O SER d 67 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL d 71 " --> pdb=" O PHE d 68 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR d 73 " --> pdb=" O PHE d 70 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU d 76 " --> pdb=" O TYR d 73 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS d 77 " --> pdb=" O TYR d 74 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP d 80 " --> pdb=" O LYS d 77 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR d 81 " --> pdb=" O ARG d 78 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET d 82 " --> pdb=" O GLN d 79 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR d 83 " --> pdb=" O ASP d 80 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL d 85 " --> pdb=" O MET d 82 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG d 86 " --> pdb=" O TYR d 83 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP d 89 " --> pdb=" O ARG d 86 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE d 91 " --> pdb=" O HIS d 88 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER d 92 " --> pdb=" O ASP d 89 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE d 94 " --> pdb=" O PHE d 91 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS d 95 " --> pdb=" O SER d 92 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER d 96 " --> pdb=" O TYR d 93 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS d 97 " --> pdb=" O ILE d 94 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 43 removed outlier: 4.187A pdb=" N GLU e 38 " --> pdb=" O ALA e 34 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP e 39 " --> pdb=" O PHE e 35 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE e 40 " --> pdb=" O GLU e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 67 removed outlier: 3.513A pdb=" N GLU e 58 " --> pdb=" O CYS e 55 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE e 59 " --> pdb=" O LYS e 56 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU e 60 " --> pdb=" O ILE e 57 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP e 61 " --> pdb=" O GLU e 58 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU e 66 " --> pdb=" O ARG e 63 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU e 67 " --> pdb=" O GLU e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 84 removed outlier: 3.861A pdb=" N ARG e 74 " --> pdb=" O LYS e 70 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA e 77 " --> pdb=" O LYS e 73 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE e 78 " --> pdb=" O ARG e 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 33 removed outlier: 4.205A pdb=" N VAL f 16 " --> pdb=" O VAL f 12 " (cutoff:3.500A) Proline residue: f 17 - end of helix removed outlier: 4.012A pdb=" N ASN f 30 " --> pdb=" O LEU f 26 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP f 31 " --> pdb=" O ASP f 27 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLU f 32 " --> pdb=" O ARG f 28 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS f 33 " --> pdb=" O LYS f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 4 through 9 removed outlier: 3.982A pdb=" N VAL f 7 " --> pdb=" O LEU f 4 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG f 8 " --> pdb=" O GLN f 5 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP f 9 " --> pdb=" O VAL f 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 4 through 9' Processing helix chain 'g' and resid 51 through 74 removed outlier: 3.571A pdb=" N ILE g 55 " --> pdb=" O PRO g 51 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP g 56 " --> pdb=" O ALA g 52 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG g 59 " --> pdb=" O ILE g 55 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL g 60 " --> pdb=" O TRP g 56 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N PHE g 62 " --> pdb=" O MET g 58 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE g 63 " --> pdb=" O ARG g 59 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY g 65 " --> pdb=" O VAL g 61 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE g 66 " --> pdb=" O PHE g 62 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU g 70 " --> pdb=" O PHE g 66 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL g 71 " --> pdb=" O SER g 67 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY g 73 " --> pdb=" O VAL g 69 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER g 74 " --> pdb=" O LEU g 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 86 through 103 removed outlier: 4.247A pdb=" N ARG g 90 " --> pdb=" O GLN g 86 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG g 91 " --> pdb=" O GLU g 87 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG g 95 " --> pdb=" O ARG g 91 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU g 96 " --> pdb=" O GLU g 92 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS g 98 " --> pdb=" O GLU g 94 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR g 99 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA g 102 " --> pdb=" O LYS g 98 " (cutoff:3.500A) Processing helix chain 'h' and resid 17 through 43 removed outlier: 3.711A pdb=" N PHE h 21 " --> pdb=" O TYR h 17 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU h 22 " --> pdb=" O ASP h 18 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR h 28 " --> pdb=" O LEU h 24 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR h 32 " --> pdb=" O TYR h 28 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE h 34 " --> pdb=" O LEU h 30 " (cutoff:3.500A) Proline residue: h 35 - end of helix removed outlier: 3.719A pdb=" N THR h 41 " --> pdb=" O ALA h 37 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE h 43 " --> pdb=" O GLY h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 70 through 78 removed outlier: 3.607A pdb=" N UNK h 74 " --> pdb=" O UNK h 70 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N UNK h 78 " --> pdb=" O UNK h 74 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 116 removed outlier: 3.707A pdb=" N UNK h 88 " --> pdb=" O UNK h 84 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N UNK h 91 " --> pdb=" O UNK h 87 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N UNK h 99 " --> pdb=" O UNK h 95 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N UNK h 100 " --> pdb=" O UNK h 96 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N UNK h 108 " --> pdb=" O UNK h 104 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N UNK h 109 " --> pdb=" O UNK h 105 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N UNK h 112 " --> pdb=" O UNK h 108 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N UNK h 116 " --> pdb=" O UNK h 112 " (cutoff:3.500A) Processing helix chain 'i' and resid 6 through 23 removed outlier: 5.906A pdb=" N ARG i 10 " --> pdb=" O GLU i 6 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU i 11 " --> pdb=" O GLU i 7 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN i 13 " --> pdb=" O LEU i 9 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU i 16 " --> pdb=" O GLN i 12 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU i 17 " --> pdb=" O GLN i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 42 through 51 removed outlier: 3.651A pdb=" N UNK i 48 " --> pdb=" O UNK i 44 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N UNK i 51 " --> pdb=" O UNK i 47 " (cutoff:3.500A) Processing helix chain 'i' and resid 57 through 86 removed outlier: 3.547A pdb=" N UNK i 61 " --> pdb=" O UNK i 57 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N UNK i 62 " --> pdb=" O UNK i 58 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N UNK i 64 " --> pdb=" O UNK i 60 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N UNK i 69 " --> pdb=" O UNK i 65 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N UNK i 70 " --> pdb=" O UNK i 66 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N UNK i 72 " --> pdb=" O UNK i 68 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N UNK i 75 " --> pdb=" O UNK i 71 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N UNK i 76 " --> pdb=" O UNK i 72 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N UNK i 77 " --> pdb=" O UNK i 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N UNK i 80 " --> pdb=" O UNK i 76 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N UNK i 83 " --> pdb=" O UNK i 79 " (cutoff:3.500A) Processing helix chain 'j' and resid 19 through 40 removed outlier: 3.672A pdb=" N UNK j 27 " --> pdb=" O UNK j 23 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N UNK j 28 " --> pdb=" O UNK j 24 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N UNK j 31 " --> pdb=" O UNK j 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N UNK j 33 " --> pdb=" O UNK j 29 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N UNK j 36 " --> pdb=" O UNK j 32 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N UNK j 39 " --> pdb=" O UNK j 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 15 through 21 removed outlier: 5.533A pdb=" N UNK k 19 " --> pdb=" O UNK k 15 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 72 removed outlier: 4.021A pdb=" N UNK k 59 " --> pdb=" O UNK k 55 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N UNK k 69 " --> pdb=" O UNK k 65 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N UNK k 72 " --> pdb=" O UNK k 68 " (cutoff:3.500A) Processing helix chain 'l' and resid 17 through 25 removed outlier: 3.890A pdb=" N UNK l 21 " --> pdb=" O UNK l 17 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N UNK l 22 " --> pdb=" O UNK l 18 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N UNK l 24 " --> pdb=" O UNK l 20 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N UNK l 25 " --> pdb=" O UNK l 21 " (cutoff:3.500A) Processing helix chain 'l' and resid 98 through 118 removed outlier: 3.708A pdb=" N UNK l 102 " --> pdb=" O UNK l 98 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N UNK l 103 " --> pdb=" O UNK l 99 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N UNK l 109 " --> pdb=" O UNK l 105 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N UNK l 112 " --> pdb=" O UNK l 108 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N UNK l 115 " --> pdb=" O UNK l 111 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N UNK l 116 " --> pdb=" O UNK l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 49 removed outlier: 3.536A pdb=" N UNK m 30 " --> pdb=" O UNK m 26 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA m 33 " --> pdb=" O UNK m 29 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE m 38 " --> pdb=" O GLU m 34 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU m 45 " --> pdb=" O ARG m 41 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR m 46 " --> pdb=" O LEU m 42 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 63 through 72 removed outlier: 4.085A pdb=" N ARG m 71 " --> pdb=" O TRP m 67 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 116 removed outlier: 3.528A pdb=" N LEU m 91 " --> pdb=" O LEU m 87 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY m 95 " --> pdb=" O LEU m 91 " (cutoff:3.500A) Proline residue: m 96 - end of helix removed outlier: 3.909A pdb=" N TYR m 102 " --> pdb=" O VAL m 98 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL m 103 " --> pdb=" O PHE m 99 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS m 105 " --> pdb=" O TYR m 101 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR m 106 " --> pdb=" O TYR m 102 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP m 107 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS m 113 " --> pdb=" O ASP m 109 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU m 114 " --> pdb=" O ARG m 110 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE m 115 " --> pdb=" O LYS m 111 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN m 116 " --> pdb=" O GLU m 112 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 29 removed outlier: 3.605A pdb=" N ARG n 24 " --> pdb=" O LYS n 20 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU n 27 " --> pdb=" O LEU n 23 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER n 28 " --> pdb=" O ARG n 24 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP n 29 " --> pdb=" O HIS n 25 " (cutoff:3.500A) Processing helix chain 'n' and resid 34 through 53 removed outlier: 3.699A pdb=" N CYS n 41 " --> pdb=" O ARG n 37 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU n 42 " --> pdb=" O TYR n 38 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG n 46 " --> pdb=" O LEU n 42 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU n 49 " --> pdb=" O ALA n 45 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN n 52 " --> pdb=" O ASP n 48 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLU n 53 " --> pdb=" O GLU n 49 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 72 removed outlier: 4.532A pdb=" N THR n 60 " --> pdb=" O MET n 56 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU n 67 " --> pdb=" O LEU n 63 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU n 68 " --> pdb=" O ARG n 64 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLU n 69 " --> pdb=" O GLU n 65 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) removed outlier: 6.199A 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: 3.662A pdb=" N ARG n 121 " --> pdb=" O TYR n 117 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 58 through 71 removed outlier: 3.596A pdb=" N ILE o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG o 64 " --> pdb=" O HIS o 60 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE o 65 " --> pdb=" O TYR o 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU o 66 " --> pdb=" O LEU o 62 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS o 69 " --> pdb=" O PHE o 65 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 113 removed outlier: 3.782A pdb=" N ASP o 85 " --> pdb=" O HIS o 81 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TRP o 86 " --> pdb=" O GLU o 82 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU o 90 " --> pdb=" O TRP o 86 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL o 95 " --> pdb=" O HIS o 91 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG o 113 " --> pdb=" O GLN o 109 " (cutoff:3.500A) Processing helix chain 'p' and resid 29 through 55 removed outlier: 3.821A pdb=" N UNK p 38 " --> pdb=" O UNK p 34 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N UNK p 41 " --> pdb=" O UNK p 37 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N UNK p 42 " --> pdb=" O UNK p 38 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N UNK p 43 " --> pdb=" O UNK p 39 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N UNK p 44 " --> pdb=" O UNK p 40 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N UNK p 55 " --> pdb=" O UNK p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 116 removed outlier: 3.643A pdb=" N ALA p 87 " --> pdb=" O CYS p 83 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP p 91 " --> pdb=" O ALA p 87 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU p 100 " --> pdb=" O LYS p 96 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN p 103 " --> pdb=" O GLN p 99 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS p 112 " --> pdb=" O ARG p 108 " (cutoff:3.500A) Processing helix chain 'p' and resid 126 through 139 removed outlier: 3.523A pdb=" N VAL p 134 " --> pdb=" O GLN p 130 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS p 136 " --> pdb=" O THR p 132 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA p 137 " --> pdb=" O GLN p 133 " (cutoff:3.500A) Processing helix chain 'p' and resid 153 through 172 removed outlier: 3.600A pdb=" N UNK p 158 " --> pdb=" O UNK p 155 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N UNK p 160 " --> pdb=" O UNK p 157 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N UNK p 161 " --> pdb=" O UNK p 158 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N UNK p 163 " --> pdb=" O UNK p 160 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N UNK p 164 " --> pdb=" O UNK p 161 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N UNK p 165 " --> pdb=" O UNK p 162 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N UNK p 166 " --> pdb=" O UNK p 163 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N UNK p 167 " --> pdb=" O UNK p 164 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N UNK p 168 " --> pdb=" O UNK p 165 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N UNK p 169 " --> pdb=" O UNK p 166 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N UNK p 170 " --> pdb=" O UNK p 167 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N UNK p 171 " --> pdb=" O UNK p 168 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N UNK p 172 " --> pdb=" O UNK p 169 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 16 removed outlier: 3.583A pdb=" N LEU q 7 " --> pdb=" O LEU q 3 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY q 10 " --> pdb=" O VAL q 6 " (cutoff:3.500A) Processing helix chain 'q' and resid 21 through 27 Processing helix chain 'r' and resid 5 through 14 removed outlier: 3.917A pdb=" N UNK r 9 " --> pdb=" O UNK r 5 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N UNK r 10 " --> pdb=" O UNK r 6 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N UNK r 13 " --> pdb=" O UNK r 9 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N UNK r 14 " --> pdb=" O UNK r 10 " (cutoff:3.500A) Processing helix chain 's' and resid 11 through 20 removed outlier: 4.029A pdb=" N UNK s 15 " --> pdb=" O UNK s 11 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N UNK s 17 " --> pdb=" O UNK s 13 " (cutoff:3.500A) removed outlier: 3.532A 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: 4.345A pdb=" N ILE B 87 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE B 50 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA B 89 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY B 90 " --> pdb=" O MET B 116 " (cutoff:3.500A) removed outlier: 3.520A 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: 3.770A pdb=" N SER C 74 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 76 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE C 92 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER C 103 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C 47 " --> pdb=" O CYS C 44 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL C 40 " --> pdb=" O CYS C 51 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLN C 39 " --> pdb=" O UNK r 69 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N UNK r 69 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 4.604A 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 51 removed outlier: 3.819A pdb=" N LEU D 49 " --> pdb=" O MET D 66 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET D 66 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE D 51 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU D 64 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG D 63 " --> pdb=" O HIS D 79 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N HIS D 79 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.560A 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: 3.721A pdb=" N GLY D 361 " --> pdb=" O SER D 380 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER D 380 " --> pdb=" O GLY D 361 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE D 367 " --> pdb=" O PHE D 374 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 374 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 375 " --> pdb=" O LYS D 392 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS D 390 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 379 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 5.143A 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: 3.755A pdb=" N THR E 138 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE E 140 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E 102 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N MET E 153 " --> pdb=" O CYS E 103 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE E 156 " --> pdb=" O ASN E 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 174 through 179 removed outlier: 4.210A pdb=" N THR F 221 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL F 94 " --> pdb=" O THR F 221 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 265 through 269 removed outlier: 3.617A pdb=" N ILE F 258 " --> pdb=" O CYS F 266 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE F 256 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL F 336 " --> pdb=" O SER F 259 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA F 333 " --> pdb=" O GLY F 300 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY F 300 " --> pdb=" O ALA F 333 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE F 335 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE F 298 " --> pdb=" O ILE F 335 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N MET F 337 " --> pdb=" O ALA F 296 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA F 296 " --> pdb=" O MET F 337 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL F 297 " --> pdb=" O ILE F 307 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.566A pdb=" N GLN G 16 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 20 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N TRP G 77 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE G 12 " --> pdb=" O TRP G 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 223 through 227 removed outlier: 6.264A pdb=" N UNK G 223 " --> pdb=" O UNK G 242 " (cutoff:3.500A) removed outlier: 4.464A 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: 6.602A pdb=" N UNK G 422 " --> pdb=" O UNK G 406 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N UNK G 408 " --> pdb=" O UNK G 422 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N UNK G 407 " --> pdb=" O UNK G 378 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N UNK G 380 " --> pdb=" O UNK G 407 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N UNK G 450 " --> pdb=" O UNK G 377 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N UNK G 379 " --> pdb=" O UNK G 450 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N UNK G 452 " --> pdb=" O UNK G 379 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N UNK G 381 " --> pdb=" O UNK G 452 " (cutoff:3.500A) removed outlier: 4.726A 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: 5.059A pdb=" N ALA G 207 " --> pdb=" O ILE G 149 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR G 209 " --> pdb=" O LYS G 147 " (cutoff:3.500A) removed outlier: 9.916A pdb=" N VAL G 146 " --> pdb=" O LYS G 140 " (cutoff:3.500A) removed outlier: 8.881A 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: 3.680A pdb=" N UNK G 292 " --> pdb=" O UNK G 284 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N UNK G 284 " --> pdb=" O UNK G 292 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N UNK G 294 " --> pdb=" O UNK G 282 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N UNK G 282 " --> pdb=" O UNK G 294 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N UNK G 558 " --> pdb=" O UNK G 285 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N UNK G 545 " --> pdb=" O UNK G 558 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N UNK G 560 " --> pdb=" O UNK G 545 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N UNK G 547 " --> pdb=" O UNK G 560 " (cutoff:3.500A) removed outlier: 6.129A 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: 4.056A pdb=" N UNK G 316 " --> pdb=" O UNK G 525 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N UNK G 527 " --> pdb=" O UNK G 316 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N UNK G 529 " --> pdb=" O UNK G 318 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N UNK G 342 " --> pdb=" O UNK G 315 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N UNK G 317 " --> pdb=" O UNK G 342 " (cutoff:3.500A) removed outlier: 3.652A 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: 4.518A pdb=" N ALA I 66 " --> pdb=" O VAL I 132 " (cutoff:3.500A) 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 removed outlier: 6.510A pdb=" N LEU L 78 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER L 64 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET L 82 " --> pdb=" O GLU L 60 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLU L 60 " --> pdb=" O MET L 82 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLN L 59 " --> pdb=" O UNK i 98 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N UNK i 98 " --> pdb=" O GLN L 59 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU L 61 " --> pdb=" O UNK i 96 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N UNK i 96 " --> pdb=" O LEU L 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 219 through 224 removed outlier: 3.774A pdb=" N VAL O 172 " --> pdb=" O LEU O 221 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL O 174 " --> pdb=" O TYR O 223 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP O 173 " --> pdb=" O UNK O 28 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL O 122 " --> pdb=" O UNK O 23 " (cutoff:3.500A) removed outlier: 4.551A 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: 4.912A pdb=" N UNK P 45 " --> pdb=" O UNK P 67 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N UNK P 69 " --> pdb=" O UNK P 45 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N UNK P 21 " --> pdb=" O UNK P 44 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N UNK P 46 " --> pdb=" O UNK P 21 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N UNK P 23 " --> pdb=" O UNK P 46 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N UNK P 25 " --> pdb=" O UNK P 48 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N UNK P 90 " --> pdb=" O UNK P 20 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N UNK P 22 " --> pdb=" O UNK P 90 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N UNK P 24 " --> pdb=" O UNK P 92 " (cutoff:3.500A) removed outlier: 4.407A 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: 3.526A pdb=" N UNK P 164 " --> pdb=" O UNK P 129 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N UNK P 131 " --> pdb=" O UNK P 164 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N UNK P 165 " --> pdb=" O UNK P 226 " (cutoff:3.500A) removed outlier: 3.700A 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: 3.566A pdb=" N UNK Q 104 " --> pdb=" O UNK Q 35 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N UNK Q 37 " --> pdb=" O UNK Q 104 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N UNK Q 106 " --> pdb=" O UNK Q 37 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N UNK Q 39 " --> pdb=" O UNK Q 106 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N UNK Q 36 " --> pdb=" O UNK Q 58 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N UNK Q 58 " --> pdb=" O UNK Q 36 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N UNK Q 56 " --> pdb=" O UNK Q 38 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N UNK Q 57 " --> pdb=" O UNK Q 84 " (cutoff:3.500A) removed outlier: 4.399A 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: 5.903A pdb=" N UNK R 55 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 4.214A 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: 4.800A pdb=" N GLY R 82 " --> pdb=" O PHE R 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 52 through 55 removed outlier: 5.702A pdb=" N ILE S 18 " --> pdb=" O LEU S 53 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ARG S 55 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE S 20 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU S 17 " --> pdb=" O ARG S 67 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG S 19 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS S 21 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS S 63 " --> pdb=" O HIS S 21 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'q' and resid 39 through 42 removed outlier: 3.757A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TYR q 48 " --> pdb=" O GLY q 40 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP q 42 " --> pdb=" O ASN q 46 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN q 46 " --> pdb=" O ASP q 42 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N GLY q 45 " --> pdb=" O TYR q 64 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR q 64 " --> pdb=" O GLY q 45 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS q 47 " --> pdb=" O VAL q 62 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL q 62 " --> pdb=" O LYS q 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 1742 hydrogen bonds defined for protein. 4659 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: 13.30 Time building geometry restraints manager: 11.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 21360 1.43 - 1.65: 30681 1.65 - 1.87: 510 1.87 - 2.09: 0 2.09 - 2.30: 80 Bond restraints: 52631 Sorted by residual: bond pdb=" C LYS D 29 " pdb=" N PRO D 30 " ideal model delta sigma weight residual 1.331 1.390 -0.058 8.70e-03 1.32e+04 4.50e+01 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 3.66e+01 bond pdb=" C5A FMN F 501 " pdb=" C9A FMN F 501 " ideal model delta sigma weight residual 1.390 1.504 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C7 FMN F 501 " pdb=" C8 FMN F 501 " ideal model delta sigma weight residual 1.390 1.503 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C GLU V 105 " pdb=" N PRO V 106 " ideal model delta sigma weight residual 1.329 1.393 -0.063 1.18e-02 7.18e+03 2.88e+01 ... (remaining 52626 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.30: 72207 12.30 - 24.61: 53 24.61 - 36.91: 0 36.91 - 49.21: 0 49.21 - 61.51: 2 Bond angle restraints: 72262 Sorted by residual: angle pdb=" O ARG i 30 " pdb=" C ARG i 30 " pdb=" N GLU i 31 " ideal model delta sigma weight residual 122.41 60.90 61.51 1.60e+00 3.91e-01 1.48e+03 angle pdb=" CA ARG i 30 " pdb=" C ARG i 30 " pdb=" N GLU i 31 " ideal model delta sigma weight residual 118.59 179.99 -61.40 1.63e+00 3.76e-01 1.42e+03 angle pdb=" N ARG i 30 " pdb=" CA ARG i 30 " pdb=" C ARG i 30 " ideal model delta sigma weight residual 113.19 99.32 13.87 1.19e+00 7.06e-01 1.36e+02 angle pdb=" O ALA H 216 " pdb=" C ALA H 216 " pdb=" N ALA H 217 " ideal model delta sigma weight residual 122.59 136.47 -13.88 1.33e+00 5.65e-01 1.09e+02 angle pdb=" N VAL D 36 " pdb=" CA VAL D 36 " pdb=" C VAL D 36 " ideal model delta sigma weight residual 110.21 121.36 -11.15 1.13e+00 7.83e-01 9.74e+01 ... (remaining 72257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.99: 30756 33.99 - 67.98: 639 67.98 - 101.97: 24 101.97 - 135.96: 0 135.96 - 169.94: 1 Dihedral angle restraints: 31420 sinusoidal: 8313 harmonic: 23107 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 -132.80 -47.20 0 5.00e+00 4.00e-02 8.91e+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 93.00 161.34 -68.34 1 1.00e+01 1.00e-02 6.06e+01 dihedral pdb=" CB CYS p 76 " pdb=" SG CYS p 76 " pdb=" SG CYS p 83 " pdb=" CB CYS p 83 " ideal model delta sinusoidal sigma weight residual 93.00 153.46 -60.46 1 1.00e+01 1.00e-02 4.87e+01 ... (remaining 31417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.260: 8839 4.260 - 8.520: 0 8.520 - 12.780: 0 12.780 - 17.040: 0 17.040 - 21.300: 24 Chirality restraints: 8863 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 -10.75 21.30 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 10.73 -21.28 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 10.72 -21.27 2.00e-01 2.50e+01 1.13e+04 ... (remaining 8860 not shown) Planarity restraints: 9468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 16 " -0.122 5.00e-02 4.00e+02 1.72e-01 4.73e+01 pdb=" N PRO E 17 " 0.297 5.00e-02 4.00e+02 pdb=" CA PRO E 17 " -0.097 5.00e-02 4.00e+02 pdb=" CD PRO E 17 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN e 24 " -0.116 5.00e-02 4.00e+02 1.62e-01 4.21e+01 pdb=" N PRO e 25 " 0.280 5.00e-02 4.00e+02 pdb=" CA PRO e 25 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO e 25 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN g 41 " 0.115 5.00e-02 4.00e+02 1.60e-01 4.12e+01 pdb=" N PRO g 42 " -0.277 5.00e-02 4.00e+02 pdb=" CA PRO g 42 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO g 42 " 0.075 5.00e-02 4.00e+02 ... (remaining 9465 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 14 2.25 - 2.91: 18707 2.91 - 3.57: 69724 3.57 - 4.24: 106271 4.24 - 4.90: 180571 Nonbonded interactions: 375287 Sorted by model distance: nonbonded pdb=" CD PRO D 6 " pdb=" OG1 THR N 303 " model vdw 1.587 3.440 nonbonded pdb=" O ALA E 46 " pdb=" CD PRO E 49 " model vdw 1.738 3.440 nonbonded pdb=" CG PRO D 31 " pdb=" NE2 GLN N 174 " model vdw 1.752 3.520 nonbonded pdb=" O GLU V 17 " pdb=" CD PRO V 19 " model vdw 1.925 3.440 nonbonded pdb=" O ASN E 15 " pdb=" CD PRO E 17 " model vdw 1.981 3.440 ... (remaining 375282 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: 3.050 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: 0.030 Extract box with map and model: 1.460 Check model and map are aligned: 0.310 Set scattering table: 0.360 Process input model: 96.980 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.220 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:2.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 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 52631 Z= 0.566 Angle : 1.472 61.514 72262 Z= 0.923 Chirality : 1.107 21.300 8863 Planarity : 0.008 0.172 9461 Dihedral : 14.694 169.944 16278 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 3.68 % Allowed : 8.63 % Favored : 87.69 % Rotamer: Outliers : 3.67 % Allowed : 8.52 % Favored : 87.81 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 0.33 % 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: -4.81 (0.08), residues: 5840 helix: -3.31 (0.06), residues: 2975 sheet: -1.02 (0.42), residues: 158 loop : -3.13 (0.10), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 68 HIS 0.006 0.001 HIS R 68 PHE 0.015 0.001 PHE J 57 TYR 0.015 0.001 TYR M 406 ARG 0.003 0.000 ARG L 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1711 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1579 time to evaluate : 4.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9248 (mt) cc_final: 0.8848 (mt) REVERT: A 93 PHE cc_start: 0.8722 (t80) cc_final: 0.8077 (t80) REVERT: B 59 MET cc_start: 0.8464 (tmm) cc_final: 0.8243 (tmm) REVERT: B 60 MET cc_start: 0.7749 (mtt) cc_final: 0.7485 (mtp) REVERT: B 67 TYR cc_start: 0.7856 (m-80) cc_final: 0.6741 (m-80) REVERT: B 85 VAL cc_start: 0.9471 (t) cc_final: 0.9201 (p) REVERT: B 116 MET cc_start: 0.8674 (ttp) cc_final: 0.8468 (ttp) REVERT: B 131 SER cc_start: 0.9114 (p) cc_final: 0.8658 (m) REVERT: B 143 ASP cc_start: 0.8713 (m-30) cc_final: 0.8423 (t0) REVERT: B 150 PRO cc_start: 0.9159 (Cg_exo) cc_final: 0.8750 (Cg_endo) REVERT: C 58 ILE cc_start: 0.9318 (mt) cc_final: 0.8955 (tt) REVERT: C 73 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7855 (ttmt) REVERT: C 92 ILE cc_start: 0.8534 (mt) cc_final: 0.8164 (mm) REVERT: C 108 LYS cc_start: 0.8293 (mttt) cc_final: 0.8078 (mtmm) REVERT: C 124 TYR cc_start: 0.6668 (t80) cc_final: 0.6375 (t80) REVERT: C 131 GLU cc_start: 0.8959 (mt-10) cc_final: 0.7984 (mt-10) REVERT: C 133 GLU cc_start: 0.8374 (tt0) cc_final: 0.7905 (tm-30) REVERT: C 134 ILE cc_start: 0.9120 (mt) cc_final: 0.8903 (mm) REVERT: C 152 LEU cc_start: 0.8799 (mt) cc_final: 0.8573 (mt) REVERT: C 173 GLU cc_start: 0.7462 (pm20) cc_final: 0.6629 (pm20) REVERT: C 174 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8010 (tp) REVERT: C 196 LYS cc_start: 0.8616 (tmmm) cc_final: 0.7827 (pttp) REVERT: D 82 LEU cc_start: 0.8131 (mt) cc_final: 0.7827 (mm) REVERT: D 97 LEU cc_start: 0.9296 (tt) cc_final: 0.9009 (tt) REVERT: D 156 THR cc_start: 0.9002 (p) cc_final: 0.8401 (t) REVERT: D 169 TRP cc_start: 0.8439 (m100) cc_final: 0.8111 (m100) REVERT: D 189 MET cc_start: 0.8449 (mtp) cc_final: 0.8103 (mtp) REVERT: D 259 MET cc_start: 0.6966 (mmm) cc_final: 0.6093 (mmp) REVERT: D 277 VAL cc_start: 0.8053 (t) cc_final: 0.7717 (p) REVERT: D 304 MET cc_start: 0.8941 (mmm) cc_final: 0.8220 (tpp) REVERT: D 311 ILE cc_start: 0.9545 (mt) cc_final: 0.9157 (tt) REVERT: D 323 ILE cc_start: 0.8968 (mm) cc_final: 0.8639 (pt) REVERT: D 338 MET cc_start: 0.9028 (ptm) cc_final: 0.8715 (ppp) REVERT: F 366 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.6794 (mtm110) REVERT: F 370 ASP cc_start: 0.8401 (m-30) cc_final: 0.7994 (p0) REVERT: F 383 ASP cc_start: 0.7335 (m-30) cc_final: 0.6947 (m-30) REVERT: F 390 ASP cc_start: 0.8029 (t70) cc_final: 0.7380 (t70) REVERT: F 394 GLU cc_start: 0.8083 (mt-10) cc_final: 0.6665 (tp30) REVERT: F 395 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8036 (tt) REVERT: F 409 ASP cc_start: 0.8301 (m-30) cc_final: 0.6356 (m-30) REVERT: F 415 VAL cc_start: 0.9377 (t) cc_final: 0.8938 (p) REVERT: G 88 LYS cc_start: 0.9187 (mttt) cc_final: 0.8834 (mtmm) REVERT: G 121 MET cc_start: 0.8705 (tpt) cc_final: 0.8496 (tpp) REVERT: H 22 LEU cc_start: 0.9095 (mt) cc_final: 0.8809 (mt) REVERT: H 24 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8397 (mt-10) REVERT: H 31 MET cc_start: 0.9250 (mmm) cc_final: 0.8955 (tpp) REVERT: H 183 MET cc_start: 0.7979 (mmt) cc_final: 0.7565 (tpt) REVERT: H 230 ASN cc_start: 0.8625 (m-40) cc_final: 0.8244 (m-40) REVERT: H 234 MET cc_start: 0.8396 (mmt) cc_final: 0.8078 (mmp) REVERT: H 253 GLU cc_start: 0.6684 (mt-10) cc_final: 0.4400 (tt0) REVERT: H 291 LYS cc_start: 0.7338 (tptm) cc_final: 0.6978 (tttm) REVERT: H 301 CYS cc_start: 0.8125 (t) cc_final: 0.7839 (t) REVERT: H 303 TRP cc_start: 0.8460 (t-100) cc_final: 0.8194 (t-100) REVERT: H 304 HIS cc_start: 0.8349 (m-70) cc_final: 0.8007 (m90) REVERT: I 19 ASP cc_start: 0.7792 (p0) cc_final: 0.7509 (t70) REVERT: I 26 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6728 (pt) REVERT: I 32 ARG cc_start: 0.7375 (ttt-90) cc_final: 0.6540 (tpp-160) REVERT: I 128 VAL cc_start: 0.9381 (OUTLIER) cc_final: 0.8944 (t) REVERT: I 140 SER cc_start: 0.7934 (p) cc_final: 0.7611 (m) REVERT: I 144 HIS cc_start: 0.6676 (m-70) cc_final: 0.5476 (p-80) REVERT: J 47 PHE cc_start: 0.7100 (m-80) cc_final: 0.6899 (m-80) REVERT: J 99 MET cc_start: 0.7713 (mmm) cc_final: 0.7450 (tpt) REVERT: J 154 VAL cc_start: 0.9461 (t) cc_final: 0.8918 (p) REVERT: K 5 TYR cc_start: 0.7691 (m-80) cc_final: 0.7471 (m-80) REVERT: K 25 HIS cc_start: 0.7621 (m-70) cc_final: 0.7104 (m170) REVERT: K 30 LEU cc_start: 0.8935 (mt) cc_final: 0.8074 (mp) REVERT: K 55 LEU cc_start: 0.7934 (mt) cc_final: 0.7654 (tp) REVERT: K 59 MET cc_start: 0.7896 (mmp) cc_final: 0.7350 (mmp) REVERT: K 66 PHE cc_start: 0.8652 (m-80) cc_final: 0.7732 (m-10) REVERT: K 69 CYS cc_start: 0.8880 (m) cc_final: 0.8519 (t) REVERT: K 78 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7322 (tt) REVERT: K 79 VAL cc_start: 0.9274 (t) cc_final: 0.9043 (t) REVERT: L 101 MET cc_start: 0.8337 (mmm) cc_final: 0.7589 (mmm) REVERT: L 102 GLU cc_start: 0.8119 (pt0) cc_final: 0.6668 (tm-30) REVERT: L 103 PHE cc_start: 0.7845 (m-80) cc_final: 0.7534 (m-80) REVERT: L 104 SER cc_start: 0.9361 (m) cc_final: 0.8314 (p) REVERT: L 229 LEU cc_start: 0.7027 (mt) cc_final: 0.6709 (mm) REVERT: L 237 MET cc_start: 0.8327 (mmp) cc_final: 0.8016 (mmp) REVERT: L 299 LYS cc_start: 0.8077 (mttt) cc_final: 0.7051 (mtpt) REVERT: L 302 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8661 (tt) REVERT: L 326 PHE cc_start: 0.7368 (p90) cc_final: 0.7075 (p90) REVERT: L 330 CYS cc_start: 0.8403 (m) cc_final: 0.7910 (t) REVERT: L 332 HIS cc_start: 0.8842 (t-90) cc_final: 0.8610 (t70) REVERT: L 393 ASP cc_start: 0.8277 (m-30) cc_final: 0.7988 (m-30) REVERT: L 458 LEU cc_start: 0.8689 (mt) cc_final: 0.8380 (tp) REVERT: L 536 LEU cc_start: 0.8613 (tt) cc_final: 0.7914 (tt) REVERT: L 544 MET cc_start: 0.6715 (mtp) cc_final: 0.6223 (tmm) REVERT: L 556 ILE cc_start: 0.8395 (mp) cc_final: 0.8032 (mp) REVERT: L 571 MET cc_start: 0.7320 (tpt) cc_final: 0.6395 (ttp) REVERT: L 592 LEU cc_start: 0.9008 (mt) cc_final: 0.8766 (tp) REVERT: M 30 HIS cc_start: 0.7861 (m-70) cc_final: 0.7659 (m170) REVERT: M 41 LEU cc_start: 0.8248 (mt) cc_final: 0.7771 (tp) REVERT: M 42 MET cc_start: 0.7763 (tpp) cc_final: 0.7377 (tmm) REVERT: M 65 LEU cc_start: 0.9045 (tp) cc_final: 0.8726 (tp) REVERT: M 143 LEU cc_start: 0.8579 (mt) cc_final: 0.8216 (mp) REVERT: M 175 ASN cc_start: 0.8417 (p0) cc_final: 0.7972 (p0) REVERT: M 179 LEU cc_start: 0.7661 (tp) cc_final: 0.7455 (tt) REVERT: M 204 MET cc_start: 0.8255 (mmp) cc_final: 0.7158 (mtp) REVERT: M 207 MET cc_start: 0.8413 (mmm) cc_final: 0.8013 (mmm) REVERT: M 237 LYS cc_start: 0.9225 (mtmm) cc_final: 0.8879 (mttm) REVERT: M 238 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7567 (pp) REVERT: M 247 THR cc_start: 0.8315 (m) cc_final: 0.7828 (t) REVERT: M 269 MET cc_start: 0.8404 (mmm) cc_final: 0.7628 (ttp) REVERT: M 319 HIS cc_start: 0.7206 (t70) cc_final: 0.6914 (t-90) REVERT: M 325 MET cc_start: 0.8446 (tpt) cc_final: 0.7740 (tpp) REVERT: M 329 LEU cc_start: 0.8801 (mt) cc_final: 0.8177 (mp) REVERT: M 335 GLU cc_start: 0.8236 (pt0) cc_final: 0.7766 (mt-10) REVERT: M 354 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8619 (tt) REVERT: N 9 ILE cc_start: 0.9254 (mt) cc_final: 0.8991 (tp) REVERT: N 10 LEU cc_start: 0.8890 (tp) cc_final: 0.8683 (tp) REVERT: N 14 MET cc_start: 0.7032 (mmm) cc_final: 0.6814 (mmt) REVERT: N 63 GLN cc_start: 0.8990 (tt0) cc_final: 0.7841 (tt0) REVERT: N 100 MET cc_start: 0.8642 (mmm) cc_final: 0.8286 (tmm) REVERT: N 159 VAL cc_start: 0.8242 (t) cc_final: 0.7719 (p) REVERT: N 211 MET cc_start: 0.8054 (ttm) cc_final: 0.7007 (ttm) REVERT: N 215 MET cc_start: 0.8351 (mmm) cc_final: 0.7826 (tpp) REVERT: N 251 MET cc_start: 0.8969 (mmm) cc_final: 0.8043 (tpp) REVERT: N 260 PHE cc_start: 0.8525 (t80) cc_final: 0.8296 (t80) REVERT: N 269 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6138 (mm-30) REVERT: N 272 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8305 (mtpt) REVERT: N 282 MET cc_start: 0.8862 (mmm) cc_final: 0.8601 (mtp) REVERT: N 294 MET cc_start: 0.8757 (mmp) cc_final: 0.8382 (mmm) REVERT: O 108 TYR cc_start: 0.8778 (t80) cc_final: 0.8262 (t80) REVERT: O 114 HIS cc_start: 0.8652 (t-90) cc_final: 0.8137 (t70) REVERT: O 132 PHE cc_start: 0.8748 (p90) cc_final: 0.8455 (p90) REVERT: O 162 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7483 (tp30) REVERT: V 48 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7084 (mt-10) REVERT: V 52 ASN cc_start: 0.8735 (m-40) cc_final: 0.8166 (p0) REVERT: W 84 LYS cc_start: 0.9103 (ttmm) cc_final: 0.8805 (tptm) REVERT: W 86 LYS cc_start: 0.8860 (mttt) cc_final: 0.8618 (tttm) REVERT: W 95 VAL cc_start: 0.8129 (t) cc_final: 0.7847 (m) REVERT: X 48 GLU cc_start: 0.7905 (mt-10) cc_final: 0.6758 (tp30) REVERT: X 49 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7296 (mp0) REVERT: X 68 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7363 (tm-30) REVERT: X 97 ARG cc_start: 0.7617 (mmm160) cc_final: 0.7161 (mmm160) REVERT: Y 79 VAL cc_start: 0.6104 (t) cc_final: 0.5753 (p) REVERT: Y 89 TYR cc_start: 0.8236 (m-80) cc_final: 0.6145 (m-80) REVERT: Z 34 MET cc_start: 0.7994 (ttt) cc_final: 0.7489 (tmm) REVERT: Z 46 TYR cc_start: 0.8500 (m-80) cc_final: 0.8140 (m-80) REVERT: Z 55 GLU cc_start: 0.8143 (tp30) cc_final: 0.7842 (tm-30) REVERT: Z 59 LEU cc_start: 0.9318 (mt) cc_final: 0.9115 (pp) REVERT: Z 62 GLU cc_start: 0.8051 (tt0) cc_final: 0.7709 (tp30) REVERT: Z 73 LEU cc_start: 0.8935 (tt) cc_final: 0.8654 (tt) REVERT: Z 74 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8059 (tt) REVERT: Z 77 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7435 (mt-10) REVERT: b 33 THR cc_start: 0.8902 (p) cc_final: 0.8626 (t) REVERT: d 30 ARG cc_start: 0.8438 (mtm180) cc_final: 0.7617 (mpt180) REVERT: d 39 TYR cc_start: 0.9012 (t80) cc_final: 0.8522 (t80) REVERT: d 73 TYR cc_start: 0.8987 (t80) cc_final: 0.8779 (t80) REVERT: d 74 TYR cc_start: 0.8355 (m-80) cc_final: 0.8139 (m-10) REVERT: e 83 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7540 (mm-30) REVERT: f 21 VAL cc_start: 0.8480 (t) cc_final: 0.8126 (p) REVERT: g 58 MET cc_start: 0.6718 (mmt) cc_final: 0.5608 (mmm) REVERT: g 64 PHE cc_start: 0.6680 (m-80) cc_final: 0.6444 (t80) REVERT: g 69 VAL cc_start: 0.9431 (t) cc_final: 0.9122 (p) REVERT: g 71 VAL cc_start: 0.8573 (t) cc_final: 0.8302 (t) REVERT: g 72 LEU cc_start: 0.9252 (mt) cc_final: 0.8983 (tt) REVERT: g 80 LEU cc_start: 0.8816 (mt) cc_final: 0.8522 (mt) REVERT: h 19 LYS cc_start: 0.8756 (mmtt) cc_final: 0.7947 (mtmt) REVERT: m 42 LEU cc_start: 0.8281 (mt) cc_final: 0.8080 (mt) REVERT: m 43 LYS cc_start: 0.8895 (tttt) cc_final: 0.8609 (tppt) REVERT: m 48 LEU cc_start: 0.9242 (mt) cc_final: 0.8904 (tt) REVERT: m 49 GLN cc_start: 0.9033 (mt0) cc_final: 0.8665 (mt0) REVERT: m 71 ARG cc_start: 0.7748 (ttm110) cc_final: 0.7010 (mmt180) REVERT: m 75 ILE cc_start: 0.8653 (mt) cc_final: 0.8360 (mm) REVERT: m 111 LYS cc_start: 0.8904 (mttt) cc_final: 0.8597 (ptpp) REVERT: n 36 TYR cc_start: 0.7551 (t80) cc_final: 0.7324 (t80) REVERT: p 100 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7647 (mt-10) REVERT: p 109 LEU cc_start: 0.8943 (tp) cc_final: 0.8672 (tp) REVERT: p 133 GLN cc_start: 0.8289 (mt0) cc_final: 0.8026 (tm-30) outliers start: 132 outliers final: 9 residues processed: 1650 average time/residue: 0.5011 time to fit residues: 1376.9337 Evaluate side-chains 942 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 923 time to evaluate : 4.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 687 random chunks: chunk 580 optimal weight: 50.0000 chunk 520 optimal weight: 5.9990 chunk 288 optimal weight: 0.0970 chunk 177 optimal weight: 20.0000 chunk 351 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 538 optimal weight: 4.9990 chunk 208 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 chunk 400 optimal weight: 0.9990 chunk 623 optimal weight: 20.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 HIS B 82 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS C 160 HIS D 84 HIS D 114 ASN D 135 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN D 316 ASN D 348 HIS F 373 ASN F 398 GLN F 421 HIS G 100 ASN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 HIS L 295 GLN M 279 GLN ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 434 ASN N 47 ASN N 48 HIS N 171 ASN N 174 GLN X 64 GLN X 72 GLN X 105 GLN Z 53 ASN a 44 GLN ** d 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 HIS p 106 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.279 52631 Z= 0.614 Angle : 1.857 51.544 72262 Z= 1.183 Chirality : 0.328 6.688 8863 Planarity : 0.007 0.154 9461 Dihedral : 5.930 166.215 8296 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 1.51 % Allowed : 8.61 % Favored : 89.88 % Rotamer: Outliers : 0.22 % Allowed : 5.15 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: -3.14 (0.09), residues: 5840 helix: -1.58 (0.08), residues: 3017 sheet: -0.73 (0.40), residues: 168 loop : -2.77 (0.11), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 129 HIS 0.020 0.002 HIS I 65 PHE 0.043 0.002 PHE L 418 TYR 0.035 0.002 TYR Y 89 ARG 0.011 0.001 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1063 time to evaluate : 4.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8202 (ptp) cc_final: 0.7964 (ptt) REVERT: B 67 TYR cc_start: 0.7780 (m-80) cc_final: 0.7204 (m-10) REVERT: B 121 ASN cc_start: 0.9073 (m-40) cc_final: 0.8829 (m-40) REVERT: C 73 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7521 (ttmt) REVERT: C 77 ASP cc_start: 0.7757 (m-30) cc_final: 0.6439 (m-30) REVERT: C 92 ILE cc_start: 0.8571 (mt) cc_final: 0.8311 (mt) REVERT: C 124 TYR cc_start: 0.6353 (t80) cc_final: 0.6145 (t80) REVERT: C 131 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8334 (mt-10) REVERT: C 133 GLU cc_start: 0.8690 (tt0) cc_final: 0.8464 (tm-30) REVERT: C 154 ASP cc_start: 0.8373 (t0) cc_final: 0.7774 (t0) REVERT: C 196 LYS cc_start: 0.8379 (ttpt) cc_final: 0.7889 (pttm) REVERT: D 90 LEU cc_start: 0.8841 (tp) cc_final: 0.8514 (tt) REVERT: D 127 ASN cc_start: 0.8683 (m110) cc_final: 0.8343 (m-40) REVERT: D 156 THR cc_start: 0.9123 (p) cc_final: 0.8753 (t) REVERT: D 169 TRP cc_start: 0.8563 (m100) cc_final: 0.8202 (m100) REVERT: D 172 GLU cc_start: 0.6887 (tp30) cc_final: 0.6371 (tp30) REVERT: D 259 MET cc_start: 0.7536 (mmm) cc_final: 0.6504 (mmp) REVERT: D 303 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8558 (tm-30) REVERT: D 304 MET cc_start: 0.9056 (mmm) cc_final: 0.8354 (tpp) REVERT: D 338 MET cc_start: 0.9036 (ptm) cc_final: 0.8519 (ppp) REVERT: D 379 VAL cc_start: 0.9430 (m) cc_final: 0.9213 (p) REVERT: D 392 LYS cc_start: 0.8082 (mttt) cc_final: 0.7626 (mmtm) REVERT: F 376 MET cc_start: 0.9351 (mmm) cc_final: 0.9150 (tpt) REVERT: F 380 VAL cc_start: 0.9013 (t) cc_final: 0.8654 (p) REVERT: F 390 ASP cc_start: 0.8588 (t70) cc_final: 0.8184 (t70) REVERT: F 394 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8432 (mt-10) REVERT: G 94 MET cc_start: 0.8930 (mmm) cc_final: 0.8632 (mmm) REVERT: H 31 MET cc_start: 0.9224 (mmm) cc_final: 0.8753 (tpp) REVERT: H 85 MET cc_start: 0.8295 (tpp) cc_final: 0.8093 (tpt) REVERT: H 183 MET cc_start: 0.8531 (mmt) cc_final: 0.8256 (mmp) REVERT: H 230 ASN cc_start: 0.8589 (m-40) cc_final: 0.8110 (m110) REVERT: H 251 MET cc_start: 0.8315 (tpt) cc_final: 0.7569 (tpp) REVERT: H 253 GLU cc_start: 0.6272 (mt-10) cc_final: 0.4544 (mp0) REVERT: H 254 LEU cc_start: 0.8552 (tp) cc_final: 0.8162 (tp) REVERT: H 304 HIS cc_start: 0.8803 (m90) cc_final: 0.8290 (m-70) REVERT: I 19 ASP cc_start: 0.7744 (p0) cc_final: 0.7356 (t70) REVERT: I 129 ASP cc_start: 0.8806 (t0) cc_final: 0.8476 (t0) REVERT: I 144 HIS cc_start: 0.6937 (m-70) cc_final: 0.6424 (m170) REVERT: J 24 PRO cc_start: 0.7294 (Cg_endo) cc_final: 0.6218 (Cg_exo) REVERT: J 46 ASN cc_start: 0.8568 (m-40) cc_final: 0.7724 (t0) REVERT: J 54 LEU cc_start: 0.9155 (mt) cc_final: 0.8933 (mt) REVERT: J 154 VAL cc_start: 0.9306 (t) cc_final: 0.9031 (p) REVERT: K 25 HIS cc_start: 0.7879 (m-70) cc_final: 0.7374 (m170) REVERT: K 34 GLU cc_start: 0.8929 (mp0) cc_final: 0.8689 (mp0) REVERT: K 66 PHE cc_start: 0.8292 (m-80) cc_final: 0.7934 (m-10) REVERT: K 69 CYS cc_start: 0.8886 (m) cc_final: 0.8483 (t) REVERT: L 21 MET cc_start: 0.8382 (ttt) cc_final: 0.7950 (tpp) REVERT: L 101 MET cc_start: 0.8666 (mmm) cc_final: 0.8134 (tpp) REVERT: L 102 GLU cc_start: 0.8409 (pt0) cc_final: 0.8099 (pt0) REVERT: L 103 PHE cc_start: 0.7622 (m-80) cc_final: 0.7398 (m-80) REVERT: L 104 SER cc_start: 0.9416 (m) cc_final: 0.8276 (t) REVERT: L 130 ILE cc_start: 0.9413 (mt) cc_final: 0.9113 (mm) REVERT: L 137 LEU cc_start: 0.8767 (tp) cc_final: 0.7861 (tp) REVERT: L 139 GLN cc_start: 0.8862 (tp40) cc_final: 0.8311 (tm-30) REVERT: L 140 LEU cc_start: 0.9098 (tp) cc_final: 0.8850 (tp) REVERT: L 211 MET cc_start: 0.8020 (tpp) cc_final: 0.7777 (tmm) REVERT: L 237 MET cc_start: 0.8756 (mmp) cc_final: 0.8170 (mmp) REVERT: L 249 SER cc_start: 0.8198 (p) cc_final: 0.6815 (t) REVERT: L 330 CYS cc_start: 0.8666 (m) cc_final: 0.8210 (t) REVERT: L 353 GLU cc_start: 0.7437 (tp30) cc_final: 0.7147 (tp30) REVERT: L 393 ASP cc_start: 0.8243 (m-30) cc_final: 0.7904 (m-30) REVERT: L 429 PHE cc_start: 0.7481 (t80) cc_final: 0.7073 (t80) REVERT: L 544 MET cc_start: 0.7088 (mtp) cc_final: 0.6573 (tmm) REVERT: L 571 MET cc_start: 0.7423 (tpt) cc_final: 0.6901 (tmm) REVERT: M 70 MET cc_start: 0.9236 (mmm) cc_final: 0.8956 (mmp) REVERT: M 141 GLU cc_start: 0.7782 (pt0) cc_final: 0.7581 (pt0) REVERT: M 200 MET cc_start: 0.8738 (mmm) cc_final: 0.8458 (mmm) REVERT: M 204 MET cc_start: 0.8229 (mmp) cc_final: 0.7743 (ptp) REVERT: M 257 MET cc_start: 0.8260 (mtp) cc_final: 0.7832 (mmp) REVERT: M 269 MET cc_start: 0.8770 (mmm) cc_final: 0.7916 (mmm) REVERT: M 270 ILE cc_start: 0.9290 (mp) cc_final: 0.8939 (mm) REVERT: M 310 MET cc_start: 0.7510 (mmt) cc_final: 0.6805 (mmm) REVERT: M 319 HIS cc_start: 0.7438 (t70) cc_final: 0.6704 (t-90) REVERT: M 325 MET cc_start: 0.8296 (tpt) cc_final: 0.7882 (tpp) REVERT: M 360 LEU cc_start: 0.9295 (tp) cc_final: 0.9082 (tp) REVERT: M 383 MET cc_start: 0.8578 (mtm) cc_final: 0.8163 (mtp) REVERT: M 394 ILE cc_start: 0.8864 (mt) cc_final: 0.8343 (tt) REVERT: N 14 MET cc_start: 0.7472 (mmm) cc_final: 0.7265 (mmt) REVERT: N 46 LYS cc_start: 0.8566 (mmmt) cc_final: 0.8261 (mmtt) REVERT: N 193 VAL cc_start: 0.9162 (t) cc_final: 0.8936 (m) REVERT: N 211 MET cc_start: 0.8357 (ttm) cc_final: 0.7184 (ttm) REVERT: N 215 MET cc_start: 0.8341 (mmm) cc_final: 0.8092 (tpp) REVERT: N 248 LEU cc_start: 0.8873 (mm) cc_final: 0.8561 (mm) REVERT: N 251 MET cc_start: 0.8992 (mmm) cc_final: 0.8329 (tpp) REVERT: N 265 MET cc_start: 0.8496 (mpp) cc_final: 0.8106 (mpp) REVERT: N 267 ILE cc_start: 0.8824 (mt) cc_final: 0.8344 (mt) REVERT: N 268 GLN cc_start: 0.7491 (tm-30) cc_final: 0.6987 (tm-30) REVERT: N 269 GLU cc_start: 0.7649 (mm-30) cc_final: 0.6586 (mm-30) REVERT: N 272 LYS cc_start: 0.8936 (mtpp) cc_final: 0.8191 (mtpt) REVERT: N 282 MET cc_start: 0.8668 (mmm) cc_final: 0.8395 (mtp) REVERT: N 294 MET cc_start: 0.8868 (mmp) cc_final: 0.8472 (mmm) REVERT: O 108 TYR cc_start: 0.9002 (t80) cc_final: 0.8734 (t80) REVERT: O 114 HIS cc_start: 0.8857 (t-90) cc_final: 0.8105 (t70) REVERT: O 162 GLU cc_start: 0.8600 (mt-10) cc_final: 0.7662 (tp30) REVERT: V 48 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7783 (mt-10) REVERT: V 49 GLN cc_start: 0.7838 (pt0) cc_final: 0.7229 (pt0) REVERT: V 52 ASN cc_start: 0.8971 (m-40) cc_final: 0.8738 (p0) REVERT: X 48 GLU cc_start: 0.8015 (mt-10) cc_final: 0.6953 (tp30) REVERT: Z 34 MET cc_start: 0.8134 (ttt) cc_final: 0.7830 (tmm) REVERT: Z 55 GLU cc_start: 0.8399 (tp30) cc_final: 0.7951 (tm-30) REVERT: Z 62 GLU cc_start: 0.8250 (tt0) cc_final: 0.7958 (tp30) REVERT: a 12 MET cc_start: 0.8367 (mmp) cc_final: 0.8137 (tpp) REVERT: a 46 TYR cc_start: 0.7426 (t80) cc_final: 0.7205 (t80) REVERT: b 33 THR cc_start: 0.8992 (p) cc_final: 0.8766 (t) REVERT: d 45 ASP cc_start: 0.8423 (p0) cc_final: 0.7936 (t0) REVERT: d 70 PHE cc_start: 0.8466 (t80) cc_final: 0.8234 (t80) REVERT: d 79 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8221 (tm-30) REVERT: e 69 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8747 (tp40) REVERT: f 16 VAL cc_start: 0.7713 (t) cc_final: 0.7369 (t) REVERT: g 58 MET cc_start: 0.6043 (mmt) cc_final: 0.5715 (tpp) REVERT: g 80 LEU cc_start: 0.8837 (mt) cc_final: 0.8297 (mt) REVERT: g 94 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7840 (mm-30) REVERT: h 19 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8139 (mtmt) REVERT: m 45 GLU cc_start: 0.8979 (tp30) cc_final: 0.8300 (tp30) REVERT: m 48 LEU cc_start: 0.9126 (mt) cc_final: 0.8784 (tt) REVERT: m 71 ARG cc_start: 0.8023 (ttm110) cc_final: 0.7215 (mpt180) REVERT: m 75 ILE cc_start: 0.8951 (mt) cc_final: 0.8736 (mm) REVERT: m 87 LEU cc_start: 0.7708 (mp) cc_final: 0.7045 (tp) REVERT: m 111 LYS cc_start: 0.9036 (mttt) cc_final: 0.8799 (ptpp) REVERT: n 56 MET cc_start: 0.7630 (tpt) cc_final: 0.7066 (tmm) REVERT: n 68 GLU cc_start: 0.8611 (mp0) cc_final: 0.8022 (mp0) REVERT: p 100 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7908 (mt-10) REVERT: p 126 LYS cc_start: 0.8887 (tmtt) cc_final: 0.8248 (tmtt) REVERT: p 133 GLN cc_start: 0.8682 (mt0) cc_final: 0.8481 (tm-30) outliers start: 8 outliers final: 1 residues processed: 1066 average time/residue: 0.4910 time to fit residues: 899.0066 Evaluate side-chains 795 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 794 time to evaluate : 4.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 687 random chunks: chunk 346 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 519 optimal weight: 4.9990 chunk 424 optimal weight: 40.0000 chunk 172 optimal weight: 10.0000 chunk 624 optimal weight: 9.9990 chunk 675 optimal weight: 20.0000 chunk 556 optimal weight: 5.9990 chunk 619 optimal weight: 20.0000 chunk 213 optimal weight: 9.9990 chunk 501 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 85 ASN ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 HIS L 72 GLN ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 328 HIS L 348 HIS L 400 ASN L 405 ASN ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 434 ASN M 440 HIS N 36 ASN N 144 GLN N 232 HIS N 268 GLN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN O 114 HIS O 151 HIS X 34 GLN X 63 ASN X 64 GLN X 72 GLN X 94 GLN X 105 GLN Z 89 ASN n 32 HIS p 99 GLN ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.273 52631 Z= 0.737 Angle : 1.962 51.273 72262 Z= 1.220 Chirality : 0.335 6.654 8863 Planarity : 0.008 0.163 9461 Dihedral : 6.809 160.600 8296 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 1.40 % Allowed : 10.92 % Favored : 87.67 % Rotamer: Outliers : 0.33 % Allowed : 7.74 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.05 % 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: -2.83 (0.10), residues: 5840 helix: -1.13 (0.08), residues: 3115 sheet: -1.02 (0.39), residues: 167 loop : -2.90 (0.11), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP C 129 HIS 0.025 0.004 HIS I 65 PHE 0.044 0.004 PHE L 335 TYR 0.037 0.004 TYR H 30 ARG 0.019 0.001 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 878 time to evaluate : 4.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8518 (tm-30) REVERT: B 94 ASN cc_start: 0.9283 (m110) cc_final: 0.9050 (m110) REVERT: B 137 ASP cc_start: 0.8707 (m-30) cc_final: 0.7799 (m-30) REVERT: C 73 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7441 (ttmt) REVERT: C 77 ASP cc_start: 0.8110 (m-30) cc_final: 0.7706 (m-30) REVERT: C 83 ILE cc_start: 0.8700 (tp) cc_final: 0.8417 (tp) REVERT: C 92 ILE cc_start: 0.8410 (mt) cc_final: 0.8028 (mt) REVERT: C 93 VAL cc_start: 0.8873 (t) cc_final: 0.8662 (t) REVERT: C 108 LYS cc_start: 0.8823 (mtpp) cc_final: 0.8501 (mtmm) REVERT: C 124 TYR cc_start: 0.6851 (t80) cc_final: 0.6592 (t80) REVERT: C 131 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8307 (mt-10) REVERT: C 133 GLU cc_start: 0.9027 (tt0) cc_final: 0.8715 (tm-30) REVERT: C 154 ASP cc_start: 0.8687 (t0) cc_final: 0.8285 (m-30) REVERT: D 156 THR cc_start: 0.9226 (p) cc_final: 0.8855 (t) REVERT: D 169 TRP cc_start: 0.8446 (m100) cc_final: 0.7878 (m100) REVERT: D 189 MET cc_start: 0.8378 (mtp) cc_final: 0.7852 (mtp) REVERT: D 193 TYR cc_start: 0.8808 (t80) cc_final: 0.8381 (t80) REVERT: D 259 MET cc_start: 0.8027 (mmm) cc_final: 0.7805 (mmm) REVERT: D 338 MET cc_start: 0.9287 (ptm) cc_final: 0.8919 (ppp) REVERT: F 380 VAL cc_start: 0.9083 (t) cc_final: 0.8840 (p) REVERT: F 390 ASP cc_start: 0.9068 (t70) cc_final: 0.8657 (t70) REVERT: G 53 ARG cc_start: 0.8921 (mmm-85) cc_final: 0.8614 (tpp80) REVERT: G 94 MET cc_start: 0.9041 (mmm) cc_final: 0.8472 (tpp) REVERT: G 154 ILE cc_start: 0.8992 (pt) cc_final: 0.8542 (pt) REVERT: H 21 THR cc_start: 0.8627 (p) cc_final: 0.8270 (p) REVERT: H 24 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8722 (mt-10) REVERT: H 31 MET cc_start: 0.9323 (mmm) cc_final: 0.8946 (mmt) REVERT: H 149 ILE cc_start: 0.9487 (mt) cc_final: 0.9259 (tp) REVERT: H 183 MET cc_start: 0.8830 (mmt) cc_final: 0.8569 (tpp) REVERT: H 230 ASN cc_start: 0.8618 (m110) cc_final: 0.8023 (m110) REVERT: H 251 MET cc_start: 0.8459 (tpt) cc_final: 0.7724 (tpp) REVERT: H 253 GLU cc_start: 0.6952 (mt-10) cc_final: 0.5197 (mp0) REVERT: H 254 LEU cc_start: 0.8708 (tp) cc_final: 0.8336 (tp) REVERT: I 117 ILE cc_start: 0.9207 (pt) cc_final: 0.8429 (mt) REVERT: I 144 HIS cc_start: 0.7938 (m-70) cc_final: 0.7467 (m170) REVERT: I 164 GLU cc_start: 0.8622 (mp0) cc_final: 0.7955 (mp0) REVERT: J 24 PRO cc_start: 0.8864 (Cg_endo) cc_final: 0.8255 (Cg_exo) REVERT: J 74 MET cc_start: 0.8961 (mmm) cc_final: 0.8755 (mmm) REVERT: J 90 LEU cc_start: 0.6563 (mt) cc_final: 0.6168 (mt) REVERT: K 59 MET cc_start: 0.8626 (mmp) cc_final: 0.8235 (mmt) REVERT: K 69 CYS cc_start: 0.9138 (m) cc_final: 0.8876 (m) REVERT: L 21 MET cc_start: 0.8313 (ttt) cc_final: 0.7929 (tpp) REVERT: L 87 MET cc_start: 0.8704 (tpt) cc_final: 0.8293 (tpt) REVERT: L 101 MET cc_start: 0.9072 (mmm) cc_final: 0.8808 (mmt) REVERT: L 102 GLU cc_start: 0.8372 (pt0) cc_final: 0.7189 (tm-30) REVERT: L 103 PHE cc_start: 0.8093 (m-80) cc_final: 0.7574 (m-80) REVERT: L 104 SER cc_start: 0.9437 (m) cc_final: 0.8351 (t) REVERT: L 237 MET cc_start: 0.8650 (mmp) cc_final: 0.8224 (mmp) REVERT: L 279 CYS cc_start: 0.8632 (t) cc_final: 0.8293 (t) REVERT: L 405 ASN cc_start: 0.7527 (OUTLIER) cc_final: 0.6903 (t0) REVERT: L 429 PHE cc_start: 0.8069 (t80) cc_final: 0.7599 (t80) REVERT: L 544 MET cc_start: 0.7062 (mtp) cc_final: 0.6252 (tmm) REVERT: L 571 MET cc_start: 0.7644 (tpt) cc_final: 0.7393 (tmm) REVERT: M 76 MET cc_start: 0.8020 (mtt) cc_final: 0.7498 (ptt) REVERT: M 178 MET cc_start: 0.7264 (pmm) cc_final: 0.7049 (pmm) REVERT: M 269 MET cc_start: 0.9178 (mmm) cc_final: 0.8536 (mmm) REVERT: M 319 HIS cc_start: 0.7593 (t70) cc_final: 0.7336 (t70) REVERT: M 325 MET cc_start: 0.8582 (tpt) cc_final: 0.8357 (tpp) REVERT: M 342 MET cc_start: 0.9008 (mmm) cc_final: 0.8697 (tpp) REVERT: M 354 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8946 (tt) REVERT: M 360 LEU cc_start: 0.9309 (tp) cc_final: 0.9100 (tp) REVERT: N 14 MET cc_start: 0.7768 (mmm) cc_final: 0.7384 (mmt) REVERT: N 174 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8712 (mp10) REVERT: N 187 MET cc_start: 0.8866 (mmm) cc_final: 0.8600 (mmt) REVERT: N 211 MET cc_start: 0.8515 (ttm) cc_final: 0.7085 (ttm) REVERT: N 251 MET cc_start: 0.9113 (mmm) cc_final: 0.8502 (tpp) REVERT: N 269 GLU cc_start: 0.7916 (mm-30) cc_final: 0.6980 (mm-30) REVERT: N 270 MET cc_start: 0.9010 (mtt) cc_final: 0.8596 (mtt) REVERT: N 272 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8506 (mtpt) REVERT: N 294 MET cc_start: 0.8978 (mmp) cc_final: 0.8713 (mmm) REVERT: N 304 MET cc_start: 0.8245 (ttm) cc_final: 0.7985 (ttm) REVERT: O 101 TYR cc_start: 0.8691 (t80) cc_final: 0.8310 (t80) REVERT: O 113 GLU cc_start: 0.8889 (pp20) cc_final: 0.8556 (pp20) REVERT: O 131 ASP cc_start: 0.8372 (t0) cc_final: 0.7930 (t0) REVERT: O 162 GLU cc_start: 0.8694 (mt-10) cc_final: 0.7772 (tp30) REVERT: V 48 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7816 (mt-10) REVERT: W 74 ASP cc_start: 0.8007 (t0) cc_final: 0.7751 (t0) REVERT: W 87 MET cc_start: 0.8722 (mtp) cc_final: 0.8492 (mtp) REVERT: X 48 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7287 (tp30) REVERT: Y 50 GLU cc_start: 0.7979 (tp30) cc_final: 0.7747 (tp30) REVERT: Z 48 SER cc_start: 0.9099 (m) cc_final: 0.8756 (m) REVERT: Z 50 MET cc_start: 0.7648 (ptt) cc_final: 0.7332 (ptt) REVERT: Z 55 GLU cc_start: 0.8723 (tp30) cc_final: 0.7906 (tm-30) REVERT: Z 59 LEU cc_start: 0.9242 (pp) cc_final: 0.8954 (mp) REVERT: Z 62 GLU cc_start: 0.8342 (tt0) cc_final: 0.8086 (tp30) REVERT: Z 87 ARG cc_start: 0.8075 (ptm160) cc_final: 0.7286 (ptm160) REVERT: a 4 GLU cc_start: 0.8213 (pt0) cc_final: 0.7888 (pt0) REVERT: b 42 LEU cc_start: 0.9203 (mt) cc_final: 0.8972 (mm) REVERT: c 31 LEU cc_start: 0.8744 (mt) cc_final: 0.8541 (mt) REVERT: d 70 PHE cc_start: 0.8720 (t80) cc_final: 0.8424 (t80) REVERT: d 79 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8292 (tm-30) REVERT: d 80 ASP cc_start: 0.8958 (m-30) cc_final: 0.8649 (m-30) REVERT: e 36 GLU cc_start: 0.9109 (tp30) cc_final: 0.8885 (tp30) REVERT: f 16 VAL cc_start: 0.8354 (t) cc_final: 0.8024 (t) REVERT: h 19 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8449 (mtmt) REVERT: m 45 GLU cc_start: 0.9113 (tp30) cc_final: 0.8490 (tp30) REVERT: m 75 ILE cc_start: 0.9003 (mt) cc_final: 0.8766 (mm) REVERT: m 87 LEU cc_start: 0.8241 (mp) cc_final: 0.7537 (tp) REVERT: m 109 ASP cc_start: 0.8450 (m-30) cc_final: 0.8207 (m-30) REVERT: n 27 GLU cc_start: 0.8470 (pp20) cc_final: 0.8131 (tm-30) REVERT: n 51 LYS cc_start: 0.8289 (tttm) cc_final: 0.7935 (tptt) REVERT: n 56 MET cc_start: 0.7906 (tpt) cc_final: 0.7315 (tmm) REVERT: n 57 VAL cc_start: 0.8773 (t) cc_final: 0.8489 (p) REVERT: n 68 GLU cc_start: 0.8383 (mp0) cc_final: 0.7849 (mp0) REVERT: n 69 GLU cc_start: 0.7379 (mp0) cc_final: 0.7059 (mp0) REVERT: p 133 GLN cc_start: 0.8680 (mt0) cc_final: 0.8387 (tm-30) outliers start: 12 outliers final: 4 residues processed: 890 average time/residue: 0.4732 time to fit residues: 722.6112 Evaluate side-chains 691 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 685 time to evaluate : 4.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 687 random chunks: chunk 617 optimal weight: 20.0000 chunk 469 optimal weight: 9.9990 chunk 324 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 298 optimal weight: 0.9980 chunk 419 optimal weight: 6.9990 chunk 627 optimal weight: 10.0000 chunk 664 optimal weight: 20.0000 chunk 327 optimal weight: 6.9990 chunk 594 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 23 GLN ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 269 ASN L 309 GLN M 279 GLN M 415 GLN N 144 GLN N 232 HIS ** N 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 273 ASN V 36 HIS ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 GLN b 45 ASN ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 130 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.272 52631 Z= 0.662 Angle : 1.876 51.596 72262 Z= 1.187 Chirality : 0.331 6.482 8863 Planarity : 0.006 0.159 9461 Dihedral : 6.529 162.587 8296 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 1.25 % Allowed : 10.02 % Favored : 88.73 % Rotamer: Outliers : 0.06 % Allowed : 5.43 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.05 % 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: -2.54 (0.10), residues: 5840 helix: -0.82 (0.09), residues: 3103 sheet: -0.96 (0.39), residues: 182 loop : -2.88 (0.12), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 129 HIS 0.013 0.002 HIS I 65 PHE 0.075 0.002 PHE O 134 TYR 0.037 0.002 TYR H 142 ARG 0.018 0.001 ARG O 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 880 time to evaluate : 4.067 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 62 PHE cc_start: 0.9269 (t80) cc_final: 0.9009 (t80) REVERT: A 65 PHE cc_start: 0.8291 (m-10) cc_final: 0.7894 (m-10) REVERT: A 68 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8644 (tm-30) REVERT: A 69 ILE cc_start: 0.9300 (pt) cc_final: 0.9043 (pt) REVERT: B 91 THR cc_start: 0.9154 (m) cc_final: 0.8939 (p) REVERT: B 137 ASP cc_start: 0.8616 (m-30) cc_final: 0.8232 (m-30) REVERT: C 73 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7044 (mttt) REVERT: C 92 ILE cc_start: 0.8427 (mt) cc_final: 0.8099 (mt) REVERT: C 131 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8344 (mt-10) REVERT: C 133 GLU cc_start: 0.9097 (tt0) cc_final: 0.8663 (tm-30) REVERT: C 154 ASP cc_start: 0.8634 (t0) cc_final: 0.8398 (t0) REVERT: D 83 LEU cc_start: 0.9520 (tp) cc_final: 0.9220 (tt) REVERT: D 90 LEU cc_start: 0.9004 (tp) cc_final: 0.8797 (tt) REVERT: D 111 MET cc_start: 0.7691 (mmp) cc_final: 0.7092 (mmm) REVERT: D 115 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7802 (mt-10) REVERT: D 169 TRP cc_start: 0.8708 (m100) cc_final: 0.8053 (m100) REVERT: D 193 TYR cc_start: 0.8755 (t80) cc_final: 0.8252 (t80) REVERT: D 304 MET cc_start: 0.9192 (tpp) cc_final: 0.8750 (tpp) REVERT: D 338 MET cc_start: 0.9243 (ptm) cc_final: 0.8778 (ppp) REVERT: F 380 VAL cc_start: 0.9047 (t) cc_final: 0.8838 (p) REVERT: F 390 ASP cc_start: 0.9048 (t70) cc_final: 0.8691 (t70) REVERT: F 418 LEU cc_start: 0.9024 (mm) cc_final: 0.8586 (tt) REVERT: H 24 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8337 (mt-10) REVERT: H 25 ARG cc_start: 0.8115 (mpt-90) cc_final: 0.7789 (mmt180) REVERT: H 26 LYS cc_start: 0.9391 (ttmm) cc_final: 0.9069 (ttpp) REVERT: H 31 MET cc_start: 0.9322 (mmm) cc_final: 0.8860 (mmt) REVERT: H 140 ILE cc_start: 0.8722 (pt) cc_final: 0.8233 (pt) REVERT: H 143 GLU cc_start: 0.7720 (mp0) cc_final: 0.7349 (mp0) REVERT: H 230 ASN cc_start: 0.8447 (m110) cc_final: 0.8098 (m-40) REVERT: H 233 MET cc_start: 0.8459 (mmm) cc_final: 0.8170 (mmm) REVERT: H 304 HIS cc_start: 0.9192 (m-70) cc_final: 0.8716 (m-70) REVERT: I 164 GLU cc_start: 0.8552 (mp0) cc_final: 0.7553 (mp0) REVERT: J 24 PRO cc_start: 0.8804 (Cg_endo) cc_final: 0.8309 (Cg_exo) REVERT: K 5 TYR cc_start: 0.8358 (m-80) cc_final: 0.8143 (m-80) REVERT: K 21 MET cc_start: 0.7790 (mtp) cc_final: 0.7580 (mtm) REVERT: K 58 MET cc_start: 0.7293 (ttt) cc_final: 0.6709 (ttt) REVERT: K 59 MET cc_start: 0.8539 (mmp) cc_final: 0.8062 (mmt) REVERT: K 70 GLU cc_start: 0.8037 (pm20) cc_final: 0.7828 (pm20) REVERT: K 88 ASP cc_start: 0.7743 (m-30) cc_final: 0.7528 (m-30) REVERT: L 21 MET cc_start: 0.8244 (ttt) cc_final: 0.7934 (tpp) REVERT: L 83 ASP cc_start: 0.7555 (t70) cc_final: 0.7238 (t0) REVERT: L 87 MET cc_start: 0.8569 (tpt) cc_final: 0.8347 (tpt) REVERT: L 101 MET cc_start: 0.9059 (mmm) cc_final: 0.8729 (mmt) REVERT: L 102 GLU cc_start: 0.8303 (pt0) cc_final: 0.7862 (pt0) REVERT: L 103 PHE cc_start: 0.8078 (m-80) cc_final: 0.7794 (m-80) REVERT: L 104 SER cc_start: 0.9484 (m) cc_final: 0.8395 (t) REVERT: L 105 MET cc_start: 0.8971 (mmp) cc_final: 0.8696 (mmm) REVERT: L 237 MET cc_start: 0.8747 (mmp) cc_final: 0.8416 (mmp) REVERT: L 252 MET cc_start: 0.8148 (tpt) cc_final: 0.7947 (tpt) REVERT: L 279 CYS cc_start: 0.8530 (t) cc_final: 0.8139 (t) REVERT: L 393 ASP cc_start: 0.8196 (m-30) cc_final: 0.7792 (m-30) REVERT: L 429 PHE cc_start: 0.8044 (t80) cc_final: 0.7634 (t80) REVERT: L 544 MET cc_start: 0.7106 (mtp) cc_final: 0.6290 (tmm) REVERT: M 10 MET cc_start: 0.8799 (mmm) cc_final: 0.8418 (ttm) REVERT: M 41 LEU cc_start: 0.8526 (mp) cc_final: 0.8011 (tp) REVERT: M 76 MET cc_start: 0.8076 (mtt) cc_final: 0.7507 (ptt) REVERT: M 204 MET cc_start: 0.8272 (mmp) cc_final: 0.8008 (ptp) REVERT: M 257 MET cc_start: 0.8370 (mtp) cc_final: 0.7546 (mmm) REVERT: M 269 MET cc_start: 0.8918 (mmm) cc_final: 0.8367 (mmm) REVERT: M 294 MET cc_start: 0.8898 (mmt) cc_final: 0.8448 (mmm) REVERT: M 342 MET cc_start: 0.8822 (mmm) cc_final: 0.8127 (mmm) REVERT: M 360 LEU cc_start: 0.9299 (tp) cc_final: 0.9086 (tp) REVERT: N 14 MET cc_start: 0.7843 (mmm) cc_final: 0.7380 (mmp) REVERT: N 68 MET cc_start: 0.8933 (mmt) cc_final: 0.8701 (mmt) REVERT: N 71 MET cc_start: 0.9506 (mmm) cc_final: 0.9280 (mmm) REVERT: N 72 MET cc_start: 0.9053 (tpp) cc_final: 0.8818 (tpp) REVERT: N 96 MET cc_start: 0.8687 (tpp) cc_final: 0.7561 (tmm) REVERT: N 190 MET cc_start: 0.8107 (mmt) cc_final: 0.7664 (mmm) REVERT: N 211 MET cc_start: 0.8558 (ttm) cc_final: 0.7174 (ttm) REVERT: N 248 LEU cc_start: 0.9114 (mm) cc_final: 0.8627 (mm) REVERT: N 251 MET cc_start: 0.9205 (mmm) cc_final: 0.8385 (tpp) REVERT: N 268 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7474 (tm-30) REVERT: N 269 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7642 (mm-30) REVERT: N 270 MET cc_start: 0.9097 (mtt) cc_final: 0.8448 (mtt) REVERT: N 294 MET cc_start: 0.8824 (mmp) cc_final: 0.8586 (mmm) REVERT: N 304 MET cc_start: 0.8451 (ttm) cc_final: 0.7969 (ttm) REVERT: O 113 GLU cc_start: 0.8928 (pp20) cc_final: 0.8544 (pp20) REVERT: O 131 ASP cc_start: 0.8204 (t0) cc_final: 0.7912 (t0) REVERT: O 162 GLU cc_start: 0.8636 (mt-10) cc_final: 0.7742 (tp30) REVERT: O 167 HIS cc_start: 0.7572 (m-70) cc_final: 0.6723 (m-70) REVERT: W 33 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: W 74 ASP cc_start: 0.7959 (t0) cc_final: 0.7751 (t0) REVERT: W 87 MET cc_start: 0.8643 (mtp) cc_final: 0.8420 (mtp) REVERT: X 48 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7357 (tp30) REVERT: X 50 LYS cc_start: 0.6332 (tttt) cc_final: 0.5115 (tptp) REVERT: Z 55 GLU cc_start: 0.8607 (tp30) cc_final: 0.8007 (tm-30) REVERT: Z 59 LEU cc_start: 0.9204 (pp) cc_final: 0.8903 (mp) REVERT: Z 81 ARG cc_start: 0.6939 (ttt180) cc_final: 0.6109 (tmt170) REVERT: Z 87 ARG cc_start: 0.8179 (ptm160) cc_final: 0.7441 (ptm160) REVERT: a 4 GLU cc_start: 0.8414 (pt0) cc_final: 0.8182 (pt0) REVERT: c 31 LEU cc_start: 0.8747 (mt) cc_final: 0.8524 (mt) REVERT: d 70 PHE cc_start: 0.8721 (t80) cc_final: 0.8411 (t80) REVERT: f 15 LEU cc_start: 0.8269 (tp) cc_final: 0.7795 (tp) REVERT: f 16 VAL cc_start: 0.8690 (t) cc_final: 0.8446 (t) REVERT: g 60 VAL cc_start: 0.7109 (t) cc_final: 0.6889 (t) REVERT: g 80 LEU cc_start: 0.9231 (mt) cc_final: 0.8950 (mt) REVERT: g 87 GLU cc_start: 0.9135 (tp30) cc_final: 0.8295 (pm20) REVERT: h 19 LYS cc_start: 0.8977 (mmtt) cc_final: 0.8407 (mtmt) REVERT: m 45 GLU cc_start: 0.8978 (tp30) cc_final: 0.8381 (tp30) REVERT: m 75 ILE cc_start: 0.9043 (mt) cc_final: 0.8776 (mm) REVERT: m 87 LEU cc_start: 0.8234 (mp) cc_final: 0.7718 (tp) REVERT: m 109 ASP cc_start: 0.8542 (m-30) cc_final: 0.8317 (m-30) REVERT: n 56 MET cc_start: 0.7671 (tpt) cc_final: 0.7121 (tmm) REVERT: n 68 GLU cc_start: 0.8593 (mp0) cc_final: 0.7929 (mp0) REVERT: n 69 GLU cc_start: 0.7277 (mp0) cc_final: 0.6982 (mp0) outliers start: 2 outliers final: 1 residues processed: 881 average time/residue: 0.4698 time to fit residues: 715.1888 Evaluate side-chains 688 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 686 time to evaluate : 3.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 687 random chunks: chunk 553 optimal weight: 3.9990 chunk 376 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 494 optimal weight: 8.9990 chunk 273 optimal weight: 0.6980 chunk 566 optimal weight: 1.9990 chunk 459 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 339 optimal weight: 6.9990 chunk 596 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS ** C 41 GLN ** 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 421 HIS ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN H 38 ASN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN L 170 GLN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 232 HIS V 49 GLN ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 GLN ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.267 52631 Z= 0.611 Angle : 1.825 50.959 72262 Z= 1.165 Chirality : 0.332 6.470 8863 Planarity : 0.005 0.145 9461 Dihedral : 6.143 165.667 8296 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 1.10 % Allowed : 9.86 % Favored : 89.04 % Rotamer: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 1.32 % 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: -2.24 (0.11), residues: 5840 helix: -0.51 (0.09), residues: 3083 sheet: -1.13 (0.40), residues: 174 loop : -2.78 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 129 HIS 0.012 0.002 HIS M 319 PHE 0.034 0.002 PHE L 335 TYR 0.031 0.002 TYR H 282 ARG 0.018 0.001 ARG H 281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 908 time to evaluate : 4.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8258 (m-10) cc_final: 0.7758 (m-10) REVERT: A 67 LEU cc_start: 0.9331 (mt) cc_final: 0.9090 (mm) REVERT: A 68 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8567 (tm-30) REVERT: A 69 ILE cc_start: 0.9279 (pt) cc_final: 0.8938 (pt) REVERT: A 100 VAL cc_start: 0.9205 (t) cc_final: 0.8999 (p) REVERT: B 33 LEU cc_start: 0.8044 (tp) cc_final: 0.7834 (tt) REVERT: C 73 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7363 (mttt) REVERT: C 92 ILE cc_start: 0.8201 (mt) cc_final: 0.7843 (mt) REVERT: C 108 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8271 (mtmm) REVERT: C 131 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8258 (mt-10) REVERT: C 133 GLU cc_start: 0.9100 (tt0) cc_final: 0.8680 (tm-30) REVERT: D 83 LEU cc_start: 0.9527 (tp) cc_final: 0.9215 (tt) REVERT: D 156 THR cc_start: 0.9223 (p) cc_final: 0.8850 (t) REVERT: D 169 TRP cc_start: 0.8726 (m100) cc_final: 0.7892 (m100) REVERT: D 193 TYR cc_start: 0.8571 (t80) cc_final: 0.8178 (t80) REVERT: D 259 MET cc_start: 0.8049 (mmm) cc_final: 0.7736 (mmm) REVERT: D 338 MET cc_start: 0.9210 (ptm) cc_final: 0.8743 (ppp) REVERT: F 380 VAL cc_start: 0.9043 (t) cc_final: 0.8825 (p) REVERT: F 390 ASP cc_start: 0.8946 (t70) cc_final: 0.8582 (t70) REVERT: G 53 ARG cc_start: 0.8930 (mmm-85) cc_final: 0.8259 (tpp80) REVERT: H 31 MET cc_start: 0.9280 (mmm) cc_final: 0.8428 (mmm) REVERT: H 91 MET cc_start: 0.8552 (tpp) cc_final: 0.8187 (mmm) REVERT: H 172 MET cc_start: 0.5775 (mmp) cc_final: 0.5336 (mmp) REVERT: H 230 ASN cc_start: 0.8319 (m110) cc_final: 0.7929 (m110) REVERT: H 233 MET cc_start: 0.8475 (mmm) cc_final: 0.8074 (mmm) REVERT: H 290 TRP cc_start: 0.8797 (m100) cc_final: 0.8324 (m-10) REVERT: H 304 HIS cc_start: 0.9012 (m-70) cc_final: 0.8421 (m-70) REVERT: I 37 THR cc_start: 0.9156 (p) cc_final: 0.8894 (p) REVERT: I 147 LEU cc_start: 0.9075 (tp) cc_final: 0.8754 (tp) REVERT: I 164 GLU cc_start: 0.8536 (mp0) cc_final: 0.7518 (mp0) REVERT: J 24 PRO cc_start: 0.8781 (Cg_endo) cc_final: 0.8248 (Cg_exo) REVERT: J 65 MET cc_start: 0.8331 (mtm) cc_final: 0.8118 (mtm) REVERT: J 99 MET cc_start: 0.8465 (tpp) cc_final: 0.8162 (tpp) REVERT: J 168 ILE cc_start: 0.9374 (mt) cc_final: 0.9077 (tt) REVERT: K 25 HIS cc_start: 0.8391 (m-70) cc_final: 0.7525 (m90) REVERT: K 38 LEU cc_start: 0.9112 (tp) cc_final: 0.8800 (tt) REVERT: K 58 MET cc_start: 0.7380 (ttt) cc_final: 0.6766 (ttt) REVERT: K 59 MET cc_start: 0.8393 (mmp) cc_final: 0.8027 (mmt) REVERT: L 21 MET cc_start: 0.8252 (ttt) cc_final: 0.7993 (tpp) REVERT: L 87 MET cc_start: 0.8599 (tpt) cc_final: 0.8308 (tpt) REVERT: L 101 MET cc_start: 0.9040 (mmm) cc_final: 0.8644 (mmt) REVERT: L 102 GLU cc_start: 0.8140 (pt0) cc_final: 0.6730 (tm-30) REVERT: L 103 PHE cc_start: 0.7947 (m-80) cc_final: 0.7385 (m-80) REVERT: L 104 SER cc_start: 0.9556 (m) cc_final: 0.8443 (t) REVERT: L 105 MET cc_start: 0.8950 (mmp) cc_final: 0.8610 (mmm) REVERT: L 131 LEU cc_start: 0.9637 (tp) cc_final: 0.9416 (tp) REVERT: L 139 GLN cc_start: 0.8811 (tp40) cc_final: 0.8198 (tp40) REVERT: L 237 MET cc_start: 0.8603 (mmp) cc_final: 0.8312 (mmp) REVERT: L 248 HIS cc_start: 0.8648 (m-70) cc_final: 0.8428 (m170) REVERT: L 252 MET cc_start: 0.8031 (tpt) cc_final: 0.7805 (tpt) REVERT: L 279 CYS cc_start: 0.8446 (t) cc_final: 0.8091 (t) REVERT: L 314 MET cc_start: 0.7975 (mmm) cc_final: 0.7731 (mmm) REVERT: L 353 GLU cc_start: 0.7644 (tp30) cc_final: 0.7391 (tp30) REVERT: L 393 ASP cc_start: 0.8189 (m-30) cc_final: 0.7768 (m-30) REVERT: L 429 PHE cc_start: 0.8174 (t80) cc_final: 0.7665 (t80) REVERT: L 544 MET cc_start: 0.7034 (mtp) cc_final: 0.6253 (tmm) REVERT: M 10 MET cc_start: 0.8717 (mmm) cc_final: 0.8252 (ttm) REVERT: M 12 MET cc_start: 0.7376 (tmm) cc_final: 0.6950 (tmm) REVERT: M 30 HIS cc_start: 0.8305 (m90) cc_final: 0.7844 (m90) REVERT: M 41 LEU cc_start: 0.8473 (mp) cc_final: 0.8011 (tp) REVERT: M 70 MET cc_start: 0.9254 (mmm) cc_final: 0.8716 (mmm) REVERT: M 76 MET cc_start: 0.7808 (mtt) cc_final: 0.7218 (mtm) REVERT: M 222 GLU cc_start: 0.8502 (tp30) cc_final: 0.7559 (tp30) REVERT: M 257 MET cc_start: 0.8386 (mtp) cc_final: 0.7511 (mmm) REVERT: M 342 MET cc_start: 0.8864 (mmm) cc_final: 0.8067 (mmm) REVERT: M 355 MET cc_start: 0.9150 (mmm) cc_final: 0.8927 (tpp) REVERT: M 364 LEU cc_start: 0.9260 (mt) cc_final: 0.9060 (mt) REVERT: M 394 ILE cc_start: 0.8938 (mm) cc_final: 0.8415 (tp) REVERT: M 437 MET cc_start: 0.9142 (mmt) cc_final: 0.8477 (mmt) REVERT: N 14 MET cc_start: 0.7810 (mmm) cc_final: 0.7279 (mmp) REVERT: N 63 GLN cc_start: 0.8796 (mt0) cc_final: 0.8560 (mt0) REVERT: N 72 MET cc_start: 0.8712 (tpp) cc_final: 0.8435 (tpt) REVERT: N 88 LYS cc_start: 0.8668 (mtmt) cc_final: 0.8425 (mtmt) REVERT: N 96 MET cc_start: 0.8436 (tpp) cc_final: 0.7343 (tmm) REVERT: N 100 MET cc_start: 0.8502 (tmm) cc_final: 0.8228 (tmm) REVERT: N 211 MET cc_start: 0.8748 (ttm) cc_final: 0.8169 (ttm) REVERT: N 248 LEU cc_start: 0.8859 (mm) cc_final: 0.8288 (mm) REVERT: N 251 MET cc_start: 0.9038 (mmm) cc_final: 0.8707 (tpp) REVERT: N 268 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7695 (tm-30) REVERT: N 269 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7602 (mm-30) REVERT: N 270 MET cc_start: 0.9121 (mtt) cc_final: 0.8510 (mtt) REVERT: N 304 MET cc_start: 0.8455 (ttm) cc_final: 0.8087 (ttm) REVERT: O 113 GLU cc_start: 0.8863 (pp20) cc_final: 0.8496 (pp20) REVERT: O 131 ASP cc_start: 0.8265 (t0) cc_final: 0.7738 (t0) REVERT: O 162 GLU cc_start: 0.8603 (mt-10) cc_final: 0.7713 (tp30) REVERT: O 167 HIS cc_start: 0.7601 (m-70) cc_final: 0.7162 (m-70) REVERT: W 33 GLU cc_start: 0.8400 (pm20) cc_final: 0.8128 (mp0) REVERT: W 86 LYS cc_start: 0.9149 (tttm) cc_final: 0.8646 (tttt) REVERT: X 48 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7213 (tp30) REVERT: X 84 TYR cc_start: 0.8511 (t80) cc_final: 0.8124 (t80) REVERT: Y 94 CYS cc_start: 0.8024 (m) cc_final: 0.7422 (t) REVERT: Z 48 SER cc_start: 0.9065 (m) cc_final: 0.8722 (t) REVERT: Z 55 GLU cc_start: 0.8491 (tp30) cc_final: 0.8006 (tm-30) REVERT: Z 57 ARG cc_start: 0.9076 (mmp80) cc_final: 0.8543 (mmm-85) REVERT: Z 81 ARG cc_start: 0.6900 (ttt180) cc_final: 0.6141 (tmt170) REVERT: Z 87 ARG cc_start: 0.8222 (ptm160) cc_final: 0.7460 (ptm160) REVERT: a 21 MET cc_start: 0.8785 (tpp) cc_final: 0.8569 (tpp) REVERT: d 70 PHE cc_start: 0.8614 (t80) cc_final: 0.8359 (t80) REVERT: e 36 GLU cc_start: 0.8882 (tp30) cc_final: 0.8539 (tt0) REVERT: f 15 LEU cc_start: 0.8462 (tp) cc_final: 0.8043 (tp) REVERT: g 60 VAL cc_start: 0.6582 (t) cc_final: 0.6377 (t) REVERT: g 80 LEU cc_start: 0.9193 (mt) cc_final: 0.8922 (mt) REVERT: g 87 GLU cc_start: 0.9057 (tp30) cc_final: 0.8349 (pm20) REVERT: h 19 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8380 (mtmt) REVERT: m 45 GLU cc_start: 0.8881 (tp30) cc_final: 0.8257 (tp30) REVERT: m 75 ILE cc_start: 0.8882 (mt) cc_final: 0.8621 (mm) REVERT: m 87 LEU cc_start: 0.8190 (mp) cc_final: 0.7744 (tt) REVERT: m 109 ASP cc_start: 0.8586 (m-30) cc_final: 0.8366 (m-30) REVERT: n 56 MET cc_start: 0.7634 (tpt) cc_final: 0.7083 (tmm) REVERT: n 68 GLU cc_start: 0.8732 (mp0) cc_final: 0.8116 (mp0) REVERT: n 69 GLU cc_start: 0.7168 (mp0) cc_final: 0.6899 (mp0) REVERT: p 127 GLU cc_start: 0.7524 (pm20) cc_final: 0.7079 (pm20) outliers start: 1 outliers final: 0 residues processed: 908 average time/residue: 0.4748 time to fit residues: 743.5647 Evaluate side-chains 724 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 724 time to evaluate : 4.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 687 random chunks: chunk 223 optimal weight: 4.9990 chunk 598 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 389 optimal weight: 1.9990 chunk 163 optimal weight: 30.0000 chunk 664 optimal weight: 20.0000 chunk 551 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 chunk 348 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** 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 421 HIS G 119 GLN H 5 ASN ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 399 ASN ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 GLN ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 99 GLN ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.270 52631 Z= 0.605 Angle : 1.811 50.998 72262 Z= 1.159 Chirality : 0.331 6.502 8863 Planarity : 0.005 0.138 9461 Dihedral : 5.907 167.376 8296 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 1.04 % Allowed : 9.35 % Favored : 89.61 % Rotamer: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 0.99 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.11), residues: 5840 helix: -0.36 (0.09), residues: 3074 sheet: -1.01 (0.40), residues: 172 loop : -2.71 (0.12), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP g 88 HIS 0.009 0.001 HIS L 248 PHE 0.037 0.002 PHE M 95 TYR 0.059 0.002 TYR G 42 ARG 0.025 0.001 ARG G 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 913 time to evaluate : 4.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8185 (m-10) cc_final: 0.7794 (m-10) REVERT: A 67 LEU cc_start: 0.9200 (mt) cc_final: 0.8994 (mm) REVERT: A 68 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8532 (tm-30) REVERT: A 73 LEU cc_start: 0.9412 (mt) cc_final: 0.8914 (mt) REVERT: B 33 LEU cc_start: 0.8006 (tp) cc_final: 0.7785 (tt) REVERT: B 84 ASP cc_start: 0.8287 (p0) cc_final: 0.8009 (p0) REVERT: B 94 ASN cc_start: 0.9273 (m110) cc_final: 0.8870 (m110) REVERT: B 106 GLN cc_start: 0.8345 (tp-100) cc_final: 0.7880 (tp-100) REVERT: B 137 ASP cc_start: 0.8344 (m-30) cc_final: 0.8010 (m-30) REVERT: C 92 ILE cc_start: 0.8283 (mt) cc_final: 0.7953 (mt) REVERT: C 108 LYS cc_start: 0.8716 (mtpp) cc_final: 0.8271 (mtmm) REVERT: C 131 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8174 (mt-10) REVERT: C 133 GLU cc_start: 0.9100 (tt0) cc_final: 0.8686 (tm-30) REVERT: C 154 ASP cc_start: 0.8544 (t0) cc_final: 0.8139 (t0) REVERT: C 167 PRO cc_start: 0.6315 (Cg_endo) cc_final: 0.5991 (Cg_exo) REVERT: D 62 LEU cc_start: 0.9019 (mt) cc_final: 0.8110 (mt) REVERT: D 83 LEU cc_start: 0.9411 (tp) cc_final: 0.9126 (tt) REVERT: D 156 THR cc_start: 0.9192 (p) cc_final: 0.8870 (t) REVERT: D 169 TRP cc_start: 0.8808 (m100) cc_final: 0.7965 (m100) REVERT: D 193 TYR cc_start: 0.8464 (t80) cc_final: 0.8124 (t80) REVERT: D 338 MET cc_start: 0.9149 (ptm) cc_final: 0.8733 (ppp) REVERT: F 380 VAL cc_start: 0.9028 (t) cc_final: 0.8823 (p) REVERT: F 390 ASP cc_start: 0.8927 (t70) cc_final: 0.8558 (t70) REVERT: G 53 ARG cc_start: 0.9003 (mmm-85) cc_final: 0.8385 (tpp80) REVERT: H 8 MET cc_start: 0.8004 (ttt) cc_final: 0.7791 (ttm) REVERT: H 24 GLU cc_start: 0.8893 (tp30) cc_final: 0.8578 (tt0) REVERT: H 31 MET cc_start: 0.9337 (mmm) cc_final: 0.8667 (mmm) REVERT: H 126 LYS cc_start: 0.5156 (mppt) cc_final: 0.4833 (mppt) REVERT: H 172 MET cc_start: 0.5683 (mmp) cc_final: 0.5426 (mmp) REVERT: H 230 ASN cc_start: 0.8323 (m110) cc_final: 0.7913 (m110) REVERT: H 251 MET cc_start: 0.8313 (tpt) cc_final: 0.7694 (tpp) REVERT: H 253 GLU cc_start: 0.6828 (mt-10) cc_final: 0.5332 (mp0) REVERT: H 254 LEU cc_start: 0.8586 (tp) cc_final: 0.8280 (tp) REVERT: H 290 TRP cc_start: 0.8848 (m100) cc_final: 0.8462 (m-10) REVERT: H 304 HIS cc_start: 0.8984 (m-70) cc_final: 0.8228 (m-70) REVERT: I 27 TRP cc_start: 0.6851 (m100) cc_final: 0.6314 (m100) REVERT: I 129 ASP cc_start: 0.9008 (t0) cc_final: 0.8561 (t0) REVERT: I 143 THR cc_start: 0.7814 (p) cc_final: 0.7585 (t) REVERT: I 147 LEU cc_start: 0.8966 (tp) cc_final: 0.8639 (tp) REVERT: J 24 PRO cc_start: 0.8921 (Cg_endo) cc_final: 0.8712 (Cg_exo) REVERT: J 74 MET cc_start: 0.8923 (mmm) cc_final: 0.8576 (mmm) REVERT: J 90 LEU cc_start: 0.7721 (mt) cc_final: 0.7206 (mt) REVERT: K 25 HIS cc_start: 0.8334 (m-70) cc_final: 0.7502 (m90) REVERT: K 59 MET cc_start: 0.8195 (mmp) cc_final: 0.7977 (mmp) REVERT: L 71 ILE cc_start: 0.8085 (mm) cc_final: 0.7570 (mm) REVERT: L 87 MET cc_start: 0.8546 (tpt) cc_final: 0.8311 (tpt) REVERT: L 101 MET cc_start: 0.9028 (mmm) cc_final: 0.8598 (mmt) REVERT: L 102 GLU cc_start: 0.7838 (pt0) cc_final: 0.6424 (tm-30) REVERT: L 103 PHE cc_start: 0.7821 (m-80) cc_final: 0.7380 (m-80) REVERT: L 104 SER cc_start: 0.9550 (m) cc_final: 0.8500 (t) REVERT: L 105 MET cc_start: 0.8929 (mmp) cc_final: 0.8612 (mmm) REVERT: L 131 LEU cc_start: 0.9643 (tp) cc_final: 0.9422 (tp) REVERT: L 139 GLN cc_start: 0.8825 (tp40) cc_final: 0.8198 (tp40) REVERT: L 237 MET cc_start: 0.8634 (mmp) cc_final: 0.8401 (mmp) REVERT: L 248 HIS cc_start: 0.8658 (m-70) cc_final: 0.8397 (m170) REVERT: L 279 CYS cc_start: 0.8448 (t) cc_final: 0.8092 (t) REVERT: L 353 GLU cc_start: 0.7627 (tp30) cc_final: 0.7408 (tp30) REVERT: L 393 ASP cc_start: 0.8197 (m-30) cc_final: 0.7767 (m-30) REVERT: L 429 PHE cc_start: 0.8116 (t80) cc_final: 0.7602 (t80) REVERT: L 544 MET cc_start: 0.7010 (mtp) cc_final: 0.6218 (tmm) REVERT: M 10 MET cc_start: 0.8700 (mmm) cc_final: 0.8383 (ttm) REVERT: M 30 HIS cc_start: 0.8259 (m90) cc_final: 0.7730 (m90) REVERT: M 41 LEU cc_start: 0.8387 (mp) cc_final: 0.7947 (tp) REVERT: M 76 MET cc_start: 0.7811 (mtt) cc_final: 0.7075 (mtm) REVERT: M 120 ILE cc_start: 0.9281 (pt) cc_final: 0.8693 (mt) REVERT: M 222 GLU cc_start: 0.8477 (tp30) cc_final: 0.7518 (tp30) REVERT: M 253 MET cc_start: 0.6659 (mmt) cc_final: 0.6424 (tpt) REVERT: M 257 MET cc_start: 0.8368 (mtp) cc_final: 0.7437 (mmm) REVERT: M 342 MET cc_start: 0.8915 (mmm) cc_final: 0.8174 (mmm) REVERT: M 348 LEU cc_start: 0.8044 (mt) cc_final: 0.7573 (mt) REVERT: M 355 MET cc_start: 0.9175 (mmm) cc_final: 0.8764 (tpt) REVERT: M 383 MET cc_start: 0.9009 (mpp) cc_final: 0.8553 (mpp) REVERT: M 394 ILE cc_start: 0.9056 (mm) cc_final: 0.8594 (tp) REVERT: M 434 ASN cc_start: 0.8984 (m-40) cc_final: 0.8777 (m-40) REVERT: N 14 MET cc_start: 0.7685 (mmm) cc_final: 0.7262 (mmt) REVERT: N 96 MET cc_start: 0.8478 (tpp) cc_final: 0.7369 (tmm) REVERT: N 215 MET cc_start: 0.8765 (tpp) cc_final: 0.8500 (tpp) REVERT: N 240 MET cc_start: 0.8819 (tpt) cc_final: 0.8449 (tpp) REVERT: N 248 LEU cc_start: 0.8840 (mm) cc_final: 0.8520 (mm) REVERT: N 251 MET cc_start: 0.9019 (mmm) cc_final: 0.8725 (mmt) REVERT: N 268 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7777 (tm-30) REVERT: N 269 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7508 (mm-30) REVERT: N 270 MET cc_start: 0.9037 (mtt) cc_final: 0.8415 (mtt) REVERT: N 304 MET cc_start: 0.8329 (ttm) cc_final: 0.8073 (ttm) REVERT: O 113 GLU cc_start: 0.8792 (pp20) cc_final: 0.8489 (pp20) REVERT: O 131 ASP cc_start: 0.7966 (t0) cc_final: 0.7410 (t0) REVERT: O 162 GLU cc_start: 0.8590 (mt-10) cc_final: 0.7711 (tp30) REVERT: O 167 HIS cc_start: 0.7675 (m-70) cc_final: 0.7194 (m-70) REVERT: W 33 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: W 86 LYS cc_start: 0.9081 (tttm) cc_final: 0.8660 (tppp) REVERT: X 31 TYR cc_start: 0.8468 (t80) cc_final: 0.8154 (t80) REVERT: X 48 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7218 (tp30) REVERT: X 67 LEU cc_start: 0.8812 (tt) cc_final: 0.8455 (mt) REVERT: X 84 TYR cc_start: 0.8529 (t80) cc_final: 0.8164 (t80) REVERT: Y 94 CYS cc_start: 0.7994 (m) cc_final: 0.7392 (t) REVERT: Z 48 SER cc_start: 0.9017 (m) cc_final: 0.8752 (t) REVERT: Z 55 GLU cc_start: 0.8451 (tp30) cc_final: 0.7987 (tm-30) REVERT: Z 57 ARG cc_start: 0.9129 (mmp80) cc_final: 0.8534 (mmm-85) REVERT: Z 81 ARG cc_start: 0.6962 (ttt180) cc_final: 0.6246 (tmt170) REVERT: Z 87 ARG cc_start: 0.8285 (ptm160) cc_final: 0.7490 (ptm160) REVERT: b 24 ILE cc_start: 0.8902 (tp) cc_final: 0.8601 (tp) REVERT: f 15 LEU cc_start: 0.8397 (tp) cc_final: 0.8048 (tp) REVERT: g 60 VAL cc_start: 0.6634 (t) cc_final: 0.6417 (t) REVERT: g 80 LEU cc_start: 0.9200 (mt) cc_final: 0.8965 (mt) REVERT: g 87 GLU cc_start: 0.8950 (tp30) cc_final: 0.8299 (pm20) REVERT: h 19 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8355 (mtmt) REVERT: m 45 GLU cc_start: 0.8838 (tp30) cc_final: 0.8369 (tp30) REVERT: m 75 ILE cc_start: 0.8621 (mt) cc_final: 0.8402 (mm) REVERT: m 87 LEU cc_start: 0.8217 (mp) cc_final: 0.7891 (tt) REVERT: m 109 ASP cc_start: 0.8621 (m-30) cc_final: 0.8379 (m-30) REVERT: n 56 MET cc_start: 0.7715 (tpt) cc_final: 0.7172 (tmm) REVERT: n 68 GLU cc_start: 0.8713 (mp0) cc_final: 0.8157 (mp0) REVERT: n 69 GLU cc_start: 0.7158 (mp0) cc_final: 0.6895 (mp0) REVERT: p 88 GLU cc_start: 0.9140 (tt0) cc_final: 0.8554 (tp30) outliers start: 1 outliers final: 0 residues processed: 914 average time/residue: 0.4869 time to fit residues: 771.8572 Evaluate side-chains 745 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 744 time to evaluate : 4.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 687 random chunks: chunk 640 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 378 optimal weight: 5.9990 chunk 485 optimal weight: 6.9990 chunk 376 optimal weight: 10.0000 chunk 559 optimal weight: 30.0000 chunk 371 optimal weight: 6.9990 chunk 662 optimal weight: 6.9990 chunk 414 optimal weight: 0.4980 chunk 403 optimal weight: 0.0980 chunk 305 optimal weight: 9.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** 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 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN H 38 ASN ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 GLN Y 128 GLN ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.272 52631 Z= 0.627 Angle : 1.841 51.088 72262 Z= 1.172 Chirality : 0.331 6.490 8863 Planarity : 0.005 0.142 9461 Dihedral : 6.043 167.713 8296 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.91 % Allowed : 10.62 % Favored : 88.48 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 1.65 % 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: -2.03 (0.11), residues: 5840 helix: -0.28 (0.09), residues: 3084 sheet: -1.06 (0.41), residues: 173 loop : -2.77 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 196 HIS 0.011 0.002 HIS C 160 PHE 0.031 0.002 PHE b 22 TYR 0.048 0.002 TYR L 159 ARG 0.009 0.001 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 883 time to evaluate : 4.043 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: A 68 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8435 (tm-30) REVERT: A 69 ILE cc_start: 0.9253 (pt) cc_final: 0.8823 (pt) REVERT: B 94 ASN cc_start: 0.9280 (m110) cc_final: 0.8986 (m110) REVERT: B 106 GLN cc_start: 0.8580 (tp-100) cc_final: 0.8187 (tp-100) REVERT: C 73 LYS cc_start: 0.8080 (mttt) cc_final: 0.7394 (mttt) REVERT: C 92 ILE cc_start: 0.8335 (mt) cc_final: 0.7863 (mt) REVERT: C 108 LYS cc_start: 0.8841 (mtpp) cc_final: 0.8340 (mtmm) REVERT: C 131 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8115 (mt-10) REVERT: C 133 GLU cc_start: 0.9084 (tt0) cc_final: 0.8736 (tm-30) REVERT: C 137 MET cc_start: 0.7532 (mtp) cc_final: 0.6697 (ttt) REVERT: C 154 ASP cc_start: 0.8643 (t0) cc_final: 0.8203 (t0) REVERT: C 167 PRO cc_start: 0.6823 (Cg_endo) cc_final: 0.6520 (Cg_exo) REVERT: D 83 LEU cc_start: 0.9366 (tp) cc_final: 0.9057 (tt) REVERT: D 111 MET cc_start: 0.8673 (mmm) cc_final: 0.8313 (mmm) REVERT: D 156 THR cc_start: 0.9184 (p) cc_final: 0.8896 (t) REVERT: D 169 TRP cc_start: 0.8737 (m100) cc_final: 0.7817 (m100) REVERT: D 193 TYR cc_start: 0.8672 (t80) cc_final: 0.8297 (t80) REVERT: D 338 MET cc_start: 0.9178 (ptm) cc_final: 0.8817 (ppp) REVERT: F 390 ASP cc_start: 0.8955 (t70) cc_final: 0.8567 (t70) REVERT: G 53 ARG cc_start: 0.9104 (mmm-85) cc_final: 0.8660 (tpp80) REVERT: G 94 MET cc_start: 0.9009 (tpp) cc_final: 0.8624 (tpp) REVERT: H 8 MET cc_start: 0.8053 (ttt) cc_final: 0.7852 (ttm) REVERT: H 25 ARG cc_start: 0.8078 (mpt-90) cc_final: 0.7869 (mmt180) REVERT: H 31 MET cc_start: 0.9403 (mmm) cc_final: 0.8662 (tpp) REVERT: H 85 MET cc_start: 0.8627 (tpp) cc_final: 0.8348 (tpp) REVERT: H 91 MET cc_start: 0.8247 (tpp) cc_final: 0.7932 (mmm) REVERT: H 126 LYS cc_start: 0.5761 (mppt) cc_final: 0.4698 (mmmt) REVERT: H 142 TYR cc_start: 0.7261 (m-10) cc_final: 0.6943 (m-10) REVERT: H 230 ASN cc_start: 0.8423 (m110) cc_final: 0.8005 (m-40) REVERT: H 251 MET cc_start: 0.8376 (tpt) cc_final: 0.7813 (tpp) REVERT: H 253 GLU cc_start: 0.6908 (mt-10) cc_final: 0.5525 (mp0) REVERT: H 254 LEU cc_start: 0.8724 (tp) cc_final: 0.8429 (tp) REVERT: H 285 LEU cc_start: 0.9113 (tp) cc_final: 0.8617 (tp) REVERT: H 290 TRP cc_start: 0.9005 (m100) cc_final: 0.8619 (m-10) REVERT: H 304 HIS cc_start: 0.9026 (m-70) cc_final: 0.8463 (m-70) REVERT: H 305 VAL cc_start: 0.9650 (t) cc_final: 0.9394 (p) REVERT: I 111 ILE cc_start: 0.8991 (mt) cc_final: 0.8749 (mt) REVERT: I 117 ILE cc_start: 0.8939 (pt) cc_final: 0.8213 (mt) REVERT: I 129 ASP cc_start: 0.9100 (t0) cc_final: 0.8763 (t0) REVERT: I 164 GLU cc_start: 0.8489 (mp0) cc_final: 0.7564 (mp0) REVERT: J 24 PRO cc_start: 0.8978 (Cg_endo) cc_final: 0.8770 (Cg_exo) REVERT: J 74 MET cc_start: 0.8979 (mmm) cc_final: 0.8671 (mmm) REVERT: J 99 MET cc_start: 0.8341 (tpp) cc_final: 0.7863 (tpt) REVERT: K 25 HIS cc_start: 0.8430 (m-70) cc_final: 0.7555 (m90) REVERT: K 37 MET cc_start: 0.8715 (mmp) cc_final: 0.8339 (mmm) REVERT: K 38 LEU cc_start: 0.9202 (tp) cc_final: 0.8952 (tt) REVERT: K 58 MET cc_start: 0.7521 (ttt) cc_final: 0.7255 (ttt) REVERT: K 59 MET cc_start: 0.8225 (mmp) cc_final: 0.7972 (mmp) REVERT: L 101 MET cc_start: 0.9022 (mmm) cc_final: 0.8090 (mmm) REVERT: L 102 GLU cc_start: 0.7970 (pt0) cc_final: 0.6546 (tp30) REVERT: L 103 PHE cc_start: 0.7998 (m-80) cc_final: 0.7531 (m-80) REVERT: L 104 SER cc_start: 0.9583 (m) cc_final: 0.8291 (t) REVERT: L 105 MET cc_start: 0.8882 (mmp) cc_final: 0.8260 (mmt) REVERT: L 131 LEU cc_start: 0.9626 (tp) cc_final: 0.9398 (tp) REVERT: L 150 MET cc_start: 0.8829 (mmp) cc_final: 0.8550 (mmt) REVERT: L 186 MET cc_start: 0.8867 (tpp) cc_final: 0.8626 (tpp) REVERT: L 203 MET cc_start: 0.8565 (ppp) cc_final: 0.8364 (ppp) REVERT: L 237 MET cc_start: 0.8704 (mmp) cc_final: 0.8334 (mmp) REVERT: L 249 SER cc_start: 0.8688 (p) cc_final: 0.8248 (t) REVERT: L 279 CYS cc_start: 0.8497 (t) cc_final: 0.8155 (t) REVERT: L 393 ASP cc_start: 0.8256 (m-30) cc_final: 0.7808 (m-30) REVERT: L 426 ILE cc_start: 0.9519 (mt) cc_final: 0.9283 (tt) REVERT: L 429 PHE cc_start: 0.8002 (t80) cc_final: 0.7556 (t80) REVERT: L 544 MET cc_start: 0.7080 (mtp) cc_final: 0.6182 (tmm) REVERT: M 10 MET cc_start: 0.8760 (mmm) cc_final: 0.8291 (ttm) REVERT: M 30 HIS cc_start: 0.8384 (m90) cc_final: 0.7921 (m90) REVERT: M 41 LEU cc_start: 0.8351 (mp) cc_final: 0.7991 (tp) REVERT: M 76 MET cc_start: 0.8179 (mtt) cc_final: 0.7461 (mtm) REVERT: M 120 ILE cc_start: 0.9463 (pt) cc_final: 0.8884 (mt) REVERT: M 178 MET cc_start: 0.8107 (pmm) cc_final: 0.7418 (mmm) REVERT: M 222 GLU cc_start: 0.8572 (tp30) cc_final: 0.7500 (tp30) REVERT: M 255 ASP cc_start: 0.8808 (p0) cc_final: 0.8605 (p0) REVERT: M 257 MET cc_start: 0.8280 (mtp) cc_final: 0.7527 (mmm) REVERT: M 310 MET cc_start: 0.7649 (mmt) cc_final: 0.6889 (mmm) REVERT: M 342 MET cc_start: 0.8932 (mmm) cc_final: 0.8125 (mmm) REVERT: M 383 MET cc_start: 0.9059 (mpp) cc_final: 0.8578 (mpp) REVERT: M 394 ILE cc_start: 0.8800 (mm) cc_final: 0.8295 (tp) REVERT: M 437 MET cc_start: 0.8969 (mmt) cc_final: 0.8663 (mmp) REVERT: N 14 MET cc_start: 0.7846 (mmm) cc_final: 0.7403 (mmt) REVERT: N 54 GLU cc_start: 0.8263 (tt0) cc_final: 0.7277 (tp30) REVERT: N 63 GLN cc_start: 0.8867 (mt0) cc_final: 0.8548 (mt0) REVERT: N 96 MET cc_start: 0.8579 (tpp) cc_final: 0.7365 (tmm) REVERT: N 100 MET cc_start: 0.8552 (tmm) cc_final: 0.8311 (tmm) REVERT: N 215 MET cc_start: 0.8822 (tpp) cc_final: 0.8579 (tpp) REVERT: N 248 LEU cc_start: 0.8825 (mm) cc_final: 0.8438 (mm) REVERT: N 268 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7680 (tm-30) REVERT: N 269 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7551 (mm-30) REVERT: N 270 MET cc_start: 0.9065 (mtt) cc_final: 0.8412 (mtt) REVERT: N 304 MET cc_start: 0.8502 (ttm) cc_final: 0.8072 (ttm) REVERT: O 113 GLU cc_start: 0.8831 (pp20) cc_final: 0.8533 (pp20) REVERT: O 131 ASP cc_start: 0.8043 (t0) cc_final: 0.7468 (t0) REVERT: O 162 GLU cc_start: 0.8616 (mt-10) cc_final: 0.7779 (tp30) REVERT: O 167 HIS cc_start: 0.7858 (m-70) cc_final: 0.6877 (m-70) REVERT: V 54 LYS cc_start: 0.8792 (mttt) cc_final: 0.8558 (tptt) REVERT: W 86 LYS cc_start: 0.9193 (tttm) cc_final: 0.8594 (tttt) REVERT: X 48 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7193 (tp30) REVERT: X 67 LEU cc_start: 0.8888 (tt) cc_final: 0.8562 (mt) REVERT: X 84 TYR cc_start: 0.8622 (t80) cc_final: 0.8162 (t80) REVERT: Z 48 SER cc_start: 0.9073 (m) cc_final: 0.8787 (t) REVERT: Z 55 GLU cc_start: 0.8548 (tp30) cc_final: 0.7950 (tm-30) REVERT: Z 57 ARG cc_start: 0.9148 (mmp80) cc_final: 0.8786 (mmm-85) REVERT: Z 81 ARG cc_start: 0.7011 (ttt180) cc_final: 0.6078 (tmt170) REVERT: Z 87 ARG cc_start: 0.8258 (ptm160) cc_final: 0.7483 (ptm160) REVERT: Z 89 ASN cc_start: 0.8724 (m110) cc_final: 0.8032 (m110) REVERT: Z 90 LEU cc_start: 0.9022 (mt) cc_final: 0.8675 (mt) REVERT: Z 93 GLU cc_start: 0.8421 (mp0) cc_final: 0.8130 (pm20) REVERT: Z 97 MET cc_start: 0.7849 (mpp) cc_final: 0.7543 (mpp) REVERT: a 4 GLU cc_start: 0.8217 (pt0) cc_final: 0.7857 (pt0) REVERT: d 46 ASN cc_start: 0.8514 (m-40) cc_final: 0.6929 (t0) REVERT: d 70 PHE cc_start: 0.8750 (t80) cc_final: 0.8523 (t80) REVERT: e 36 GLU cc_start: 0.8772 (tp30) cc_final: 0.8477 (tt0) REVERT: f 15 LEU cc_start: 0.8547 (tp) cc_final: 0.7973 (tp) REVERT: g 60 VAL cc_start: 0.6909 (t) cc_final: 0.6440 (t) REVERT: g 87 GLU cc_start: 0.9038 (tp30) cc_final: 0.8354 (pm20) REVERT: h 19 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8409 (mtmt) REVERT: m 45 GLU cc_start: 0.8915 (tp30) cc_final: 0.8330 (tp30) REVERT: m 49 GLN cc_start: 0.9103 (mt0) cc_final: 0.8821 (mt0) REVERT: m 87 LEU cc_start: 0.8395 (mp) cc_final: 0.8016 (tp) REVERT: m 109 ASP cc_start: 0.8736 (m-30) cc_final: 0.8518 (m-30) REVERT: n 56 MET cc_start: 0.7717 (tpt) cc_final: 0.7180 (tmm) REVERT: n 68 GLU cc_start: 0.8741 (mp0) cc_final: 0.8184 (mp0) REVERT: n 69 GLU cc_start: 0.7246 (mp0) cc_final: 0.6992 (mp0) REVERT: p 88 GLU cc_start: 0.9223 (tt0) cc_final: 0.8569 (tp30) outliers start: 0 outliers final: 0 residues processed: 883 average time/residue: 0.4909 time to fit residues: 749.8565 Evaluate side-chains 716 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 716 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 687 random chunks: chunk 409 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 395 optimal weight: 0.9980 chunk 199 optimal weight: 30.0000 chunk 130 optimal weight: 7.9990 chunk 128 optimal weight: 0.0040 chunk 420 optimal weight: 0.7980 chunk 451 optimal weight: 20.0000 chunk 327 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 520 optimal weight: 6.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** 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 421 HIS H 5 ASN ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 ASN ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN M 26 ASN M 83 HIS M 168 GLN ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 63 GLN N 197 ASN X 72 GLN X 105 GLN Y 128 GLN ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 25 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.272 52631 Z= 0.603 Angle : 1.811 50.869 72262 Z= 1.159 Chirality : 0.330 6.446 8863 Planarity : 0.005 0.138 9461 Dihedral : 5.757 169.983 8296 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.21 % Favored : 89.91 % Rotamer: Outliers : 0.03 % Allowed : 1.64 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 1.32 % 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: -1.89 (0.11), residues: 5840 helix: -0.17 (0.09), residues: 3053 sheet: -0.95 (0.41), residues: 168 loop : -2.66 (0.12), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 196 HIS 0.010 0.001 HIS L 248 PHE 0.037 0.002 PHE H 237 TYR 0.052 0.002 TYR L 159 ARG 0.009 0.001 ARG D 388 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 924 time to evaluate : 4.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8185 (m-10) cc_final: 0.7947 (m-10) REVERT: A 68 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8509 (tm-30) REVERT: A 69 ILE cc_start: 0.9059 (pt) cc_final: 0.8784 (pt) REVERT: A 108 GLN cc_start: 0.8228 (mm110) cc_final: 0.6921 (pm20) REVERT: B 43 SER cc_start: 0.9056 (t) cc_final: 0.8661 (m) REVERT: B 48 MET cc_start: 0.8720 (tpp) cc_final: 0.8361 (tpp) REVERT: B 60 MET cc_start: 0.8297 (mtp) cc_final: 0.7875 (ttm) REVERT: B 67 TYR cc_start: 0.7503 (m-10) cc_final: 0.7287 (m-10) REVERT: B 84 ASP cc_start: 0.8341 (p0) cc_final: 0.8042 (p0) REVERT: B 104 TYR cc_start: 0.8798 (t80) cc_final: 0.8496 (t80) REVERT: B 106 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7897 (tp-100) REVERT: C 61 LEU cc_start: 0.9158 (mm) cc_final: 0.8851 (tp) REVERT: C 73 LYS cc_start: 0.8215 (mttt) cc_final: 0.7614 (mttt) REVERT: C 92 ILE cc_start: 0.8305 (mt) cc_final: 0.7964 (mt) REVERT: C 108 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8444 (mtmm) REVERT: C 110 TYR cc_start: 0.5638 (t80) cc_final: 0.5143 (m-80) REVERT: C 131 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8203 (mt-10) REVERT: C 133 GLU cc_start: 0.9118 (tt0) cc_final: 0.8631 (tm-30) REVERT: C 137 MET cc_start: 0.7289 (mtp) cc_final: 0.6198 (ttt) REVERT: C 154 ASP cc_start: 0.8455 (t0) cc_final: 0.8078 (t0) REVERT: D 62 LEU cc_start: 0.9045 (mt) cc_final: 0.8100 (mt) REVERT: D 83 LEU cc_start: 0.9262 (tp) cc_final: 0.8994 (tt) REVERT: D 156 THR cc_start: 0.9166 (p) cc_final: 0.8895 (t) REVERT: D 169 TRP cc_start: 0.8764 (m100) cc_final: 0.7108 (m100) REVERT: D 193 TYR cc_start: 0.8327 (t80) cc_final: 0.8105 (t80) REVERT: D 248 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6572 (tp30) REVERT: D 338 MET cc_start: 0.9105 (ptm) cc_final: 0.8757 (ppp) REVERT: F 390 ASP cc_start: 0.8878 (t70) cc_final: 0.8541 (t70) REVERT: G 53 ARG cc_start: 0.9032 (mmm-85) cc_final: 0.8503 (tpp80) REVERT: G 104 ASP cc_start: 0.8492 (m-30) cc_final: 0.8158 (m-30) REVERT: H 8 MET cc_start: 0.8041 (ttt) cc_final: 0.7817 (ttm) REVERT: H 25 ARG cc_start: 0.7954 (mpt-90) cc_final: 0.7699 (mmt180) REVERT: H 31 MET cc_start: 0.9103 (mmm) cc_final: 0.8561 (mmt) REVERT: H 85 MET cc_start: 0.8657 (tpp) cc_final: 0.8275 (tpp) REVERT: H 126 LYS cc_start: 0.5026 (mppt) cc_final: 0.4371 (mmmt) REVERT: H 154 LEU cc_start: 0.9174 (mm) cc_final: 0.8920 (tp) REVERT: H 183 MET cc_start: 0.8729 (tpp) cc_final: 0.8372 (tpt) REVERT: H 230 ASN cc_start: 0.8278 (m110) cc_final: 0.7865 (m-40) REVERT: H 290 TRP cc_start: 0.8739 (m100) cc_final: 0.8392 (m100) REVERT: H 301 CYS cc_start: 0.8701 (t) cc_final: 0.8484 (t) REVERT: H 304 HIS cc_start: 0.8951 (m-70) cc_final: 0.8423 (m-70) REVERT: I 40 TYR cc_start: 0.6902 (t80) cc_final: 0.6655 (t80) REVERT: I 48 ILE cc_start: 0.9128 (mp) cc_final: 0.8744 (pt) REVERT: I 117 ILE cc_start: 0.8693 (pt) cc_final: 0.7858 (pt) REVERT: I 129 ASP cc_start: 0.9065 (t0) cc_final: 0.8598 (t0) REVERT: J 24 PRO cc_start: 0.8724 (Cg_endo) cc_final: 0.8452 (Cg_exo) REVERT: J 74 MET cc_start: 0.8925 (mmm) cc_final: 0.8466 (mmm) REVERT: J 99 MET cc_start: 0.8328 (tpp) cc_final: 0.7951 (tpt) REVERT: K 25 HIS cc_start: 0.7932 (m-70) cc_final: 0.7336 (m170) REVERT: K 37 MET cc_start: 0.8669 (mmp) cc_final: 0.8319 (mmm) REVERT: L 71 ILE cc_start: 0.7976 (mm) cc_final: 0.7491 (mm) REVERT: L 83 ASP cc_start: 0.7750 (t0) cc_final: 0.7415 (t0) REVERT: L 101 MET cc_start: 0.9068 (mmm) cc_final: 0.8574 (mmt) REVERT: L 102 GLU cc_start: 0.7855 (pt0) cc_final: 0.6439 (tm-30) REVERT: L 103 PHE cc_start: 0.7846 (m-80) cc_final: 0.7416 (m-80) REVERT: L 104 SER cc_start: 0.9540 (m) cc_final: 0.8515 (t) REVERT: L 105 MET cc_start: 0.8803 (mmp) cc_final: 0.8587 (mmm) REVERT: L 131 LEU cc_start: 0.9588 (tp) cc_final: 0.9338 (tp) REVERT: L 142 ILE cc_start: 0.8821 (mp) cc_final: 0.8592 (tt) REVERT: L 150 MET cc_start: 0.8847 (mmp) cc_final: 0.8543 (mmt) REVERT: L 186 MET cc_start: 0.8848 (tpp) cc_final: 0.8579 (tpp) REVERT: L 237 MET cc_start: 0.8597 (mmp) cc_final: 0.7479 (ppp) REVERT: L 249 SER cc_start: 0.8660 (p) cc_final: 0.8172 (t) REVERT: L 279 CYS cc_start: 0.8436 (t) cc_final: 0.8093 (t) REVERT: L 297 ASP cc_start: 0.8819 (t0) cc_final: 0.8365 (t0) REVERT: L 341 MET cc_start: 0.8020 (tpt) cc_final: 0.7428 (tpt) REVERT: L 393 ASP cc_start: 0.8204 (m-30) cc_final: 0.7666 (m-30) REVERT: L 426 ILE cc_start: 0.9367 (mt) cc_final: 0.9166 (tt) REVERT: L 429 PHE cc_start: 0.7887 (t80) cc_final: 0.7585 (t80) REVERT: L 544 MET cc_start: 0.7111 (mtp) cc_final: 0.6283 (tmm) REVERT: M 10 MET cc_start: 0.8695 (mmm) cc_final: 0.8381 (ttm) REVERT: M 30 HIS cc_start: 0.8403 (m90) cc_final: 0.7894 (m90) REVERT: M 41 LEU cc_start: 0.8396 (mp) cc_final: 0.8057 (tp) REVERT: M 76 MET cc_start: 0.8072 (mtt) cc_final: 0.7346 (mtm) REVERT: M 120 ILE cc_start: 0.9380 (pt) cc_final: 0.8772 (mt) REVERT: M 178 MET cc_start: 0.7952 (pmm) cc_final: 0.7360 (mmm) REVERT: M 222 GLU cc_start: 0.8443 (tp30) cc_final: 0.7656 (tp30) REVERT: M 257 MET cc_start: 0.8201 (mtp) cc_final: 0.7409 (mmm) REVERT: M 310 MET cc_start: 0.7621 (mmt) cc_final: 0.7128 (mmm) REVERT: M 342 MET cc_start: 0.8943 (mmm) cc_final: 0.8174 (mmm) REVERT: M 355 MET cc_start: 0.9031 (mmm) cc_final: 0.8681 (tpt) REVERT: M 383 MET cc_start: 0.8963 (mpp) cc_final: 0.8414 (mpp) REVERT: M 394 ILE cc_start: 0.8816 (mm) cc_final: 0.8267 (tp) REVERT: M 433 GLU cc_start: 0.8620 (tp30) cc_final: 0.8212 (tp30) REVERT: N 14 MET cc_start: 0.7705 (mmm) cc_final: 0.7306 (mmt) REVERT: N 54 GLU cc_start: 0.8192 (tt0) cc_final: 0.6995 (tp30) REVERT: N 63 GLN cc_start: 0.8668 (mt0) cc_final: 0.8335 (mt0) REVERT: N 71 MET cc_start: 0.9321 (mmm) cc_final: 0.8955 (mmp) REVERT: N 245 LEU cc_start: 0.8862 (tp) cc_final: 0.8449 (tp) REVERT: N 248 LEU cc_start: 0.8818 (mm) cc_final: 0.8373 (mm) REVERT: N 268 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7323 (tm-30) REVERT: N 269 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7254 (mm-30) REVERT: N 270 MET cc_start: 0.8967 (mtt) cc_final: 0.8306 (mtt) REVERT: N 288 LEU cc_start: 0.9339 (tp) cc_final: 0.9028 (tp) REVERT: O 113 GLU cc_start: 0.8771 (pp20) cc_final: 0.8434 (pp20) REVERT: O 131 ASP cc_start: 0.7946 (t0) cc_final: 0.7354 (t0) REVERT: O 162 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7750 (tp30) REVERT: V 54 LYS cc_start: 0.8747 (mttt) cc_final: 0.8535 (tptt) REVERT: W 33 GLU cc_start: 0.8190 (mp0) cc_final: 0.7866 (mp0) REVERT: W 86 LYS cc_start: 0.9039 (tttm) cc_final: 0.8576 (tppp) REVERT: X 31 TYR cc_start: 0.7999 (t80) cc_final: 0.7750 (t80) REVERT: X 48 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7361 (tp30) REVERT: X 67 LEU cc_start: 0.8783 (tt) cc_final: 0.8425 (mt) REVERT: X 68 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7761 (tm-30) REVERT: X 84 TYR cc_start: 0.8465 (t80) cc_final: 0.8098 (t80) REVERT: Z 48 SER cc_start: 0.9000 (m) cc_final: 0.8658 (t) REVERT: Z 55 GLU cc_start: 0.8407 (tp30) cc_final: 0.7943 (tm-30) REVERT: Z 57 ARG cc_start: 0.9062 (mmp80) cc_final: 0.8390 (mmm-85) REVERT: Z 81 ARG cc_start: 0.6833 (ttt180) cc_final: 0.5942 (tmt170) REVERT: Z 87 ARG cc_start: 0.8223 (ptm160) cc_final: 0.7424 (ptm160) REVERT: a 4 GLU cc_start: 0.8015 (pt0) cc_final: 0.7729 (pt0) REVERT: b 7 PHE cc_start: 0.7468 (t80) cc_final: 0.6900 (t80) REVERT: d 46 ASN cc_start: 0.8380 (m-40) cc_final: 0.6923 (t0) REVERT: e 36 GLU cc_start: 0.8925 (tp30) cc_final: 0.8493 (mt-10) REVERT: f 15 LEU cc_start: 0.8607 (tp) cc_final: 0.8262 (tp) REVERT: g 60 VAL cc_start: 0.6690 (t) cc_final: 0.6283 (t) REVERT: g 87 GLU cc_start: 0.8938 (tp30) cc_final: 0.8572 (tp30) REVERT: h 19 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8294 (mtmt) REVERT: m 44 ARG cc_start: 0.8772 (tpp80) cc_final: 0.8290 (tpt-90) REVERT: m 45 GLU cc_start: 0.8761 (tp30) cc_final: 0.8345 (tp30) REVERT: m 109 ASP cc_start: 0.8730 (m-30) cc_final: 0.8498 (m-30) REVERT: n 56 MET cc_start: 0.7731 (tpt) cc_final: 0.7159 (tmm) REVERT: n 68 GLU cc_start: 0.8747 (mp0) cc_final: 0.8165 (mp0) REVERT: n 69 GLU cc_start: 0.7091 (mp0) cc_final: 0.6836 (mp0) REVERT: p 88 GLU cc_start: 0.9007 (tt0) cc_final: 0.8575 (tp30) REVERT: p 98 ASP cc_start: 0.8423 (t0) cc_final: 0.8086 (t0) REVERT: p 105 ILE cc_start: 0.9358 (tt) cc_final: 0.9136 (tt) outliers start: 1 outliers final: 0 residues processed: 924 average time/residue: 0.4752 time to fit residues: 757.9231 Evaluate side-chains 747 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 747 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 687 random chunks: chunk 602 optimal weight: 40.0000 chunk 634 optimal weight: 10.0000 chunk 578 optimal weight: 5.9990 chunk 617 optimal weight: 20.0000 chunk 371 optimal weight: 0.7980 chunk 268 optimal weight: 0.9980 chunk 484 optimal weight: 6.9990 chunk 189 optimal weight: 20.0000 chunk 557 optimal weight: 0.9980 chunk 583 optimal weight: 9.9990 chunk 614 optimal weight: 20.0000 overall best weight: 3.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN ** 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 421 HIS H 5 ASN H 38 ASN ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 107 GLN O 167 HIS X 72 GLN ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.262 52631 Z= 0.615 Angle : 1.824 50.910 72262 Z= 1.165 Chirality : 0.331 6.456 8863 Planarity : 0.005 0.145 9461 Dihedral : 5.792 170.704 8296 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.79 % Allowed : 10.41 % Favored : 88.80 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 1.65 % 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: -1.82 (0.11), residues: 5840 helix: -0.12 (0.09), residues: 3057 sheet: -1.12 (0.41), residues: 170 loop : -2.60 (0.12), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 196 HIS 0.011 0.002 HIS D 190 PHE 0.028 0.002 PHE g 62 TYR 0.033 0.002 TYR H 142 ARG 0.009 0.001 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 868 time to evaluate : 4.100 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 68 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8514 (tm-30) REVERT: A 69 ILE cc_start: 0.9221 (pt) cc_final: 0.8898 (pt) REVERT: A 73 LEU cc_start: 0.9340 (mt) cc_final: 0.8864 (mt) REVERT: B 60 MET cc_start: 0.8326 (mtp) cc_final: 0.7802 (ttm) REVERT: B 62 MET cc_start: 0.8903 (mmt) cc_final: 0.8620 (mmt) REVERT: B 86 MET cc_start: 0.7717 (mtp) cc_final: 0.7405 (mtm) REVERT: B 94 ASN cc_start: 0.9356 (m110) cc_final: 0.8929 (m110) REVERT: B 106 GLN cc_start: 0.8509 (tp-100) cc_final: 0.7977 (tp-100) REVERT: B 121 ASN cc_start: 0.9399 (m-40) cc_final: 0.9064 (m-40) REVERT: C 73 LYS cc_start: 0.8118 (mttt) cc_final: 0.7571 (mttt) REVERT: C 92 ILE cc_start: 0.8394 (mt) cc_final: 0.7990 (mt) REVERT: C 131 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8198 (mt-10) REVERT: C 133 GLU cc_start: 0.9173 (tt0) cc_final: 0.8679 (tm-30) REVERT: C 154 ASP cc_start: 0.8642 (t0) cc_final: 0.8213 (t0) REVERT: D 83 LEU cc_start: 0.9355 (tp) cc_final: 0.9094 (tt) REVERT: D 156 THR cc_start: 0.9223 (p) cc_final: 0.8896 (t) REVERT: D 169 TRP cc_start: 0.8733 (m100) cc_final: 0.6989 (m100) REVERT: D 193 TYR cc_start: 0.8487 (t80) cc_final: 0.8095 (t80) REVERT: D 248 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6873 (tp30) REVERT: D 338 MET cc_start: 0.9147 (ptm) cc_final: 0.8818 (ppp) REVERT: F 390 ASP cc_start: 0.8927 (t70) cc_final: 0.8569 (t70) REVERT: G 53 ARG cc_start: 0.9022 (mmm-85) cc_final: 0.8591 (tpp80) REVERT: H 8 MET cc_start: 0.8068 (ttt) cc_final: 0.7752 (ttm) REVERT: H 24 GLU cc_start: 0.9003 (tp30) cc_final: 0.8599 (tp30) REVERT: H 25 ARG cc_start: 0.8171 (mpt-90) cc_final: 0.7846 (mmt180) REVERT: H 31 MET cc_start: 0.9220 (mmm) cc_final: 0.8718 (tpp) REVERT: H 98 MET cc_start: 0.7674 (tpt) cc_final: 0.7421 (tpt) REVERT: H 126 LYS cc_start: 0.5534 (mppt) cc_final: 0.4710 (mmmt) REVERT: H 183 MET cc_start: 0.8737 (tpp) cc_final: 0.8491 (tpt) REVERT: H 230 ASN cc_start: 0.8375 (m110) cc_final: 0.7990 (m110) REVERT: H 290 TRP cc_start: 0.8884 (m100) cc_final: 0.8517 (m-10) REVERT: H 304 HIS cc_start: 0.9002 (m-70) cc_final: 0.8424 (m-70) REVERT: I 117 ILE cc_start: 0.8788 (pt) cc_final: 0.8281 (pt) REVERT: I 129 ASP cc_start: 0.9153 (t0) cc_final: 0.8948 (t0) REVERT: I 137 PHE cc_start: 0.7681 (m-10) cc_final: 0.7446 (m-10) REVERT: J 24 PRO cc_start: 0.8848 (Cg_endo) cc_final: 0.8628 (Cg_exo) REVERT: J 74 MET cc_start: 0.8956 (mmm) cc_final: 0.8441 (mmm) REVERT: K 25 HIS cc_start: 0.8018 (m-70) cc_final: 0.7172 (m170) REVERT: L 83 ASP cc_start: 0.7856 (t0) cc_final: 0.7537 (t0) REVERT: L 101 MET cc_start: 0.9099 (mmm) cc_final: 0.8506 (mmt) REVERT: L 102 GLU cc_start: 0.7886 (pt0) cc_final: 0.6660 (tm-30) REVERT: L 103 PHE cc_start: 0.7866 (m-80) cc_final: 0.7379 (m-80) REVERT: L 104 SER cc_start: 0.9556 (m) cc_final: 0.8450 (t) REVERT: L 142 ILE cc_start: 0.8814 (mp) cc_final: 0.8578 (tt) REVERT: L 237 MET cc_start: 0.8622 (mmp) cc_final: 0.8276 (mmp) REVERT: L 249 SER cc_start: 0.8791 (p) cc_final: 0.8290 (t) REVERT: L 279 CYS cc_start: 0.8470 (t) cc_final: 0.8121 (t) REVERT: L 297 ASP cc_start: 0.8880 (t0) cc_final: 0.8660 (t0) REVERT: L 341 MET cc_start: 0.8109 (tpt) cc_final: 0.7433 (tpt) REVERT: L 393 ASP cc_start: 0.8234 (m-30) cc_final: 0.7751 (m-30) REVERT: L 429 PHE cc_start: 0.8014 (t80) cc_final: 0.7675 (t80) REVERT: L 544 MET cc_start: 0.7255 (mtp) cc_final: 0.6366 (tmm) REVERT: M 10 MET cc_start: 0.8770 (mmm) cc_final: 0.8257 (ttm) REVERT: M 30 HIS cc_start: 0.8393 (m90) cc_final: 0.7851 (m90) REVERT: M 41 LEU cc_start: 0.8304 (mp) cc_final: 0.8009 (tp) REVERT: M 76 MET cc_start: 0.8182 (mtt) cc_final: 0.7402 (mtm) REVERT: M 120 ILE cc_start: 0.9470 (pt) cc_final: 0.8922 (mt) REVERT: M 178 MET cc_start: 0.7847 (pmm) cc_final: 0.7334 (mmm) REVERT: M 216 LEU cc_start: 0.9334 (tp) cc_final: 0.9044 (tt) REVERT: M 255 ASP cc_start: 0.8747 (p0) cc_final: 0.8506 (p0) REVERT: M 257 MET cc_start: 0.8229 (mtp) cc_final: 0.7497 (mmm) REVERT: M 310 MET cc_start: 0.7720 (mmt) cc_final: 0.7099 (mmm) REVERT: M 342 MET cc_start: 0.9030 (mmm) cc_final: 0.8272 (mmm) REVERT: M 383 MET cc_start: 0.8971 (mpp) cc_final: 0.8482 (mpp) REVERT: M 433 GLU cc_start: 0.8711 (tp30) cc_final: 0.8448 (tp30) REVERT: N 14 MET cc_start: 0.7825 (mmm) cc_final: 0.7422 (mmt) REVERT: N 54 GLU cc_start: 0.8012 (tt0) cc_final: 0.7064 (tp30) REVERT: N 63 GLN cc_start: 0.8613 (mt0) cc_final: 0.8258 (mt0) REVERT: N 72 MET cc_start: 0.9019 (tpp) cc_final: 0.8725 (tpt) REVERT: N 96 MET cc_start: 0.8653 (tpp) cc_final: 0.7859 (tmm) REVERT: N 211 MET cc_start: 0.9115 (ttm) cc_final: 0.8340 (ttm) REVERT: N 218 MET cc_start: 0.8886 (ttp) cc_final: 0.8621 (tmm) REVERT: N 245 LEU cc_start: 0.9002 (tp) cc_final: 0.8648 (tp) REVERT: N 248 LEU cc_start: 0.8704 (mm) cc_final: 0.8241 (mm) REVERT: N 251 MET cc_start: 0.9318 (tpp) cc_final: 0.8731 (tpp) REVERT: N 268 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7915 (tm-30) REVERT: N 270 MET cc_start: 0.8996 (mtt) cc_final: 0.8416 (mtt) REVERT: N 288 LEU cc_start: 0.9404 (tp) cc_final: 0.9104 (tp) REVERT: O 113 GLU cc_start: 0.8781 (pp20) cc_final: 0.8460 (pp20) REVERT: O 131 ASP cc_start: 0.8166 (t0) cc_final: 0.7850 (t0) REVERT: O 162 GLU cc_start: 0.8705 (mt-10) cc_final: 0.7826 (tp30) REVERT: V 54 LYS cc_start: 0.8853 (mttt) cc_final: 0.8512 (tptt) REVERT: W 33 GLU cc_start: 0.8279 (mp0) cc_final: 0.8055 (mp0) REVERT: W 86 LYS cc_start: 0.8979 (tttm) cc_final: 0.8496 (tttt) REVERT: X 31 TYR cc_start: 0.8058 (t80) cc_final: 0.7822 (t80) REVERT: X 67 LEU cc_start: 0.8847 (tt) cc_final: 0.8445 (mt) REVERT: X 68 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7807 (tm-30) REVERT: X 84 TYR cc_start: 0.8376 (t80) cc_final: 0.8072 (t80) REVERT: Z 48 SER cc_start: 0.9061 (m) cc_final: 0.8692 (t) REVERT: Z 55 GLU cc_start: 0.8506 (tp30) cc_final: 0.7939 (tm-30) REVERT: Z 57 ARG cc_start: 0.9063 (mmp80) cc_final: 0.8436 (mmm-85) REVERT: Z 81 ARG cc_start: 0.6901 (ttt180) cc_final: 0.5881 (tmt170) REVERT: Z 85 MET cc_start: 0.8784 (mmp) cc_final: 0.8532 (mmm) REVERT: Z 87 ARG cc_start: 0.8233 (ptm160) cc_final: 0.7535 (ptm160) REVERT: Z 89 ASN cc_start: 0.8646 (m110) cc_final: 0.7915 (m110) REVERT: Z 90 LEU cc_start: 0.8963 (mt) cc_final: 0.8542 (mt) REVERT: Z 93 GLU cc_start: 0.8474 (mp0) cc_final: 0.8005 (pm20) REVERT: Z 97 MET cc_start: 0.7892 (mpp) cc_final: 0.7684 (mpp) REVERT: a 4 GLU cc_start: 0.8201 (pt0) cc_final: 0.7812 (pt0) REVERT: b 7 PHE cc_start: 0.7558 (t80) cc_final: 0.6979 (t80) REVERT: b 43 MET cc_start: 0.7485 (ptm) cc_final: 0.7031 (ppp) REVERT: b 44 ILE cc_start: 0.9460 (pt) cc_final: 0.9213 (pt) REVERT: d 46 ASN cc_start: 0.8417 (m-40) cc_final: 0.6933 (t0) REVERT: e 36 GLU cc_start: 0.8822 (tp30) cc_final: 0.8459 (tt0) REVERT: f 15 LEU cc_start: 0.8566 (tp) cc_final: 0.7728 (tp) REVERT: g 60 VAL cc_start: 0.6629 (t) cc_final: 0.6049 (t) REVERT: g 80 LEU cc_start: 0.9169 (mt) cc_final: 0.8908 (mt) REVERT: g 87 GLU cc_start: 0.9022 (tp30) cc_final: 0.8625 (tp30) REVERT: h 19 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8283 (mtmt) REVERT: m 45 GLU cc_start: 0.8844 (tp30) cc_final: 0.8507 (tp30) REVERT: m 49 GLN cc_start: 0.9051 (mt0) cc_final: 0.8821 (mt0) REVERT: m 109 ASP cc_start: 0.8751 (m-30) cc_final: 0.8536 (m-30) REVERT: n 56 MET cc_start: 0.7748 (tpt) cc_final: 0.7179 (tmm) REVERT: n 68 GLU cc_start: 0.8716 (mp0) cc_final: 0.8177 (mp0) REVERT: n 69 GLU cc_start: 0.7232 (mp0) cc_final: 0.6958 (mp0) REVERT: p 88 GLU cc_start: 0.9042 (tt0) cc_final: 0.8518 (tp30) REVERT: p 89 MET cc_start: 0.8775 (mmm) cc_final: 0.8558 (mmm) REVERT: p 98 ASP cc_start: 0.8662 (t0) cc_final: 0.8408 (t0) outliers start: 0 outliers final: 0 residues processed: 868 average time/residue: 0.4664 time to fit residues: 701.0615 Evaluate side-chains 733 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 733 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 687 random chunks: chunk 405 optimal weight: 0.5980 chunk 652 optimal weight: 0.0070 chunk 398 optimal weight: 0.0470 chunk 309 optimal weight: 0.7980 chunk 453 optimal weight: 20.0000 chunk 684 optimal weight: 30.0000 chunk 629 optimal weight: 9.9990 chunk 545 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 420 optimal weight: 0.5980 chunk 334 optimal weight: 8.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 HIS H 5 ASN ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 ASN M 192 ASN ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 167 HIS X 34 GLN X 72 GLN X 105 GLN ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 30 ASN ** m 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.6442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.268 52631 Z= 0.606 Angle : 1.812 50.789 72262 Z= 1.158 Chirality : 0.330 6.457 8863 Planarity : 0.005 0.146 9461 Dihedral : 5.586 172.725 8296 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.75 % Allowed : 8.82 % Favored : 90.43 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: -1.77 (0.11), residues: 5840 helix: -0.07 (0.09), residues: 3056 sheet: -1.00 (0.41), residues: 168 loop : -2.59 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 303 HIS 0.024 0.001 HIS O 167 PHE 0.022 0.002 PHE D 103 TYR 0.040 0.002 TYR D 118 ARG 0.013 0.001 ARG D 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11680 Ramachandran restraints generated. 5840 Oldfield, 0 Emsley, 5840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 899 time to evaluate : 4.128 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: A 65 PHE cc_start: 0.8189 (m-10) cc_final: 0.7758 (m-10) REVERT: A 68 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8340 (tm-30) REVERT: A 69 ILE cc_start: 0.9157 (pt) cc_final: 0.8692 (pt) REVERT: B 43 SER cc_start: 0.8938 (t) cc_final: 0.8554 (m) REVERT: B 48 MET cc_start: 0.8555 (tpp) cc_final: 0.8253 (tpp) REVERT: B 60 MET cc_start: 0.8240 (mtp) cc_final: 0.7811 (ttm) REVERT: B 106 GLN cc_start: 0.8317 (tp-100) cc_final: 0.7981 (tp-100) REVERT: B 154 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7860 (mm-30) REVERT: C 61 LEU cc_start: 0.9111 (mm) cc_final: 0.8808 (tp) REVERT: C 73 LYS cc_start: 0.8090 (mttt) cc_final: 0.7585 (mttt) REVERT: C 92 ILE cc_start: 0.8399 (mt) cc_final: 0.8057 (mt) REVERT: C 108 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8412 (mtmm) REVERT: C 110 TYR cc_start: 0.5618 (t80) cc_final: 0.4969 (m-80) REVERT: C 131 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8206 (mt-10) REVERT: C 133 GLU cc_start: 0.9124 (tt0) cc_final: 0.8651 (tm-30) REVERT: C 137 MET cc_start: 0.7201 (mtp) cc_final: 0.6461 (ttt) REVERT: C 154 ASP cc_start: 0.8531 (t0) cc_final: 0.8098 (t0) REVERT: D 118 TYR cc_start: 0.8947 (t80) cc_final: 0.8709 (t80) REVERT: D 156 THR cc_start: 0.9186 (p) cc_final: 0.8882 (t) REVERT: D 169 TRP cc_start: 0.8811 (m100) cc_final: 0.7033 (m100) REVERT: D 248 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6737 (tp30) REVERT: D 259 MET cc_start: 0.7685 (mmm) cc_final: 0.7417 (mmm) REVERT: D 304 MET cc_start: 0.9043 (tpp) cc_final: 0.8650 (tpp) REVERT: D 338 MET cc_start: 0.9041 (ptm) cc_final: 0.8740 (ppp) REVERT: D 367 ILE cc_start: 0.9397 (tt) cc_final: 0.9196 (pt) REVERT: F 390 ASP cc_start: 0.8846 (t70) cc_final: 0.8499 (t70) REVERT: G 53 ARG cc_start: 0.9061 (mmm-85) cc_final: 0.8643 (tpp80) REVERT: G 104 ASP cc_start: 0.8385 (m-30) cc_final: 0.8177 (m-30) REVERT: H 8 MET cc_start: 0.8000 (ttt) cc_final: 0.7705 (ttm) REVERT: H 25 ARG cc_start: 0.7952 (mpt-90) cc_final: 0.7724 (mmt180) REVERT: H 31 MET cc_start: 0.9169 (mmm) cc_final: 0.8560 (mmt) REVERT: H 60 PRO cc_start: 0.6669 (Cg_endo) cc_final: 0.6190 (Cg_exo) REVERT: H 126 LYS cc_start: 0.4748 (mppt) cc_final: 0.4329 (mmmt) REVERT: H 154 LEU cc_start: 0.9160 (mm) cc_final: 0.8933 (tp) REVERT: H 183 MET cc_start: 0.8615 (tpp) cc_final: 0.8385 (tpt) REVERT: H 230 ASN cc_start: 0.8528 (m110) cc_final: 0.7894 (m110) REVERT: H 290 TRP cc_start: 0.8585 (m100) cc_final: 0.8302 (m100) REVERT: H 301 CYS cc_start: 0.8656 (t) cc_final: 0.8414 (t) REVERT: H 304 HIS cc_start: 0.8882 (m-70) cc_final: 0.8222 (m-70) REVERT: I 48 ILE cc_start: 0.9153 (mp) cc_final: 0.8792 (pt) REVERT: I 50 TYR cc_start: 0.8023 (t80) cc_final: 0.7697 (t80) REVERT: I 121 PHE cc_start: 0.8050 (m-80) cc_final: 0.7021 (m-80) REVERT: I 129 ASP cc_start: 0.9096 (t0) cc_final: 0.8890 (t0) REVERT: J 74 MET cc_start: 0.8890 (mmm) cc_final: 0.8283 (mmm) REVERT: K 25 HIS cc_start: 0.7820 (m-70) cc_final: 0.7073 (m170) REVERT: L 45 ILE cc_start: 0.8202 (pt) cc_final: 0.7985 (pt) REVERT: L 101 MET cc_start: 0.8989 (mmm) cc_final: 0.8124 (mmt) REVERT: L 102 GLU cc_start: 0.7775 (pt0) cc_final: 0.6343 (tm-30) REVERT: L 103 PHE cc_start: 0.7604 (m-80) cc_final: 0.7311 (m-80) REVERT: L 104 SER cc_start: 0.9540 (m) cc_final: 0.8349 (t) REVERT: L 142 ILE cc_start: 0.8794 (mp) cc_final: 0.8509 (tt) REVERT: L 150 MET cc_start: 0.8893 (mmp) cc_final: 0.8501 (mmm) REVERT: L 237 MET cc_start: 0.8508 (mmp) cc_final: 0.8228 (mmp) REVERT: L 249 SER cc_start: 0.8675 (p) cc_final: 0.8190 (t) REVERT: L 279 CYS cc_start: 0.8400 (t) cc_final: 0.8056 (t) REVERT: L 393 ASP cc_start: 0.8252 (m-30) cc_final: 0.7718 (m-30) REVERT: L 429 PHE cc_start: 0.7885 (t80) cc_final: 0.7625 (t80) REVERT: L 544 MET cc_start: 0.7198 (mtp) cc_final: 0.6315 (tmm) REVERT: M 10 MET cc_start: 0.8649 (mmm) cc_final: 0.8131 (ttm) REVERT: M 30 HIS cc_start: 0.8327 (m90) cc_final: 0.7732 (m90) REVERT: M 41 LEU cc_start: 0.8340 (mp) cc_final: 0.8064 (tp) REVERT: M 42 MET cc_start: 0.8648 (mmp) cc_final: 0.8443 (tpp) REVERT: M 76 MET cc_start: 0.8122 (mtt) cc_final: 0.7320 (mtm) REVERT: M 257 MET cc_start: 0.8177 (mtp) cc_final: 0.7440 (mmm) REVERT: M 310 MET cc_start: 0.7504 (mmt) cc_final: 0.7138 (mmm) REVERT: M 342 MET cc_start: 0.9092 (mmm) cc_final: 0.8185 (mmm) REVERT: M 383 MET cc_start: 0.8966 (mpp) cc_final: 0.8445 (mpp) REVERT: M 394 ILE cc_start: 0.8951 (mm) cc_final: 0.8472 (tp) REVERT: M 433 GLU cc_start: 0.8505 (tp30) cc_final: 0.8263 (tp30) REVERT: M 437 MET cc_start: 0.6914 (mmp) cc_final: 0.6432 (mmp) REVERT: N 14 MET cc_start: 0.7739 (mmm) cc_final: 0.7346 (mmt) REVERT: N 34 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8310 (mm-30) REVERT: N 37 MET cc_start: 0.7990 (mmp) cc_final: 0.7749 (mmp) REVERT: N 54 GLU cc_start: 0.7903 (tt0) cc_final: 0.6963 (tp30) REVERT: N 96 MET cc_start: 0.8355 (tpp) cc_final: 0.7648 (tmm) REVERT: N 211 MET cc_start: 0.8985 (ttm) cc_final: 0.8499 (ttm) REVERT: N 245 LEU cc_start: 0.8948 (tp) cc_final: 0.8522 (tp) REVERT: N 248 LEU cc_start: 0.8754 (mm) cc_final: 0.8192 (mm) REVERT: N 268 GLN cc_start: 0.8639 (tm-30) cc_final: 0.7359 (tm-30) REVERT: N 270 MET cc_start: 0.8975 (mtt) cc_final: 0.8542 (mtp) REVERT: N 288 LEU cc_start: 0.9359 (tp) cc_final: 0.9034 (tp) REVERT: O 113 GLU cc_start: 0.8764 (pp20) cc_final: 0.8478 (pp20) REVERT: O 131 ASP cc_start: 0.8021 (t0) cc_final: 0.7618 (t0) REVERT: O 162 GLU cc_start: 0.8752 (mt-10) cc_final: 0.7809 (tp30) REVERT: V 53 GLU cc_start: 0.8659 (pt0) cc_final: 0.8228 (tm-30) REVERT: V 54 LYS cc_start: 0.8936 (mttt) cc_final: 0.8265 (tptt) REVERT: W 33 GLU cc_start: 0.8315 (mp0) cc_final: 0.8103 (mp0) REVERT: W 86 LYS cc_start: 0.8918 (tttm) cc_final: 0.8531 (tttt) REVERT: X 41 GLU cc_start: 0.7783 (tp30) cc_final: 0.6861 (tp30) REVERT: X 43 MET cc_start: 0.7756 (mmm) cc_final: 0.7455 (mmm) REVERT: X 67 LEU cc_start: 0.8789 (tt) cc_final: 0.8419 (mt) REVERT: X 84 TYR cc_start: 0.8468 (t80) cc_final: 0.8121 (t80) REVERT: Z 48 SER cc_start: 0.9008 (m) cc_final: 0.8623 (t) REVERT: Z 55 GLU cc_start: 0.8381 (tp30) cc_final: 0.7932 (tm-30) REVERT: Z 57 ARG cc_start: 0.9009 (mmp80) cc_final: 0.8427 (mmm-85) REVERT: Z 81 ARG cc_start: 0.6838 (ttt180) cc_final: 0.6006 (tmt170) REVERT: Z 87 ARG cc_start: 0.8176 (ptm160) cc_final: 0.7461 (ptm160) REVERT: Z 89 ASN cc_start: 0.8608 (m110) cc_final: 0.7854 (m110) REVERT: Z 90 LEU cc_start: 0.8856 (mt) cc_final: 0.8449 (mt) REVERT: Z 93 GLU cc_start: 0.8424 (mp0) cc_final: 0.7854 (pm20) REVERT: a 4 GLU cc_start: 0.8019 (pt0) cc_final: 0.7689 (pt0) REVERT: a 21 MET cc_start: 0.8689 (tpp) cc_final: 0.8488 (tpp) REVERT: b 7 PHE cc_start: 0.7491 (t80) cc_final: 0.6939 (t80) REVERT: b 24 ILE cc_start: 0.8902 (tp) cc_final: 0.8485 (tp) REVERT: b 43 MET cc_start: 0.7354 (ptm) cc_final: 0.6907 (ppp) REVERT: b 44 ILE cc_start: 0.9421 (pt) cc_final: 0.9163 (pt) REVERT: d 46 ASN cc_start: 0.8311 (m-40) cc_final: 0.6948 (t0) REVERT: e 36 GLU cc_start: 0.8822 (tp30) cc_final: 0.8385 (mt-10) REVERT: f 15 LEU cc_start: 0.8847 (tp) cc_final: 0.8441 (tp) REVERT: g 60 VAL cc_start: 0.6630 (t) cc_final: 0.6235 (t) REVERT: g 80 LEU cc_start: 0.9122 (mt) cc_final: 0.8919 (mt) REVERT: g 87 GLU cc_start: 0.8991 (tp30) cc_final: 0.8564 (tp30) REVERT: h 19 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8152 (mtmt) REVERT: i 9 LEU cc_start: 0.8821 (tt) cc_final: 0.8266 (pt) REVERT: i 14 LEU cc_start: 0.9319 (mt) cc_final: 0.9108 (mt) REVERT: m 44 ARG cc_start: 0.8726 (tpp80) cc_final: 0.8480 (tpt-90) REVERT: m 45 GLU cc_start: 0.8708 (tp30) cc_final: 0.8229 (tp30) REVERT: m 109 ASP cc_start: 0.8739 (m-30) cc_final: 0.8501 (m-30) REVERT: n 56 MET cc_start: 0.7739 (tpt) cc_final: 0.7160 (tmm) REVERT: n 68 GLU cc_start: 0.8732 (mp0) cc_final: 0.8196 (mp0) REVERT: n 69 GLU cc_start: 0.7229 (mp0) cc_final: 0.6976 (mp0) REVERT: p 98 ASP cc_start: 0.8302 (t0) cc_final: 0.8060 (t0) REVERT: p 105 ILE cc_start: 0.9347 (tt) cc_final: 0.8949 (tt) outliers start: 0 outliers final: 0 residues processed: 899 average time/residue: 0.4773 time to fit residues: 746.9426 Evaluate side-chains 737 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 737 time to evaluate : 4.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 687 random chunks: chunk 432 optimal weight: 20.0000 chunk 580 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 502 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 545 optimal weight: 20.0000 chunk 228 optimal weight: 2.9990 chunk 560 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 100 optimal weight: 40.0000 overall best weight: 5.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 107 GLN ** O 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.066846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.059814 restraints weight = 293836.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.060917 restraints weight = 183931.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.061619 restraints weight = 127188.076| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.255 52631 Z= 0.652 Angle : 1.864 50.998 72262 Z= 1.180 Chirality : 0.332 6.481 8863 Planarity : 0.006 0.150 9461 Dihedral : 6.034 171.906 8296 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.82 % Allowed : 11.11 % Favored : 88.07 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 1.65 % 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: -1.89 (0.11), residues: 5840 helix: -0.17 (0.09), residues: 3075 sheet: -1.13 (0.42), residues: 159 loop : -2.66 (0.12), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP H 303 HIS 0.014 0.002 HIS O 167 PHE 0.036 0.002 PHE H 237 TYR 0.037 0.003 TYR D 118 ARG 0.012 0.001 ARG D 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12086.65 seconds wall clock time: 208 minutes 42.05 seconds (12522.05 seconds total)