Starting phenix.real_space_refine on Mon Mar 25 22:38:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lc5_4032/03_2024/5lc5_4032_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lc5_4032/03_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_4032/03_2024/5lc5_4032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lc5_4032/03_2024/5lc5_4032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lc5_4032/03_2024/5lc5_4032_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lc5_4032/03_2024/5lc5_4032_updated.pdb" } 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 Residue "A GLU 105": "OE1" <-> "OE2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 368": "OE1" <-> "OE2" Residue "L PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 51718 Number of models: 1 Model: "" Number of chains: 52 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: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 3614 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 591} Link IDs: {'PTRANS': 8, 'TRANS': 676} Unresolved non-hydrogen bonds: 1309 Unresolved non-hydrogen angles: 1884 Unresolved non-hydrogen dihedrals: 750 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 4, 'UNK:plan-1': 483, '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: 637 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: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1133 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 4, 'TRANS': 159} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'UNK:plan-1': 55, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 74 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: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 921 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 1, 'TRANS': 136} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 69 Planarities with less than four sites: {'UNK:plan-1': 69} Unresolved non-hydrogen planarities: 69 Chain: "a" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 480 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 60} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "b" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 519 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'UNK:plan-1': 35} Unresolved non-hydrogen planarities: 35 Chain: "c" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 320 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 42} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "d" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 790 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 2, 'TRANS': 111} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 45} Unresolved non-hydrogen planarities: 45 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: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 770 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 2, 'TRANS': 131} Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'UNK:plan-1': 95} Unresolved non-hydrogen planarities: 106 Chain: "i" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 616 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'UNK:plan-1': 79, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "j" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 260 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'TRANS': 51} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'UNK:plan-1': 52} Unresolved non-hydrogen planarities: 52 Chain: "k" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 370 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'TRANS': 73} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'UNK:plan-1': 74} Unresolved non-hydrogen planarities: 74 Chain: "l" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "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: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1088 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 7, 'TRANS': 158} Unresolved non-hydrogen bonds: 327 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 6, 'UNK:plan-1': 39, 'TRP:plan': 4, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 221 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: 28.42, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.32 Conformation dependent library (CDL) restraints added in 8.1 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... running ksdssp... Secondary structure from input PDB file: 281 helices and 19 sheets defined 56.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.50 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 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 56 through 71 removed outlier: 3.697A pdb=" N ILE A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 75 through 78 No H-bonds generated for 'chain 'A' and resid 75 through 78' 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 29 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 55 through 60 Processing helix chain 'B' and resid 94 through 106 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 122 Processing helix chain 'B' and resid 153 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 19 through 32 removed outlier: 3.660A pdb=" N ALA C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA C 30 " --> pdb=" O GLY C 26 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 32 " --> pdb=" O TYR C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 127 through 137 removed outlier: 3.537A pdb=" N GLU C 133 " --> pdb=" O TRP C 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 11 No H-bonds generated for 'chain 'D' and resid 8 through 11' Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.947A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 4.245A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 104' Processing helix chain 'D' and resid 116 through 125 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 165 through 184 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 208 through 226 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 248 through 251 No H-bonds generated for 'chain 'D' and resid 248 through 251' 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 295 through 305 removed outlier: 4.492A pdb=" N ARG D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.621A pdb=" N LYS D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 335 through 340' Processing helix chain 'D' and resid 342 through 350 Processing helix chain 'D' and resid 395 through 405 removed outlier: 3.832A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 3.894A 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 28 through 36 removed outlier: 3.582A pdb=" N ALA E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Proline residue: E 49 - end of helix removed outlier: 3.942A pdb=" N ALA E 54 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN E 55 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG E 56 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN E 57 " --> pdb=" O ALA E 54 " (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 109 No H-bonds generated for 'chain 'E' and resid 106 through 109' Processing helix chain 'E' and resid 114 through 123 Processing helix chain 'E' and resid 168 through 177 removed outlier: 4.008A pdb=" N LYS E 177 " --> pdb=" O ILE E 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 38 removed outlier: 3.836A pdb=" N SER F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 34 through 38' Processing helix chain 'F' and resid 45 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 80 Processing helix chain 'F' and resid 106 through 110 removed outlier: 3.710A pdb=" N ILE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 110' Processing helix chain 'F' and resid 115 through 124 removed outlier: 3.579A pdb=" N CYS F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 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 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' 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 228 No H-bonds generated for 'chain 'F' and resid 225 through 228' Processing helix chain 'F' and resid 231 through 236 Processing helix 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 322 No H-bonds generated for 'chain 'F' and resid 319 through 322' Processing helix chain 'F' and resid 343 through 357 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 366 No H-bonds generated for 'chain 'F' and resid 363 through 366' Processing helix chain 'F' and resid 369 through 381 removed outlier: 3.543A 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 388 through 399 removed outlier: 3.664A pdb=" N GLU F 394 " --> pdb=" O ASP F 390 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE F 395 " --> pdb=" O SER F 391 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN F 398 " --> pdb=" O GLU F 394 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE F 399 " --> pdb=" O ILE F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 410 No H-bonds generated for 'chain 'F' and resid 407 through 410' Processing helix chain 'F' and resid 413 through 419 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 424 through 436 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) Processing helix chain 'G' and resid 26 through 30 Processing helix chain 'G' and resid 84 through 97 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 158 through 164 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 265 through 268 No H-bonds generated for 'chain 'G' and resid 265 through 268' Processing helix chain 'G' and resid 296 through 308 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 327 through 337 Processing helix chain 'G' and resid 369 through 373 Processing helix chain 'G' and resid 389 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 427 through 432 removed outlier: 3.570A pdb=" N UNK G 431 " --> pdb=" O UNK G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 443 No H-bonds generated for 'chain 'G' and resid 440 through 443' Processing helix chain 'G' and resid 462 through 474 removed outlier: 3.533A pdb=" N UNK G 468 " --> pdb=" O UNK G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 503 Processing helix chain 'G' and resid 553 through 556 No H-bonds generated for 'chain 'G' and resid 553 through 556' Processing helix chain 'G' and resid 599 through 606 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) Processing helix chain 'G' and resid 617 through 622 removed outlier: 3.868A pdb=" N UNK G 621 " --> pdb=" O UNK G 617 " (cutoff:3.500A) Processing helix chain 'G' and resid 646 through 652 removed outlier: 3.704A pdb=" N UNK G 652 " --> pdb=" O UNK G 648 " (cutoff:3.500A) Processing helix chain 'G' and resid 682 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 11 through 18 Processing helix chain 'H' and resid 20 through 31 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 47 through 55 removed outlier: 4.201A pdb=" N ALA H 52 " --> pdb=" O PRO H 48 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE H 53 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 82 removed outlier: 4.008A pdb=" N ILE H 76 " --> pdb=" O ILE H 72 " (cutoff:3.500A) 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) Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 101 through 118 removed outlier: 3.676A pdb=" N MET H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) 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) Processing helix chain 'H' and resid 126 through 140 removed outlier: 3.718A pdb=" N ILE H 130 " --> pdb=" O LYS H 126 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY H 131 " --> pdb=" O TYR H 127 " (cutoff:3.500A) 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) Processing helix chain 'H' and resid 142 through 156 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 164 through 167 No H-bonds generated for 'chain 'H' and resid 164 through 167' Processing helix chain 'H' and resid 179 through 186 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) Processing helix chain 'H' and resid 188 through 191 Processing helix chain 'H' and resid 218 through 227 removed outlier: 3.621A pdb=" N PHE H 224 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA H 226 " --> pdb=" O LEU H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 241 Processing helix chain 'H' and resid 252 through 276 removed outlier: 3.570A pdb=" N ILE H 257 " --> pdb=" O GLU H 253 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR H 260 " --> pdb=" O THR H 256 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS H 262 " --> pdb=" O ASN H 258 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU H 266 " --> pdb=" O LYS H 262 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER H 269 " --> pdb=" O LEU H 265 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU H 271 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 276 " --> pdb=" O TRP H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 288 removed outlier: 3.944A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 310 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 15 through 25 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 29 through 34 Processing helix chain 'I' and resid 36 through 42 removed outlier: 3.779A pdb=" N TYR I 40 " --> pdb=" O MET I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 144 through 147 No H-bonds generated for 'chain 'I' and resid 144 through 147' Processing helix chain 'I' and resid 156 through 168 removed outlier: 3.634A pdb=" N ASP I 159 " --> pdb=" O ASN I 156 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS I 160 " --> pdb=" O ASN I 157 " (cutoff:3.500A) 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) Processing helix chain 'J' and resid 6 through 21 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 25 through 47 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) removed outlier: 3.824A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 60 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 62 through 70 removed outlier: 3.679A pdb=" N VAL J 66 " --> pdb=" O GLY J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 97 removed outlier: 4.003A pdb=" N ALA J 92 " --> pdb=" O ALA J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.575A pdb=" N TYR J 105 " --> pdb=" O PHE J 101 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR J 106 " --> pdb=" O PHE J 102 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL J 107 " --> pdb=" O MET J 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 101 through 107' Processing helix chain 'J' and resid 151 through 171 removed outlier: 3.704A pdb=" N ILE J 155 " --> pdb=" O THR J 151 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) 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 5 through 20 removed outlier: 3.605A pdb=" N VAL K 14 " --> pdb=" O MET K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 50 removed outlier: 3.583A pdb=" N GLU K 34 " --> pdb=" O LEU K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 67 Processing helix chain 'K' and resid 69 through 84 removed outlier: 3.705A pdb=" N LEU K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL K 79 " --> pdb=" O LEU K 75 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET K 80 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER K 82 " --> pdb=" O LEU K 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 20 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 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 85 through 105 removed outlier: 3.759A pdb=" N PHE L 89 " --> pdb=" O PHE L 85 " (cutoff:3.500A) 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) Processing helix chain 'L' and resid 114 through 132 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 150 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) Processing helix chain 'L' and resid 152 through 155 No H-bonds generated for 'chain 'L' and resid 152 through 155' Processing helix chain 'L' and resid 164 through 192 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 216 through 222 removed outlier: 3.792A pdb=" N THR L 221 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY L 222 " --> pdb=" O LEU L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 238 removed outlier: 4.009A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 249 removed outlier: 3.756A pdb=" N HIS L 248 " --> pdb=" O SER L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 262 removed outlier: 3.848A pdb=" N ALA L 255 " --> pdb=" O THR L 251 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLY L 256 " --> pdb=" O MET L 252 " (cutoff:3.500A) 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 265 through 269 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 318 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 323 through 349 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 393 through 399 Processing helix chain 'L' and resid 406 through 427 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) Processing helix chain 'L' and resid 448 through 460 removed outlier: 3.531A pdb=" N ASN L 452 " --> pdb=" O PRO L 448 " (cutoff:3.500A) 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 489 through 510 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 537 through 546 removed outlier: 3.718A pdb=" N SER L 545 " --> pdb=" O ASN L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 560 through 563 No H-bonds generated for 'chain 'L' and resid 560 through 563' Processing helix chain 'L' and resid 567 through 574 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 9 through 17 Proline residue: M 13 - end of helix removed outlier: 3.612A pdb=" N TRP M 16 " --> pdb=" O PRO M 13 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU M 17 " --> pdb=" O LEU M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 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 65 through 81 Proline residue: M 74 - end of helix removed outlier: 4.862A pdb=" N LEU M 77 " --> pdb=" O LEU M 73 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET M 78 " --> pdb=" O PRO M 74 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA M 79 " --> pdb=" O LEU M 75 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER M 80 " --> pdb=" O MET M 76 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 111 removed outlier: 4.182A pdb=" N LEU M 99 " --> pdb=" O PHE M 95 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 122 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) Processing helix chain 'M' and resid 125 through 134 removed outlier: 3.753A pdb=" N THR M 129 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE M 131 " --> pdb=" O VAL M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 150 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) Processing helix chain 'M' and resid 153 through 170 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 205 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) Processing helix chain 'M' and resid 214 through 221 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 237 Processing helix chain 'M' and resid 242 through 249 removed outlier: 4.030A pdb=" N ILE M 246 " --> pdb=" O MET M 243 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N THR M 247 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU M 248 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 275 removed outlier: 3.707A pdb=" N MET M 263 " --> pdb=" O TYR M 259 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY M 268 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET M 269 " --> pdb=" O SER M 265 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR M 272 " --> pdb=" O GLY M 268 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE M 275 " --> pdb=" O MET M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 287 removed outlier: 3.736A pdb=" N ILE M 286 " --> pdb=" O LEU M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 289 through 303 removed outlier: 3.596A pdb=" N MET M 294 " --> pdb=" O SER M 290 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 334 removed outlier: 3.982A pdb=" N MET M 310 " --> pdb=" O PRO M 306 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY M 311 " --> pdb=" O TRP M 307 " (cutoff:3.500A) 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) 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 374 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 405 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) Processing helix chain 'M' and resid 408 through 412 Processing helix chain 'M' and resid 432 through 446 removed outlier: 4.063A pdb=" N MET M 437 " --> pdb=" O GLU M 433 " (cutoff:3.500A) Proline residue: M 443 - end of helix Processing helix chain 'N' and resid 5 through 21 removed outlier: 3.673A pdb=" N ILE N 13 " --> pdb=" O ILE N 9 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET N 14 " --> pdb=" O LEU N 10 " (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 61 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) Processing helix chain 'N' and resid 64 through 79 removed outlier: 3.597A pdb=" N LEU N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 103 removed outlier: 3.973A pdb=" N LEU N 97 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 121 Processing helix chain 'N' and resid 128 through 142 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) Processing helix chain 'N' and resid 151 through 153 No H-bonds generated for 'chain 'N' and resid 151 through 153' Processing helix chain 'N' and resid 156 through 168 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) Processing helix chain 'N' and resid 175 through 193 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) Processing helix chain 'N' and resid 201 through 218 removed outlier: 3.558A pdb=" N LEU N 205 " --> pdb=" O THR N 201 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR N 217 " --> pdb=" O SER N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 230 Processing helix chain 'N' and resid 240 through 251 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 326 through 331 Processing helix chain 'N' and resid 340 through 344 Processing helix chain 'O' and resid 36 through 45 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) removed outlier: 5.073A pdb=" N UNK O 45 " --> pdb=" O UNK O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 84 Processing helix chain 'O' and resid 95 through 116 removed outlier: 3.564A pdb=" N TRP O 99 " --> pdb=" O ARG O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 139 removed outlier: 4.911A pdb=" N PHE O 132 " --> pdb=" O TYR O 129 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU O 135 " --> pdb=" O PHE O 132 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU O 136 " --> pdb=" O VAL O 133 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA O 137 " --> 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 177 through 184 removed outlier: 4.416A pdb=" N GLN O 180 " --> pdb=" O PRO O 177 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER O 181 " --> pdb=" O GLU O 178 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE O 183 " --> pdb=" O GLN O 180 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN O 184 " --> pdb=" O SER O 181 " (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 255 through 264 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 273 removed outlier: 4.671A pdb=" N TYR O 272 " --> pdb=" O GLU O 268 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR O 273 " --> pdb=" O VAL O 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 297 removed outlier: 3.748A pdb=" N GLN O 291 " --> pdb=" O HIS O 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 37 Processing helix chain 'P' and resid 53 through 59 removed outlier: 4.698A pdb=" N UNK P 58 " --> pdb=" O UNK P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 84 Processing helix chain 'P' and resid 112 through 123 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 149 through 158 Processing helix chain 'P' and resid 177 through 187 removed outlier: 3.630A pdb=" N UNK P 181 " --> pdb=" O UNK P 177 " (cutoff:3.500A) 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) removed outlier: 4.947A pdb=" N UNK P 187 " --> pdb=" O UNK P 183 " (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 238 through 248 removed outlier: 3.566A pdb=" N UNK P 248 " --> pdb=" O UNK P 244 " (cutoff:3.500A) Processing helix chain 'P' and resid 263 through 267 Processing helix chain 'P' and resid 281 through 288 removed outlier: 3.808A pdb=" N UNK P 285 " --> pdb=" O UNK P 281 " (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 'S' and resid 32 through 37 Processing helix chain 'S' and resid 40 through 46 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 12 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 46 through 58 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 67 No H-bonds generated for 'chain 'T' and resid 64 through 67' Processing helix chain 'T' and resid 73 through 80 removed outlier: 3.882A pdb=" N ASP T 78 " --> pdb=" O GLN T 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 20 removed outlier: 3.560A pdb=" N LYS U 12 " --> pdb=" O LEU U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 57 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 73 through 83 Processing helix chain 'V' and resid 22 through 34 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) 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 65 through 68 No H-bonds generated for 'chain 'V' and resid 65 through 68' Processing helix chain 'V' and resid 75 through 84 removed outlier: 3.784A pdb=" N VAL V 79 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN V 82 " --> pdb=" O GLU V 78 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 95 Processing helix chain 'W' and resid 26 through 39 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) Processing helix chain 'W' and resid 44 through 47 No H-bonds generated for 'chain 'W' and resid 44 through 47' Processing helix chain 'W' and resid 55 through 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 75 through 88 removed outlier: 3.543A pdb=" N LEU W 80 " --> pdb=" O ARG W 76 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET W 87 " --> pdb=" O ILE W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 123 removed outlier: 3.800A pdb=" N TYR W 122 " --> pdb=" O LEU W 118 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL W 123 " --> pdb=" O SER W 119 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 27 No H-bonds generated for 'chain 'X' and resid 24 through 27' Processing helix chain 'X' and resid 37 through 48 removed outlier: 3.519A pdb=" N GLU X 41 " --> pdb=" O LYS X 37 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU X 48 " --> pdb=" O LEU X 44 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 75 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 79 through 90 removed outlier: 3.589A pdb=" N ASP X 89 " --> pdb=" O TRP X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 103 No H-bonds generated for 'chain 'X' and resid 100 through 103' Processing helix chain 'X' and resid 110 through 112 No H-bonds generated for 'chain 'X' and resid 110 through 112' Processing helix chain 'Y' and resid 2 through 13 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 20 through 40 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) Processing helix chain 'Y' and resid 51 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 86 through 96 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) Processing helix chain 'Y' and resid 100 through 103 No H-bonds generated for 'chain 'Y' and resid 100 through 103' Processing helix chain 'Y' and resid 114 through 125 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 32 through 69 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) Processing helix chain 'Z' and resid 72 through 95 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 128 through 135 removed outlier: 3.854A pdb=" N UNK Z 133 " --> pdb=" O UNK Z 129 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 10 Processing helix chain 'a' and resid 12 through 30 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 '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 'b' and resid 8 through 13 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 34 removed outlier: 3.565A pdb=" N SER b 21 " --> pdb=" O LEU b 18 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA b 23 " --> pdb=" O ALA b 20 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ILE b 24 " --> pdb=" O SER b 21 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA b 25 " --> pdb=" O PHE b 22 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY b 26 " --> pdb=" O ALA b 23 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU b 27 " --> pdb=" O ILE b 24 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA b 28 " --> pdb=" O ALA b 25 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE b 30 " --> pdb=" O LEU b 27 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU b 31 " --> pdb=" O ALA b 28 " (cutoff:3.500A) Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 3.921A pdb=" N LEU b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET b 43 " --> pdb=" O LYS b 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE b 44 " --> pdb=" O TYR b 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 45 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 61 through 97 removed outlier: 3.589A pdb=" N PHE d 68 " --> pdb=" O TYR d 64 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE d 94 " --> pdb=" O MET d 90 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS d 95 " --> pdb=" O PHE d 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 42 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 46 through 49 No H-bonds generated for 'chain 'e' and resid 46 through 49' Processing helix chain 'e' and resid 56 through 66 removed outlier: 3.673A pdb=" N CYS e 65 " --> pdb=" O ASP e 61 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU e 66 " --> pdb=" O PHE e 62 " (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 4 through 9 removed outlier: 3.519A pdb=" N ARG f 8 " --> pdb=" O LEU f 4 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 31 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) Processing helix chain 'g' and resid 51 through 58 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) Processing helix chain 'g' and resid 61 through 68 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) Processing helix chain 'g' and resid 88 through 103 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 16 through 31 removed outlier: 3.516A pdb=" N ARG h 20 " --> pdb=" O PHE h 16 " (cutoff:3.500A) 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) Processing helix chain 'h' and resid 34 through 45 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: 3.569A pdb=" N UNK h 74 " --> pdb=" O UNK h 71 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N UNK h 75 " --> pdb=" O UNK h 72 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N UNK h 77 " --> pdb=" O UNK h 74 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N UNK h 78 " --> pdb=" O UNK h 75 " (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 10 through 23 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 43 through 52 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) removed outlier: 3.920A pdb=" N UNK i 52 " --> pdb=" O UNK i 48 " (cutoff:3.500A) Processing helix chain 'i' and resid 58 through 73 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) Processing helix chain 'i' and resid 75 through 86 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 20 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 17 through 22 Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.657A pdb=" N UNK k 49 " --> pdb=" O UNK k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 70 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) Processing helix chain 'l' and resid 99 through 118 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 27 through 50 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 62 through 72 removed outlier: 3.512A pdb=" N ARG m 66 " --> pdb=" O PRO m 62 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG m 71 " --> pdb=" O TRP m 67 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 91 removed outlier: 3.528A pdb=" N LEU m 91 " --> pdb=" O LEU m 87 " (cutoff:3.500A) Processing helix chain 'm' and resid 95 through 116 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 26 removed outlier: 3.605A pdb=" N ARG n 24 " --> pdb=" O LYS n 20 " (cutoff:3.500A) Processing helix chain 'n' and resid 33 through 51 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) Processing helix chain 'n' and resid 58 through 66 Processing helix chain 'n' and resid 100 through 102 No H-bonds generated for 'chain 'n' and resid 100 through 102' Processing helix chain 'n' and resid 115 through 130 removed outlier: 3.662A pdb=" N ARG n 121 " --> pdb=" O TYR n 117 " (cutoff:3.500A) Processing helix chain 'n' and resid 132 through 139 removed outlier: 3.664A pdb=" N UNK n 137 " --> pdb=" O GLU n 133 " (cutoff:3.500A) Processing helix chain 'o' and resid 59 through 72 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 81 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 28 through 39 removed outlier: 3.821A pdb=" N UNK p 38 " --> pdb=" O UNK p 34 " (cutoff:3.500A) Processing helix chain 'p' and resid 42 through 53 Processing helix chain 'p' and resid 81 through 115 removed outlier: 3.733A pdb=" N PHE p 85 " --> pdb=" O VAL p 81 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) 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 141 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) removed outlier: 3.672A pdb=" N ASP p 140 " --> pdb=" O LYS p 136 " (cutoff:3.500A) Processing helix chain 'p' and resid 151 through 171 removed outlier: 3.682A pdb=" N UNK p 155 " --> pdb=" O UNK p 151 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N UNK p 156 " --> pdb=" O UNK p 152 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N UNK p 171 " --> pdb=" O UNK p 167 " (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 28 Processing helix chain 'r' and resid 7 through 13 removed outlier: 3.540A pdb=" N UNK r 13 " --> pdb=" O UNK r 9 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 19 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= A, first strand: chain 'B' and resid 85 through 88 removed outlier: 6.375A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE B 144 " --> pdb=" O SER B 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 40 through 43 removed outlier: 4.380A pdb=" N VAL C 40 " --> pdb=" O CYS C 51 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE C 92 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 46 through 50 removed outlier: 3.602A pdb=" N LEU D 68 " --> pdb=" O LEU D 47 " (cutoff:3.500A) 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: 3.560A pdb=" N LYS D 75 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 363 through 368 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) Processing sheet with id= E, first strand: chain 'E' and resid 137 through 142 removed outlier: 7.738A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (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= F, first strand: chain 'F' and resid 222 through 224 removed outlier: 7.096A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 266 through 271 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: 4.084A pdb=" N GLU F 270 " --> pdb=" O LYS F 254 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS F 254 " --> pdb=" O GLU F 270 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL F 334 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.501A pdb=" N VAL G 20 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN G 16 " --> pdb=" O VAL G 13 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 224 through 227 Processing sheet with id= J, first strand: chain 'G' and resid 544 through 547 removed outlier: 6.960A pdb=" N UNK G 559 " --> pdb=" O UNK G 545 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N UNK G 547 " --> pdb=" O UNK G 559 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N UNK G 561 " --> pdb=" O UNK G 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'G' and resid 571 through 574 Processing sheet with id= L, first strand: chain 'G' and resid 316 through 319 removed outlier: 3.675A pdb=" N UNK G 527 " --> pdb=" O UNK G 316 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 92 through 95 Processing sheet with id= N, first strand: chain 'O' and resid 123 through 125 removed outlier: 6.866A pdb=" N UNK O 25 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL O 169 " --> pdb=" O UNK O 26 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N UNK O 28 " --> pdb=" O VAL O 169 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR O 171 " --> pdb=" O UNK O 28 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU O 219 " --> pdb=" O VAL O 170 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL O 172 " --> pdb=" O GLU O 219 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU O 221 " --> pdb=" O VAL O 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'P' and resid 46 through 49 removed outlier: 6.680A pdb=" N UNK P 69 " --> pdb=" O UNK P 47 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N UNK P 49 " --> pdb=" O UNK P 69 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N UNK P 71 " --> pdb=" O UNK P 49 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'P' and resid 166 through 168 removed outlier: 6.854A pdb=" N UNK P 228 " --> pdb=" O UNK P 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'Q' and resid 102 through 104 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: 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: 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= R, first strand: chain 'R' and resid 56 through 59 removed outlier: 4.214A pdb=" N VAL R 71 " --> pdb=" O CYS R 59 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'S' and resid 63 through 67 1583 hydrogen bonds defined for protein. 4614 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.26 Time building geometry restraints manager: 20.94 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: 21367 1.43 - 1.65: 30681 1.65 - 1.87: 510 1.87 - 2.09: 0 2.09 - 2.30: 80 Bond restraints: 52638 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 52633 not shown) Histogram of bond angle deviations from ideal: 60.90 - 84.72: 77 84.72 - 108.53: 2429 108.53 - 132.35: 69649 132.35 - 156.17: 127 156.17 - 179.99: 1 Bond angle restraints: 72283 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 72278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.99: 30743 33.99 - 67.98: 638 67.98 - 101.97: 24 101.97 - 135.96: 0 135.96 - 169.94: 1 Dihedral angle restraints: 31406 sinusoidal: 8299 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 31403 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: 18713 2.91 - 3.57: 69928 3.57 - 4.24: 106614 4.24 - 4.90: 180654 Nonbonded interactions: 375923 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 375918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'Q' selection = (chain 'l' and resid 10 through 122) } ncs_group { reference = chain 'T' selection = (chain 'U' and resid 8 through 82) } ncs_group { reference = chain 'k' selection = (chain 'r' and resid 17 through 119) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.060 Extract box with map and model: 12.790 Check model and map are aligned: 0.760 Set scattering table: 0.470 Process input model: 145.390 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.660 ------------------------------------------------------------------------------- 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 52638 Z= 0.564 Angle : 1.472 61.514 72283 Z= 0.923 Chirality : 1.107 21.300 8863 Planarity : 0.008 0.172 9468 Dihedral : 14.691 169.944 16285 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 : 5.172 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: 0.6572 time to fit residues: 1813.6259 Evaluate side-chains 942 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 923 time to evaluate : 5.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 469 optimal weight: 3.9990 chunk 421 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 435 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 264 optimal weight: 0.6980 chunk 324 optimal weight: 8.9990 chunk 504 optimal weight: 20.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 127 HIS ** C 39 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 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN D 348 HIS D 421 GLN 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 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN H 304 HIS L 295 GLN L 348 HIS ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 279 GLN ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 434 ASN N 171 ASN ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 GLN X 72 GLN X 105 GLN Z 53 ASN a 44 GLN b 45 ASN d 59 HIS ** p 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.275 52638 Z= 0.616 Angle : 1.856 51.677 72283 Z= 1.180 Chirality : 0.330 6.527 8863 Planarity : 0.007 0.155 9468 Dihedral : 6.006 165.738 8303 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 1.54 % Allowed : 7.79 % Favored : 90.67 % Rotamer: Outliers : 0.31 % Allowed : 5.76 % Favored : 93.93 % 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: -2.96 (0.10), residues: 5840 helix: -1.37 (0.08), residues: 3010 sheet: -0.80 (0.40), residues: 161 loop : -2.74 (0.11), residues: 2669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 129 HIS 0.019 0.002 HIS I 65 PHE 0.042 0.002 PHE L 418 TYR 0.038 0.002 TYR H 142 ARG 0.012 0.001 ARG H 281 *********************** 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 1066 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1055 time to evaluate : 4.723 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: A 67 LEU cc_start: 0.9225 (mt) cc_final: 0.8875 (mm) REVERT: A 68 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8497 (tm-30) REVERT: B 52 LEU cc_start: 0.8251 (mt) cc_final: 0.7997 (mt) REVERT: B 115 SER cc_start: 0.9110 (p) cc_final: 0.8790 (p) REVERT: B 116 MET cc_start: 0.8752 (ttp) cc_final: 0.8402 (ppp) REVERT: B 121 ASN cc_start: 0.9047 (m-40) cc_final: 0.8226 (m110) REVERT: C 73 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7507 (ttmt) REVERT: C 92 ILE cc_start: 0.8683 (mt) cc_final: 0.8274 (mt) REVERT: C 124 TYR cc_start: 0.6537 (t80) cc_final: 0.6112 (t80) REVERT: C 131 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8024 (mt-10) REVERT: C 133 GLU cc_start: 0.8944 (tt0) cc_final: 0.8578 (tm-30) REVERT: C 154 ASP cc_start: 0.8394 (t0) cc_final: 0.7877 (t0) REVERT: C 196 LYS cc_start: 0.8401 (ttpt) cc_final: 0.7940 (pttm) REVERT: D 62 LEU cc_start: 0.8967 (mt) cc_final: 0.8515 (mt) REVERT: D 90 LEU cc_start: 0.8861 (tp) cc_final: 0.8555 (tt) REVERT: D 115 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7629 (mt-10) REVERT: D 127 ASN cc_start: 0.8739 (m110) cc_final: 0.8420 (m-40) REVERT: D 156 THR cc_start: 0.9053 (p) cc_final: 0.8767 (t) REVERT: D 169 TRP cc_start: 0.8595 (m100) cc_final: 0.7054 (m100) REVERT: D 259 MET cc_start: 0.7472 (mmm) cc_final: 0.7212 (mmm) REVERT: D 304 MET cc_start: 0.9088 (mmm) cc_final: 0.8795 (tpp) REVERT: D 311 ILE cc_start: 0.9549 (mt) cc_final: 0.9262 (mm) REVERT: D 338 MET cc_start: 0.9053 (ptm) cc_final: 0.8544 (ppp) REVERT: F 355 LYS cc_start: 0.9307 (tptt) cc_final: 0.9105 (tppt) REVERT: F 380 VAL cc_start: 0.9002 (t) cc_final: 0.8654 (p) REVERT: F 390 ASP cc_start: 0.8722 (t70) cc_final: 0.8010 (t70) REVERT: F 394 GLU cc_start: 0.8926 (mt-10) cc_final: 0.7640 (tp30) REVERT: G 94 MET cc_start: 0.9099 (mmm) cc_final: 0.8726 (tpp) REVERT: H 24 GLU cc_start: 0.8746 (mt-10) cc_final: 0.7975 (mt-10) REVERT: H 25 ARG cc_start: 0.7939 (mpt-90) cc_final: 0.7472 (mmt180) REVERT: H 31 MET cc_start: 0.9241 (mmm) cc_final: 0.8116 (mmm) REVERT: H 85 MET cc_start: 0.8331 (tpp) cc_final: 0.8115 (tpt) REVERT: H 156 MET cc_start: 0.8765 (ttm) cc_final: 0.8478 (ttm) REVERT: H 183 MET cc_start: 0.8414 (mmt) cc_final: 0.8189 (mmp) REVERT: H 230 ASN cc_start: 0.8717 (m-40) cc_final: 0.8315 (m-40) REVERT: H 251 MET cc_start: 0.8299 (tpt) cc_final: 0.8072 (tpp) REVERT: H 253 GLU cc_start: 0.6762 (mt-10) cc_final: 0.4907 (mp0) REVERT: H 254 LEU cc_start: 0.8532 (tp) cc_final: 0.8292 (tp) REVERT: H 268 MET cc_start: 0.7684 (ttp) cc_final: 0.7363 (tmm) REVERT: H 304 HIS cc_start: 0.8832 (m90) cc_final: 0.8389 (m90) REVERT: H 305 VAL cc_start: 0.9530 (t) cc_final: 0.9218 (p) REVERT: I 37 THR cc_start: 0.9085 (p) cc_final: 0.8728 (p) REVERT: I 144 HIS cc_start: 0.7035 (m-70) cc_final: 0.6584 (m170) REVERT: J 24 PRO cc_start: 0.7625 (Cg_endo) cc_final: 0.6477 (Cg_exo) REVERT: J 46 ASN cc_start: 0.8942 (m-40) cc_final: 0.8588 (t0) REVERT: J 99 MET cc_start: 0.7873 (mmm) cc_final: 0.7587 (tpt) REVERT: J 154 VAL cc_start: 0.9331 (t) cc_final: 0.9074 (p) REVERT: K 25 HIS cc_start: 0.8006 (m-70) cc_final: 0.7490 (m170) REVERT: K 59 MET cc_start: 0.8371 (mmp) cc_final: 0.7990 (ttt) REVERT: K 69 CYS cc_start: 0.8960 (m) cc_final: 0.8757 (m) REVERT: L 17 MET cc_start: 0.8651 (mmm) cc_final: 0.8450 (ttp) REVERT: L 21 MET cc_start: 0.8330 (ttt) cc_final: 0.7940 (tpp) REVERT: L 87 MET cc_start: 0.8293 (tpp) cc_final: 0.7989 (tpp) REVERT: L 101 MET cc_start: 0.8706 (mmm) cc_final: 0.8171 (tpp) REVERT: L 102 GLU cc_start: 0.8400 (pt0) cc_final: 0.6969 (tm-30) REVERT: L 103 PHE cc_start: 0.7665 (m-80) cc_final: 0.7052 (m-80) REVERT: L 104 SER cc_start: 0.9388 (m) cc_final: 0.8359 (t) REVERT: L 130 ILE cc_start: 0.9352 (mt) cc_final: 0.9113 (mm) REVERT: L 137 LEU cc_start: 0.8776 (tp) cc_final: 0.8491 (tp) REVERT: L 211 MET cc_start: 0.7990 (tpp) cc_final: 0.7500 (tmm) REVERT: L 237 MET cc_start: 0.8797 (mmp) cc_final: 0.8388 (mmp) REVERT: L 299 LYS cc_start: 0.8424 (mttt) cc_final: 0.7420 (mtpt) REVERT: L 330 CYS cc_start: 0.8661 (m) cc_final: 0.8224 (t) REVERT: L 386 LEU cc_start: 0.7165 (tp) cc_final: 0.6957 (tp) REVERT: L 429 PHE cc_start: 0.7557 (t80) cc_final: 0.7138 (t80) REVERT: L 544 MET cc_start: 0.7196 (mtp) cc_final: 0.6644 (tmm) REVERT: L 571 MET cc_start: 0.7367 (tpt) cc_final: 0.6999 (tmm) REVERT: M 70 MET cc_start: 0.9264 (mmm) cc_final: 0.9062 (mmp) REVERT: M 73 LEU cc_start: 0.8838 (tp) cc_final: 0.7904 (tp) REVERT: M 141 GLU cc_start: 0.7894 (pt0) cc_final: 0.7674 (pt0) REVERT: M 204 MET cc_start: 0.8281 (mmp) cc_final: 0.7772 (ptp) REVERT: M 207 MET cc_start: 0.8760 (mmm) cc_final: 0.8388 (mmm) REVERT: M 257 MET cc_start: 0.8027 (mtp) cc_final: 0.7186 (mmm) REVERT: M 270 ILE cc_start: 0.9289 (mp) cc_final: 0.9013 (mm) REVERT: M 310 MET cc_start: 0.7517 (mmt) cc_final: 0.6872 (mmm) REVERT: M 335 GLU cc_start: 0.8377 (pt0) cc_final: 0.8155 (mt-10) REVERT: M 360 LEU cc_start: 0.9298 (tp) cc_final: 0.9097 (tp) REVERT: M 383 MET cc_start: 0.8489 (mtm) cc_final: 0.8236 (mtp) REVERT: N 14 MET cc_start: 0.7722 (mmm) cc_final: 0.7430 (mmt) REVERT: N 35 MET cc_start: 0.9009 (mmm) cc_final: 0.8781 (mmm) REVERT: N 179 MET cc_start: 0.9106 (mmm) cc_final: 0.8684 (mmm) REVERT: N 187 MET cc_start: 0.8874 (mmm) cc_final: 0.8642 (mmt) REVERT: N 193 VAL cc_start: 0.9243 (t) cc_final: 0.8987 (p) REVERT: N 248 LEU cc_start: 0.8845 (mm) cc_final: 0.8572 (mm) REVERT: N 265 MET cc_start: 0.8450 (mpp) cc_final: 0.8011 (mpp) REVERT: N 267 ILE cc_start: 0.8879 (mt) cc_final: 0.8415 (mt) REVERT: N 281 PHE cc_start: 0.8376 (t80) cc_final: 0.8049 (t80) REVERT: N 282 MET cc_start: 0.8663 (mmm) cc_final: 0.8454 (mtp) REVERT: O 114 HIS cc_start: 0.8873 (t-90) cc_final: 0.8134 (t70) REVERT: O 131 ASP cc_start: 0.8089 (t0) cc_final: 0.7637 (t0) REVERT: O 162 GLU cc_start: 0.8710 (mt-10) cc_final: 0.7769 (tp30) REVERT: V 48 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7613 (mt-10) REVERT: V 49 GLN cc_start: 0.7851 (pt0) cc_final: 0.7416 (pt0) REVERT: V 52 ASN cc_start: 0.8973 (m-40) cc_final: 0.8681 (p0) REVERT: W 65 MET cc_start: 0.7857 (tmm) cc_final: 0.7488 (tmm) REVERT: X 48 GLU cc_start: 0.8079 (mt-10) cc_final: 0.6884 (tp30) REVERT: X 68 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7606 (tm-30) REVERT: Z 34 MET cc_start: 0.8176 (ttt) cc_final: 0.7804 (tmm) REVERT: Z 55 GLU cc_start: 0.8422 (tp30) cc_final: 0.7859 (tm-30) REVERT: Z 64 PHE cc_start: 0.8686 (m-10) cc_final: 0.8430 (m-80) REVERT: a 18 ILE cc_start: 0.8951 (mm) cc_final: 0.8743 (mm) REVERT: a 46 TYR cc_start: 0.7399 (t80) cc_final: 0.7155 (t80) REVERT: c 31 LEU cc_start: 0.8468 (mt) cc_final: 0.8244 (mt) REVERT: d 45 ASP cc_start: 0.8516 (p0) cc_final: 0.8148 (t0) REVERT: d 70 PHE cc_start: 0.8754 (t80) cc_final: 0.8407 (t80) REVERT: e 69 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8756 (tp40) REVERT: f 16 VAL cc_start: 0.7736 (t) cc_final: 0.7141 (t) REVERT: g 58 MET cc_start: 0.5767 (mmt) cc_final: 0.5425 (tpp) REVERT: g 80 LEU cc_start: 0.8881 (mt) cc_final: 0.8515 (mt) REVERT: g 94 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7844 (mm-30) REVERT: h 19 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8009 (mtpt) REVERT: m 45 GLU cc_start: 0.8836 (tp30) cc_final: 0.8278 (tp30) REVERT: m 48 LEU cc_start: 0.9115 (mt) cc_final: 0.8752 (tt) REVERT: m 71 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7287 (mpt180) REVERT: m 75 ILE cc_start: 0.8983 (mt) cc_final: 0.8766 (mm) REVERT: m 87 LEU cc_start: 0.7722 (mp) cc_final: 0.7090 (tp) REVERT: m 111 LYS cc_start: 0.9066 (mttt) cc_final: 0.8807 (ptpp) REVERT: n 56 MET cc_start: 0.7576 (tpt) cc_final: 0.7027 (tmm) REVERT: n 68 GLU cc_start: 0.8592 (mp0) cc_final: 0.7908 (mp0) REVERT: p 100 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7865 (mt-10) REVERT: p 126 LYS cc_start: 0.8951 (tmtt) cc_final: 0.8385 (tmtt) outliers start: 11 outliers final: 1 residues processed: 1061 average time/residue: 0.5694 time to fit residues: 1031.8905 Evaluate side-chains 780 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 779 time to evaluate : 5.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 280 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 420 optimal weight: 7.9990 chunk 343 optimal weight: 0.0010 chunk 139 optimal weight: 5.9990 chunk 505 optimal weight: 20.0000 chunk 546 optimal weight: 10.0000 chunk 450 optimal weight: 0.0270 chunk 501 optimal weight: 20.0000 chunk 172 optimal weight: 3.9990 chunk 405 optimal weight: 3.9990 overall best weight: 2.2050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 135 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS D 398 HIS D 421 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 GLN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 400 ASN M 144 ASN M 169 ASN M 399 ASN M 434 ASN N 36 ASN N 47 ASN N 144 GLN N 232 HIS ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 34 GLN X 63 ASN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 72 GLN X 105 GLN Z 89 ASN d 59 HIS p 106 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.263 52638 Z= 0.592 Angle : 1.800 51.114 72283 Z= 1.156 Chirality : 0.330 6.464 8863 Planarity : 0.005 0.152 9468 Dihedral : 5.529 165.556 8303 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 1.35 % Allowed : 8.96 % Favored : 89.69 % Rotamer: Outliers : 0.17 % Allowed : 3.90 % Favored : 95.94 % 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: -2.21 (0.10), residues: 5840 helix: -0.54 (0.09), residues: 3023 sheet: -0.66 (0.41), residues: 161 loop : -2.68 (0.11), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 30 HIS 0.014 0.002 HIS I 65 PHE 0.034 0.002 PHE J 57 TYR 0.030 0.002 TYR H 142 ARG 0.016 0.001 ARG W 76 *********************** 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 1001 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 995 time to evaluate : 4.882 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: A 69 ILE cc_start: 0.9139 (pt) cc_final: 0.8729 (pt) REVERT: B 84 ASP cc_start: 0.8324 (p0) cc_final: 0.8120 (p0) REVERT: B 104 TYR cc_start: 0.8938 (t80) cc_final: 0.8738 (t80) REVERT: B 115 SER cc_start: 0.9170 (p) cc_final: 0.8945 (p) REVERT: B 121 ASN cc_start: 0.9029 (m-40) cc_final: 0.8149 (m-40) REVERT: B 154 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7731 (mm-30) REVERT: C 73 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7481 (ttmt) REVERT: C 92 ILE cc_start: 0.8601 (mt) cc_final: 0.8344 (mt) REVERT: C 124 TYR cc_start: 0.6734 (t80) cc_final: 0.6532 (t80) REVERT: C 131 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8034 (mp0) REVERT: C 154 ASP cc_start: 0.8519 (t0) cc_final: 0.7948 (m-30) REVERT: C 175 ARG cc_start: 0.7530 (mtp85) cc_final: 0.7079 (mmm-85) REVERT: C 196 LYS cc_start: 0.8463 (ttpt) cc_final: 0.7988 (pttm) REVERT: D 76 CYS cc_start: 0.8673 (t) cc_final: 0.7895 (p) REVERT: D 90 LEU cc_start: 0.8707 (tp) cc_final: 0.8483 (tt) REVERT: D 115 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7567 (mt-10) REVERT: D 127 ASN cc_start: 0.8838 (m110) cc_final: 0.8607 (m-40) REVERT: D 156 THR cc_start: 0.9058 (p) cc_final: 0.8700 (t) REVERT: D 169 TRP cc_start: 0.8639 (m100) cc_final: 0.7282 (m100) REVERT: D 193 TYR cc_start: 0.8243 (t80) cc_final: 0.7974 (t80) REVERT: D 252 ASN cc_start: 0.8115 (t0) cc_final: 0.7902 (t0) REVERT: D 303 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8529 (tm-30) REVERT: D 304 MET cc_start: 0.9023 (mmm) cc_final: 0.8599 (tpp) REVERT: D 311 ILE cc_start: 0.9573 (mt) cc_final: 0.9297 (mm) REVERT: D 338 MET cc_start: 0.9088 (ptm) cc_final: 0.8459 (ppp) REVERT: D 405 MET cc_start: 0.8929 (mmt) cc_final: 0.8643 (mmm) REVERT: F 355 LYS cc_start: 0.9376 (tptt) cc_final: 0.9156 (tppt) REVERT: F 380 VAL cc_start: 0.8991 (t) cc_final: 0.8657 (p) REVERT: F 383 ASP cc_start: 0.5713 (m-30) cc_final: 0.5100 (m-30) REVERT: F 390 ASP cc_start: 0.8688 (t70) cc_final: 0.7963 (t70) REVERT: F 394 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8521 (mt-10) REVERT: G 94 MET cc_start: 0.9059 (mmm) cc_final: 0.8650 (tpp) REVERT: G 155 GLN cc_start: 0.6544 (tt0) cc_final: 0.6124 (tt0) REVERT: H 26 LYS cc_start: 0.9451 (ttmm) cc_final: 0.9139 (ttpp) REVERT: H 31 MET cc_start: 0.9106 (mmm) cc_final: 0.8633 (tpp) REVERT: H 144 VAL cc_start: 0.9508 (t) cc_final: 0.9296 (t) REVERT: H 156 MET cc_start: 0.8706 (ttm) cc_final: 0.8002 (mtp) REVERT: H 230 ASN cc_start: 0.8771 (m110) cc_final: 0.8559 (m-40) REVERT: H 233 MET cc_start: 0.8787 (mmp) cc_final: 0.7969 (mmp) REVERT: H 251 MET cc_start: 0.8304 (tpt) cc_final: 0.7596 (tpp) REVERT: H 253 GLU cc_start: 0.6706 (mt-10) cc_final: 0.4840 (mp0) REVERT: H 254 LEU cc_start: 0.8555 (tp) cc_final: 0.8146 (tp) REVERT: H 268 MET cc_start: 0.7562 (ttp) cc_final: 0.7165 (tmm) REVERT: H 304 HIS cc_start: 0.8681 (m90) cc_final: 0.8069 (m90) REVERT: I 19 ASP cc_start: 0.7525 (p0) cc_final: 0.7043 (t70) REVERT: I 50 TYR cc_start: 0.7452 (t80) cc_final: 0.6912 (t80) REVERT: I 111 ILE cc_start: 0.9153 (mt) cc_final: 0.8853 (mt) REVERT: I 121 PHE cc_start: 0.8169 (m-80) cc_final: 0.7891 (m-80) REVERT: I 144 HIS cc_start: 0.6987 (m-70) cc_final: 0.6544 (m170) REVERT: J 24 PRO cc_start: 0.7528 (Cg_endo) cc_final: 0.6703 (Cg_exo) REVERT: J 46 ASN cc_start: 0.8609 (m-40) cc_final: 0.7893 (t0) REVERT: J 154 VAL cc_start: 0.9171 (t) cc_final: 0.8928 (p) REVERT: K 25 HIS cc_start: 0.7924 (m-70) cc_final: 0.7614 (m90) REVERT: K 27 MET cc_start: 0.9193 (mmm) cc_final: 0.8925 (mmm) REVERT: K 59 MET cc_start: 0.8210 (mmp) cc_final: 0.7930 (mmt) REVERT: L 17 MET cc_start: 0.8746 (mmm) cc_final: 0.8542 (ttt) REVERT: L 21 MET cc_start: 0.8310 (ttt) cc_final: 0.7929 (tpp) REVERT: L 102 GLU cc_start: 0.8308 (pt0) cc_final: 0.7006 (tm-30) REVERT: L 103 PHE cc_start: 0.7602 (m-80) cc_final: 0.6979 (m-80) REVERT: L 104 SER cc_start: 0.9444 (m) cc_final: 0.8470 (t) REVERT: L 237 MET cc_start: 0.8794 (mmp) cc_final: 0.8265 (mmp) REVERT: L 299 LYS cc_start: 0.8517 (mttt) cc_final: 0.7672 (mtpt) REVERT: L 330 CYS cc_start: 0.8177 (m) cc_final: 0.7939 (t) REVERT: L 393 ASP cc_start: 0.8345 (m-30) cc_final: 0.7843 (m-30) REVERT: L 429 PHE cc_start: 0.7652 (t80) cc_final: 0.7153 (t80) REVERT: L 456 ARG cc_start: 0.4081 (mtt180) cc_final: 0.3017 (tpp-160) REVERT: L 544 MET cc_start: 0.7345 (mtp) cc_final: 0.6581 (tmm) REVERT: L 571 MET cc_start: 0.7577 (tpt) cc_final: 0.7280 (tmm) REVERT: M 10 MET cc_start: 0.8482 (ttm) cc_final: 0.7932 (ttm) REVERT: M 73 LEU cc_start: 0.8921 (tp) cc_final: 0.8531 (tp) REVERT: M 87 GLU cc_start: 0.7384 (pp20) cc_final: 0.6931 (pm20) REVERT: M 120 ILE cc_start: 0.9294 (pt) cc_final: 0.8933 (mt) REVERT: M 178 MET cc_start: 0.7285 (pmm) cc_final: 0.6986 (pmm) REVERT: M 195 MET cc_start: 0.8906 (tmm) cc_final: 0.8527 (ttm) REVERT: M 216 LEU cc_start: 0.9310 (tp) cc_final: 0.8962 (tt) REVERT: M 269 MET cc_start: 0.8972 (mmm) cc_final: 0.8396 (mmm) REVERT: M 270 ILE cc_start: 0.9315 (mp) cc_final: 0.8856 (mm) REVERT: M 310 MET cc_start: 0.7740 (mmt) cc_final: 0.6942 (mmm) REVERT: M 335 GLU cc_start: 0.8421 (pt0) cc_final: 0.8134 (mt-10) REVERT: M 394 ILE cc_start: 0.8864 (mm) cc_final: 0.8272 (tt) REVERT: N 14 MET cc_start: 0.7653 (mmm) cc_final: 0.7321 (mmt) REVERT: N 35 MET cc_start: 0.8995 (mmm) cc_final: 0.8785 (mmm) REVERT: N 37 MET cc_start: 0.8403 (mmp) cc_final: 0.8202 (mmt) REVERT: N 87 MET cc_start: 0.8218 (ptt) cc_final: 0.7957 (ptp) REVERT: N 96 MET cc_start: 0.8275 (tpp) cc_final: 0.7853 (tpt) REVERT: N 174 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8882 (mm-40) REVERT: N 248 LEU cc_start: 0.8787 (mm) cc_final: 0.8324 (mm) REVERT: N 251 MET cc_start: 0.9184 (tpp) cc_final: 0.8922 (tpp) REVERT: N 267 ILE cc_start: 0.8914 (mt) cc_final: 0.8504 (mt) REVERT: N 268 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7162 (tm-30) REVERT: N 304 MET cc_start: 0.7576 (ttm) cc_final: 0.7272 (ttm) REVERT: O 113 GLU cc_start: 0.8570 (pp20) cc_final: 0.8248 (pp20) REVERT: O 114 HIS cc_start: 0.8563 (t-90) cc_final: 0.7805 (t70) REVERT: O 131 ASP cc_start: 0.8101 (t0) cc_final: 0.7899 (t0) REVERT: O 152 TYR cc_start: 0.8715 (t80) cc_final: 0.8505 (t80) REVERT: O 162 GLU cc_start: 0.8697 (mt-10) cc_final: 0.7673 (tp30) REVERT: V 53 GLU cc_start: 0.8412 (pt0) cc_final: 0.8198 (pt0) REVERT: X 48 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7140 (tp30) REVERT: X 50 LYS cc_start: 0.8681 (mppt) cc_final: 0.7543 (tptt) REVERT: X 68 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7906 (tm-30) REVERT: X 84 TYR cc_start: 0.8617 (t80) cc_final: 0.8405 (t80) REVERT: Z 34 MET cc_start: 0.8273 (ttt) cc_final: 0.7922 (tmm) REVERT: Z 48 SER cc_start: 0.9077 (m) cc_final: 0.8610 (m) REVERT: Z 55 GLU cc_start: 0.8454 (tp30) cc_final: 0.8033 (tm-30) REVERT: Z 87 ARG cc_start: 0.7876 (ptm160) cc_final: 0.7183 (ptm160) REVERT: a 4 GLU cc_start: 0.7856 (pt0) cc_final: 0.7516 (pt0) REVERT: a 21 MET cc_start: 0.8623 (tpp) cc_final: 0.8332 (tpp) REVERT: b 24 ILE cc_start: 0.8224 (tp) cc_final: 0.7960 (tp) REVERT: d 45 ASP cc_start: 0.8406 (p0) cc_final: 0.8119 (t0) REVERT: d 70 PHE cc_start: 0.8732 (t80) cc_final: 0.8475 (t80) REVERT: e 69 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8732 (tp40) REVERT: g 58 MET cc_start: 0.5987 (mmt) cc_final: 0.5486 (tpp) REVERT: g 80 LEU cc_start: 0.8905 (mt) cc_final: 0.8608 (mt) REVERT: h 19 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8066 (mtmt) REVERT: m 45 GLU cc_start: 0.8871 (tp30) cc_final: 0.8278 (tp30) REVERT: m 48 LEU cc_start: 0.9072 (mt) cc_final: 0.8698 (tt) REVERT: m 49 GLN cc_start: 0.9120 (mt0) cc_final: 0.8720 (mt0) REVERT: m 71 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7347 (mmt180) REVERT: m 75 ILE cc_start: 0.8936 (mt) cc_final: 0.7977 (mm) REVERT: m 87 LEU cc_start: 0.7774 (mp) cc_final: 0.7197 (tp) REVERT: m 109 ASP cc_start: 0.8407 (m-30) cc_final: 0.8123 (m-30) REVERT: n 56 MET cc_start: 0.7662 (tpt) cc_final: 0.7147 (tmm) REVERT: p 126 LYS cc_start: 0.9163 (tmtt) cc_final: 0.8929 (tmtt) outliers start: 6 outliers final: 4 residues processed: 1001 average time/residue: 0.6243 time to fit residues: 1071.0033 Evaluate side-chains 770 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 766 time to evaluate : 4.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 499 optimal weight: 20.0000 chunk 380 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 241 optimal weight: 10.0000 chunk 339 optimal weight: 7.9990 chunk 507 optimal weight: 20.0000 chunk 537 optimal weight: 30.0000 chunk 265 optimal weight: 6.9990 chunk 481 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 overall best weight: 6.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS C 160 HIS D 98 GLN D 266 GLN D 357 GLN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN L 139 GLN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 269 ASN L 328 HIS L 405 ASN M 30 HIS M 169 ASN M 440 HIS N 63 GLN ** N 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 273 ASN ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 36 HIS V 49 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 GLN d 46 ASN f 13 HIS ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.281 52638 Z= 0.681 Angle : 1.904 51.788 72283 Z= 1.199 Chirality : 0.329 6.534 8863 Planarity : 0.006 0.154 9468 Dihedral : 6.373 161.961 8303 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 1.34 % Allowed : 9.98 % Favored : 88.68 % Rotamer: Outliers : 0.17 % Allowed : 6.29 % Favored : 93.54 % 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: -2.28 (0.10), residues: 5840 helix: -0.59 (0.09), residues: 3085 sheet: -0.67 (0.41), residues: 155 loop : -2.76 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP C 135 HIS 0.016 0.003 HIS I 65 PHE 0.053 0.003 PHE M 95 TYR 0.044 0.003 TYR G 42 ARG 0.017 0.001 ARG B 66 *********************** 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 880 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 874 time to evaluate : 5.987 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 68 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8796 (tm-30) REVERT: B 137 ASP cc_start: 0.8045 (m-30) cc_final: 0.7242 (m-30) REVERT: C 92 ILE cc_start: 0.8574 (mt) cc_final: 0.8138 (mt) REVERT: C 131 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8267 (mt-10) REVERT: C 154 ASP cc_start: 0.8385 (t0) cc_final: 0.8055 (t0) REVERT: D 76 CYS cc_start: 0.8732 (t) cc_final: 0.8469 (p) REVERT: D 115 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7973 (mt-10) REVERT: D 169 TRP cc_start: 0.8401 (m100) cc_final: 0.6735 (m100) REVERT: D 193 TYR cc_start: 0.8799 (t80) cc_final: 0.8526 (t80) REVERT: D 304 MET cc_start: 0.9088 (mmm) cc_final: 0.8653 (tpp) REVERT: D 338 MET cc_start: 0.9238 (ptm) cc_final: 0.8747 (ppp) REVERT: D 342 MET cc_start: 0.8827 (tpp) cc_final: 0.8595 (tpp) REVERT: F 380 VAL cc_start: 0.9051 (t) cc_final: 0.8768 (p) REVERT: F 390 ASP cc_start: 0.8949 (t70) cc_final: 0.8187 (t70) REVERT: F 394 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8710 (mt-10) REVERT: G 121 MET cc_start: 0.8616 (tmm) cc_final: 0.8254 (tmm) REVERT: G 154 ILE cc_start: 0.9000 (pt) cc_final: 0.8108 (pt) REVERT: H 25 ARG cc_start: 0.8007 (mpt-90) cc_final: 0.7688 (mmt180) REVERT: H 26 LYS cc_start: 0.9534 (ttmm) cc_final: 0.9183 (ttpp) REVERT: H 31 MET cc_start: 0.9374 (mmm) cc_final: 0.8807 (mmt) REVERT: H 34 ARG cc_start: 0.9104 (ptt-90) cc_final: 0.8809 (ptt-90) REVERT: H 156 MET cc_start: 0.8796 (ttm) cc_final: 0.8408 (ttm) REVERT: H 233 MET cc_start: 0.8826 (mmp) cc_final: 0.8595 (mmm) REVERT: H 268 MET cc_start: 0.7433 (ttp) cc_final: 0.6944 (tmm) REVERT: I 48 ILE cc_start: 0.9012 (mp) cc_final: 0.8755 (pt) REVERT: I 111 ILE cc_start: 0.9161 (mt) cc_final: 0.8940 (mt) REVERT: I 117 ILE cc_start: 0.9082 (pt) cc_final: 0.8254 (mp) REVERT: I 118 TYR cc_start: 0.8078 (m-80) cc_final: 0.7864 (m-80) REVERT: I 144 HIS cc_start: 0.7362 (m-70) cc_final: 0.6906 (m170) REVERT: I 153 LYS cc_start: 0.8127 (tttt) cc_final: 0.7533 (tttm) REVERT: J 24 PRO cc_start: 0.8377 (Cg_endo) cc_final: 0.7804 (Cg_exo) REVERT: J 54 LEU cc_start: 0.9141 (mm) cc_final: 0.8926 (mm) REVERT: J 99 MET cc_start: 0.8405 (tpp) cc_final: 0.8151 (tpt) REVERT: J 103 MET cc_start: 0.8601 (ptt) cc_final: 0.8391 (ptp) REVERT: K 59 MET cc_start: 0.8392 (mmp) cc_final: 0.8148 (mmt) REVERT: L 17 MET cc_start: 0.8814 (mmm) cc_final: 0.8582 (ttt) REVERT: L 21 MET cc_start: 0.8388 (ttt) cc_final: 0.7962 (tpp) REVERT: L 101 MET cc_start: 0.9035 (mmm) cc_final: 0.8420 (tpp) REVERT: L 102 GLU cc_start: 0.8290 (pt0) cc_final: 0.6956 (tm-30) REVERT: L 103 PHE cc_start: 0.7928 (m-80) cc_final: 0.7324 (m-80) REVERT: L 104 SER cc_start: 0.9543 (m) cc_final: 0.8522 (t) REVERT: L 237 MET cc_start: 0.8644 (mmp) cc_final: 0.8232 (mmp) REVERT: L 238 GLU cc_start: 0.7058 (tt0) cc_final: 0.6856 (tt0) REVERT: L 279 CYS cc_start: 0.8542 (t) cc_final: 0.8204 (t) REVERT: L 330 CYS cc_start: 0.8664 (m) cc_final: 0.8050 (t) REVERT: L 397 GLU cc_start: 0.7890 (tp30) cc_final: 0.7383 (mm-30) REVERT: L 429 PHE cc_start: 0.8059 (t80) cc_final: 0.7519 (t80) REVERT: L 544 MET cc_start: 0.7298 (mtp) cc_final: 0.6441 (tmm) REVERT: M 10 MET cc_start: 0.8654 (ttm) cc_final: 0.7880 (ttm) REVERT: M 41 LEU cc_start: 0.8469 (mp) cc_final: 0.8023 (tp) REVERT: M 42 MET cc_start: 0.8661 (mmp) cc_final: 0.8147 (mmm) REVERT: M 76 MET cc_start: 0.8107 (mtt) cc_final: 0.7560 (ptt) REVERT: M 87 GLU cc_start: 0.8058 (pp20) cc_final: 0.6857 (mp0) REVERT: M 204 MET cc_start: 0.8342 (mmp) cc_final: 0.7919 (ptp) REVERT: M 216 LEU cc_start: 0.9355 (tp) cc_final: 0.9069 (tt) REVERT: M 342 MET cc_start: 0.9161 (mmt) cc_final: 0.8452 (mmm) REVERT: M 348 LEU cc_start: 0.8157 (mt) cc_final: 0.7575 (mt) REVERT: M 410 MET cc_start: 0.9107 (mpp) cc_final: 0.8584 (mpp) REVERT: N 14 MET cc_start: 0.7932 (mmm) cc_final: 0.7604 (mmt) REVERT: N 54 GLU cc_start: 0.8460 (tt0) cc_final: 0.8027 (tt0) REVERT: N 71 MET cc_start: 0.9487 (mmm) cc_final: 0.9113 (mmm) REVERT: N 100 MET cc_start: 0.8786 (ttp) cc_final: 0.8280 (tmm) REVERT: N 117 GLU cc_start: 0.8245 (mp0) cc_final: 0.7996 (mm-30) REVERT: N 269 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7267 (mm-30) REVERT: N 270 MET cc_start: 0.9009 (mtm) cc_final: 0.8051 (mtt) REVERT: N 272 LYS cc_start: 0.9211 (mtpp) cc_final: 0.8943 (mtpt) REVERT: N 304 MET cc_start: 0.8215 (ttm) cc_final: 0.7663 (ttm) REVERT: O 101 TYR cc_start: 0.8478 (t80) cc_final: 0.8197 (t80) REVERT: O 113 GLU cc_start: 0.8851 (pp20) cc_final: 0.8494 (pp20) REVERT: O 131 ASP cc_start: 0.8005 (t0) cc_final: 0.7780 (t0) REVERT: O 162 GLU cc_start: 0.8659 (mt-10) cc_final: 0.7749 (tp30) REVERT: W 33 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: X 48 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7191 (tp30) REVERT: X 68 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8065 (tm-30) REVERT: X 102 GLN cc_start: 0.8342 (mp10) cc_final: 0.8081 (mp10) REVERT: Z 34 MET cc_start: 0.8536 (ttt) cc_final: 0.8120 (tmm) REVERT: Z 48 SER cc_start: 0.9164 (m) cc_final: 0.8815 (m) REVERT: Z 55 GLU cc_start: 0.8769 (tp30) cc_final: 0.8014 (tm-30) REVERT: Z 57 ARG cc_start: 0.8981 (mmp80) cc_final: 0.8686 (mmm160) REVERT: Z 59 LEU cc_start: 0.9205 (pp) cc_final: 0.8912 (mp) REVERT: Z 87 ARG cc_start: 0.8015 (ptm160) cc_final: 0.7180 (ptm160) REVERT: a 4 GLU cc_start: 0.8074 (pt0) cc_final: 0.7823 (pt0) REVERT: d 70 PHE cc_start: 0.8834 (t80) cc_final: 0.8602 (t80) REVERT: d 82 MET cc_start: 0.8963 (mmm) cc_final: 0.8746 (mmt) REVERT: g 58 MET cc_start: 0.6914 (mmt) cc_final: 0.6627 (mmt) REVERT: g 80 LEU cc_start: 0.9292 (mt) cc_final: 0.9024 (mt) REVERT: h 19 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8077 (mtmt) REVERT: h 36 VAL cc_start: 0.8821 (t) cc_final: 0.8562 (p) REVERT: m 45 GLU cc_start: 0.9066 (tp30) cc_final: 0.8456 (tp30) REVERT: m 75 ILE cc_start: 0.9005 (mt) cc_final: 0.8676 (mm) REVERT: m 87 LEU cc_start: 0.7922 (mp) cc_final: 0.7232 (tt) REVERT: m 109 ASP cc_start: 0.8430 (m-30) cc_final: 0.8168 (m-30) REVERT: n 27 GLU cc_start: 0.8581 (pp20) cc_final: 0.8051 (tm-30) REVERT: n 51 LYS cc_start: 0.8304 (tttm) cc_final: 0.7943 (tptt) REVERT: n 56 MET cc_start: 0.7777 (tpt) cc_final: 0.7227 (tmm) outliers start: 6 outliers final: 2 residues processed: 879 average time/residue: 0.5641 time to fit residues: 855.2492 Evaluate side-chains 686 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 683 time to evaluate : 5.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 447 optimal weight: 20.0000 chunk 305 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 400 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 458 optimal weight: 0.0370 chunk 371 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 482 optimal weight: 0.0020 chunk 135 optimal weight: 30.0000 overall best weight: 1.5670 ------------------------------------------------------------------------------- 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** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 GLN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN J 46 ASN ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 GLN M 26 ASN M 30 HIS M 168 GLN M 169 ASN M 279 GLN ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 232 HIS ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 HIS ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 94 GLN X 105 GLN Z 89 ASN f 13 HIS ** n 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 103 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.281 52638 Z= 0.591 Angle : 1.807 50.839 72283 Z= 1.158 Chirality : 0.330 6.428 8863 Planarity : 0.005 0.141 9468 Dihedral : 5.817 163.798 8303 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 1.23 % Allowed : 8.94 % Favored : 89.83 % Rotamer: Outliers : 0.03 % Allowed : 2.78 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.11), residues: 5840 helix: -0.16 (0.09), residues: 3060 sheet: -0.47 (0.43), residues: 145 loop : -2.61 (0.12), residues: 2635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 129 HIS 0.009 0.001 HIS F 402 PHE 0.080 0.002 PHE O 134 TYR 0.038 0.002 TYR L 159 ARG 0.020 0.001 ARG O 126 *********************** 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 921 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 920 time to evaluate : 5.240 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: 0.9100 (tm-30) cc_final: 0.8691 (tm-30) REVERT: A 69 ILE cc_start: 0.9031 (pt) cc_final: 0.8625 (pt) REVERT: A 90 MET cc_start: 0.8419 (ptp) cc_final: 0.7961 (ptt) REVERT: B 94 ASN cc_start: 0.9274 (m110) cc_final: 0.9012 (m110) REVERT: B 115 SER cc_start: 0.9308 (p) cc_final: 0.9024 (p) REVERT: B 121 ASN cc_start: 0.9036 (m-40) cc_final: 0.8782 (m-40) REVERT: B 137 ASP cc_start: 0.7927 (m-30) cc_final: 0.7484 (m-30) REVERT: C 92 ILE cc_start: 0.8664 (mt) cc_final: 0.8328 (mt) REVERT: C 131 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8286 (mt-10) REVERT: C 154 ASP cc_start: 0.8086 (t0) cc_final: 0.7738 (t0) REVERT: D 83 LEU cc_start: 0.9312 (tp) cc_final: 0.9056 (tt) REVERT: D 115 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7620 (mt-10) REVERT: D 169 TRP cc_start: 0.8669 (m100) cc_final: 0.7310 (m100) REVERT: D 193 TYR cc_start: 0.8568 (t80) cc_final: 0.8246 (t80) REVERT: D 304 MET cc_start: 0.8955 (mmm) cc_final: 0.8714 (tpp) REVERT: D 338 MET cc_start: 0.9197 (ptm) cc_final: 0.8574 (ppp) REVERT: D 410 MET cc_start: 0.7353 (mmm) cc_final: 0.6848 (mmm) REVERT: F 380 VAL cc_start: 0.9024 (t) cc_final: 0.8723 (p) REVERT: F 390 ASP cc_start: 0.8864 (t70) cc_final: 0.8236 (t70) REVERT: F 418 LEU cc_start: 0.8935 (mm) cc_final: 0.8535 (tt) REVERT: G 154 ILE cc_start: 0.8522 (pt) cc_final: 0.7907 (pt) REVERT: G 160 ILE cc_start: 0.9574 (mp) cc_final: 0.9175 (tt) REVERT: H 24 GLU cc_start: 0.7744 (tt0) cc_final: 0.6924 (tt0) REVERT: H 25 ARG cc_start: 0.7920 (mpt-90) cc_final: 0.7707 (mmt180) REVERT: H 26 LYS cc_start: 0.9476 (ttmm) cc_final: 0.9180 (ttpp) REVERT: H 31 MET cc_start: 0.9333 (mmm) cc_final: 0.8688 (mmt) REVERT: H 91 MET cc_start: 0.8389 (tpp) cc_final: 0.8094 (mmm) REVERT: H 144 VAL cc_start: 0.9552 (t) cc_final: 0.9343 (t) REVERT: H 156 MET cc_start: 0.8723 (ttm) cc_final: 0.8073 (mtp) REVERT: H 230 ASN cc_start: 0.8631 (m110) cc_final: 0.8142 (m110) REVERT: H 251 MET cc_start: 0.8266 (tpt) cc_final: 0.8024 (tpp) REVERT: H 253 GLU cc_start: 0.6622 (mt-10) cc_final: 0.5134 (mp0) REVERT: H 254 LEU cc_start: 0.8611 (tp) cc_final: 0.8349 (tp) REVERT: H 268 MET cc_start: 0.7292 (ttp) cc_final: 0.6967 (tmm) REVERT: I 48 ILE cc_start: 0.9177 (mp) cc_final: 0.8845 (pt) REVERT: I 144 HIS cc_start: 0.6973 (m-70) cc_final: 0.6707 (m170) REVERT: I 164 GLU cc_start: 0.8120 (mp0) cc_final: 0.6958 (mp0) REVERT: J 24 PRO cc_start: 0.8071 (Cg_endo) cc_final: 0.7403 (Cg_exo) REVERT: J 64 MET cc_start: 0.8756 (tpp) cc_final: 0.8498 (tpp) REVERT: J 168 ILE cc_start: 0.9422 (mt) cc_final: 0.9106 (tt) REVERT: K 25 HIS cc_start: 0.7792 (m-70) cc_final: 0.7495 (m90) REVERT: K 37 MET cc_start: 0.8393 (mmp) cc_final: 0.8128 (tpp) REVERT: K 38 LEU cc_start: 0.8995 (tp) cc_final: 0.8761 (tt) REVERT: L 21 MET cc_start: 0.8285 (ttt) cc_final: 0.7957 (tpp) REVERT: L 101 MET cc_start: 0.8935 (mmm) cc_final: 0.8691 (mmt) REVERT: L 102 GLU cc_start: 0.8183 (pt0) cc_final: 0.7860 (pt0) REVERT: L 103 PHE cc_start: 0.7849 (m-80) cc_final: 0.7562 (m-80) REVERT: L 104 SER cc_start: 0.9540 (m) cc_final: 0.8554 (t) REVERT: L 279 CYS cc_start: 0.8434 (t) cc_final: 0.8065 (t) REVERT: L 299 LYS cc_start: 0.8869 (mttt) cc_final: 0.7824 (mtpt) REVERT: L 393 ASP cc_start: 0.8453 (m-30) cc_final: 0.8047 (m-30) REVERT: L 397 GLU cc_start: 0.7763 (tp30) cc_final: 0.7322 (tp30) REVERT: L 429 PHE cc_start: 0.7943 (t80) cc_final: 0.7409 (t80) REVERT: L 544 MET cc_start: 0.7420 (mtp) cc_final: 0.6677 (tmm) REVERT: M 10 MET cc_start: 0.8651 (ttm) cc_final: 0.7828 (ttm) REVERT: M 12 MET cc_start: 0.7248 (tmm) cc_final: 0.6912 (tmm) REVERT: M 42 MET cc_start: 0.8731 (mmp) cc_final: 0.8396 (mmm) REVERT: M 76 MET cc_start: 0.8021 (mtt) cc_final: 0.7319 (mtm) REVERT: M 113 MET cc_start: 0.7090 (mtt) cc_final: 0.6486 (mtt) REVERT: M 216 LEU cc_start: 0.9303 (tp) cc_final: 0.8985 (tt) REVERT: M 222 GLU cc_start: 0.8265 (tp30) cc_final: 0.7403 (tp30) REVERT: M 257 MET cc_start: 0.7738 (mtm) cc_final: 0.7258 (mmp) REVERT: M 269 MET cc_start: 0.8792 (mmm) cc_final: 0.8285 (mtt) REVERT: M 342 MET cc_start: 0.9124 (mmt) cc_final: 0.8244 (mmm) REVERT: M 394 ILE cc_start: 0.8906 (mm) cc_final: 0.8382 (tp) REVERT: M 410 MET cc_start: 0.9067 (mpp) cc_final: 0.8828 (mpp) REVERT: N 14 MET cc_start: 0.7810 (mmm) cc_final: 0.7450 (mmt) REVERT: N 100 MET cc_start: 0.9056 (ttp) cc_final: 0.8389 (tmm) REVERT: N 248 LEU cc_start: 0.8822 (mm) cc_final: 0.8465 (mm) REVERT: N 270 MET cc_start: 0.9087 (mtm) cc_final: 0.8183 (mtt) REVERT: O 101 TYR cc_start: 0.8488 (t80) cc_final: 0.8286 (t80) REVERT: O 113 GLU cc_start: 0.8784 (pp20) cc_final: 0.8398 (pp20) REVERT: O 114 HIS cc_start: 0.8588 (t70) cc_final: 0.8189 (t70) REVERT: O 131 ASP cc_start: 0.7939 (t0) cc_final: 0.7551 (t0) REVERT: O 134 PHE cc_start: 0.7948 (m-80) cc_final: 0.7619 (m-10) REVERT: O 162 GLU cc_start: 0.8614 (mt-10) cc_final: 0.7692 (tp30) REVERT: V 53 GLU cc_start: 0.8438 (pt0) cc_final: 0.8160 (pt0) REVERT: X 48 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7206 (tp30) REVERT: X 57 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8555 (mp0) REVERT: X 67 LEU cc_start: 0.8891 (tt) cc_final: 0.8582 (mt) REVERT: X 68 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7920 (tm-30) REVERT: X 84 TYR cc_start: 0.8647 (t80) cc_final: 0.8432 (t80) REVERT: X 97 ARG cc_start: 0.7454 (ttp-110) cc_final: 0.7155 (ttp-110) REVERT: Z 34 MET cc_start: 0.8414 (ttt) cc_final: 0.8059 (tmm) REVERT: Z 42 LEU cc_start: 0.9262 (mp) cc_final: 0.9057 (mp) REVERT: Z 48 SER cc_start: 0.9109 (m) cc_final: 0.8789 (m) REVERT: Z 55 GLU cc_start: 0.8729 (mm-30) cc_final: 0.7908 (tm-30) REVERT: Z 57 ARG cc_start: 0.8914 (mmp80) cc_final: 0.8554 (mmm160) REVERT: Z 59 LEU cc_start: 0.9128 (pp) cc_final: 0.8911 (mt) REVERT: Z 87 ARG cc_start: 0.8053 (ptm160) cc_final: 0.7359 (ptm160) REVERT: a 4 GLU cc_start: 0.7896 (pt0) cc_final: 0.7554 (pt0) REVERT: a 48 MET cc_start: 0.8071 (ppp) cc_final: 0.7813 (ppp) REVERT: d 70 PHE cc_start: 0.8692 (t80) cc_final: 0.8454 (t80) REVERT: d 79 GLN cc_start: 0.9252 (pp30) cc_final: 0.8997 (pp30) REVERT: d 82 MET cc_start: 0.8892 (mmm) cc_final: 0.8650 (mmt) REVERT: g 58 MET cc_start: 0.6570 (mmt) cc_final: 0.6007 (tpp) REVERT: g 60 VAL cc_start: 0.6325 (t) cc_final: 0.6064 (t) REVERT: h 19 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8155 (mtmt) REVERT: m 45 GLU cc_start: 0.8892 (tp30) cc_final: 0.8211 (tp30) REVERT: m 49 GLN cc_start: 0.9168 (mt0) cc_final: 0.8891 (mt0) REVERT: m 75 ILE cc_start: 0.8836 (mt) cc_final: 0.8484 (mm) REVERT: m 87 LEU cc_start: 0.7959 (mp) cc_final: 0.7460 (tt) REVERT: m 109 ASP cc_start: 0.8474 (m-30) cc_final: 0.8219 (m-30) REVERT: n 27 GLU cc_start: 0.8465 (pp20) cc_final: 0.8225 (pp20) REVERT: n 56 MET cc_start: 0.7849 (tpt) cc_final: 0.7147 (tmm) REVERT: n 68 GLU cc_start: 0.8442 (mp0) cc_final: 0.8052 (mp0) outliers start: 1 outliers final: 0 residues processed: 921 average time/residue: 0.5706 time to fit residues: 906.5163 Evaluate side-chains 721 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 721 time to evaluate : 5.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 180 optimal weight: 6.9990 chunk 483 optimal weight: 5.9990 chunk 106 optimal weight: 50.0000 chunk 315 optimal weight: 9.9990 chunk 132 optimal weight: 30.0000 chunk 537 optimal weight: 20.0000 chunk 446 optimal weight: 0.0010 chunk 249 optimal weight: 9.9990 chunk 44 optimal weight: 0.4980 chunk 177 optimal weight: 6.9990 chunk 282 optimal weight: 0.0470 overall best weight: 2.7088 ------------------------------------------------------------------------------- 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** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 98 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 GLN ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 ASN ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 HIS M 169 ASN ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 399 ASN N 63 GLN N 144 GLN N 232 HIS ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 GLN b 45 ASN p 103 ASN ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 130 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.260 52638 Z= 0.595 Angle : 1.806 51.014 72283 Z= 1.158 Chirality : 0.330 6.461 8863 Planarity : 0.005 0.144 9468 Dihedral : 5.718 164.341 8303 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 1.08 % Allowed : 9.91 % Favored : 89.01 % Rotamer: Outliers : 0.08 % Allowed : 2.84 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.11), residues: 5840 helix: 0.01 (0.09), residues: 3046 sheet: -0.58 (0.42), residues: 158 loop : -2.56 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP W 96 HIS 0.011 0.002 HIS I 65 PHE 0.038 0.002 PHE O 134 TYR 0.069 0.002 TYR G 42 ARG 0.021 0.001 ARG C 210 *********************** 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 896 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 893 time to evaluate : 5.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8690 (tm-30) REVERT: A 69 ILE cc_start: 0.8970 (pt) cc_final: 0.8649 (pt) REVERT: B 37 ILE cc_start: 0.8073 (tt) cc_final: 0.7776 (tt) REVERT: B 94 ASN cc_start: 0.9275 (m110) cc_final: 0.9027 (m110) REVERT: B 106 GLN cc_start: 0.8268 (tp-100) cc_final: 0.7951 (tp-100) REVERT: B 115 SER cc_start: 0.9116 (p) cc_final: 0.8868 (p) REVERT: B 121 ASN cc_start: 0.9006 (m-40) cc_final: 0.8760 (m-40) REVERT: B 137 ASP cc_start: 0.7711 (m-30) cc_final: 0.7013 (m-30) REVERT: C 77 ASP cc_start: 0.7330 (m-30) cc_final: 0.6808 (m-30) REVERT: C 92 ILE cc_start: 0.8585 (mt) cc_final: 0.8274 (mt) REVERT: C 131 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8135 (mt-10) REVERT: C 154 ASP cc_start: 0.8127 (t0) cc_final: 0.7833 (t0) REVERT: C 167 PRO cc_start: 0.6802 (Cg_endo) cc_final: 0.6402 (Cg_exo) REVERT: D 83 LEU cc_start: 0.9304 (tp) cc_final: 0.9010 (tt) REVERT: D 115 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7498 (mt-10) REVERT: D 169 TRP cc_start: 0.8669 (m100) cc_final: 0.7241 (m100) REVERT: D 193 TYR cc_start: 0.8696 (t80) cc_final: 0.8344 (t80) REVERT: D 338 MET cc_start: 0.9214 (ptm) cc_final: 0.8584 (ppp) REVERT: D 392 LYS cc_start: 0.7954 (mtpt) cc_final: 0.7547 (mmtm) REVERT: D 405 MET cc_start: 0.8937 (mmt) cc_final: 0.8704 (tpp) REVERT: F 390 ASP cc_start: 0.8961 (t70) cc_final: 0.8305 (t70) REVERT: G 54 MET cc_start: 0.8308 (tpp) cc_final: 0.8085 (tpp) REVERT: G 154 ILE cc_start: 0.8418 (pt) cc_final: 0.7933 (pt) REVERT: G 160 ILE cc_start: 0.9612 (mp) cc_final: 0.9223 (tt) REVERT: H 24 GLU cc_start: 0.8427 (tt0) cc_final: 0.6886 (tt0) REVERT: H 26 LYS cc_start: 0.9463 (ttmm) cc_final: 0.9218 (ttpp) REVERT: H 31 MET cc_start: 0.9267 (mmm) cc_final: 0.8641 (tpp) REVERT: H 77 MET cc_start: 0.9068 (mpp) cc_final: 0.8450 (mpp) REVERT: H 156 MET cc_start: 0.8724 (ttm) cc_final: 0.8511 (ttm) REVERT: H 172 MET cc_start: 0.5045 (mmp) cc_final: 0.4695 (mmm) REVERT: H 230 ASN cc_start: 0.8544 (m110) cc_final: 0.8095 (m110) REVERT: H 251 MET cc_start: 0.8134 (tpt) cc_final: 0.7784 (tpp) REVERT: H 253 GLU cc_start: 0.6870 (mt-10) cc_final: 0.5335 (tt0) REVERT: H 254 LEU cc_start: 0.8594 (tp) cc_final: 0.8216 (tp) REVERT: H 268 MET cc_start: 0.7295 (ttp) cc_final: 0.6984 (tmm) REVERT: H 290 TRP cc_start: 0.8716 (m100) cc_final: 0.8211 (m-10) REVERT: I 111 ILE cc_start: 0.8956 (mt) cc_final: 0.8637 (mt) REVERT: I 144 HIS cc_start: 0.7150 (m-70) cc_final: 0.6860 (m-70) REVERT: I 164 GLU cc_start: 0.8243 (mp0) cc_final: 0.7228 (mp0) REVERT: J 24 PRO cc_start: 0.8185 (Cg_endo) cc_final: 0.7710 (Cg_exo) REVERT: J 54 LEU cc_start: 0.9240 (mm) cc_final: 0.9036 (mm) REVERT: J 76 THR cc_start: 0.8866 (p) cc_final: 0.8608 (p) REVERT: J 168 ILE cc_start: 0.9378 (mt) cc_final: 0.9094 (tt) REVERT: K 25 HIS cc_start: 0.7843 (m-70) cc_final: 0.7460 (m90) REVERT: L 21 MET cc_start: 0.8162 (ttt) cc_final: 0.7938 (tpp) REVERT: L 69 LEU cc_start: 0.8886 (tt) cc_final: 0.8673 (tt) REVERT: L 101 MET cc_start: 0.8932 (mmm) cc_final: 0.8666 (mmt) REVERT: L 102 GLU cc_start: 0.8108 (pt0) cc_final: 0.7778 (pt0) REVERT: L 103 PHE cc_start: 0.7880 (m-80) cc_final: 0.7567 (m-80) REVERT: L 104 SER cc_start: 0.9562 (m) cc_final: 0.8599 (t) REVERT: L 237 MET cc_start: 0.8628 (mmp) cc_final: 0.8339 (mmp) REVERT: L 238 GLU cc_start: 0.7317 (tt0) cc_final: 0.6607 (pt0) REVERT: L 279 CYS cc_start: 0.8414 (t) cc_final: 0.8083 (t) REVERT: L 353 GLU cc_start: 0.8183 (tp30) cc_final: 0.7876 (tp30) REVERT: L 393 ASP cc_start: 0.8547 (m-30) cc_final: 0.8104 (m-30) REVERT: L 397 GLU cc_start: 0.7968 (tp30) cc_final: 0.7430 (tp30) REVERT: L 429 PHE cc_start: 0.8005 (t80) cc_final: 0.7454 (t80) REVERT: L 544 MET cc_start: 0.7394 (mtp) cc_final: 0.6536 (tmm) REVERT: M 10 MET cc_start: 0.8704 (ttm) cc_final: 0.8283 (ttm) REVERT: M 12 MET cc_start: 0.7306 (tmm) cc_final: 0.7054 (tmm) REVERT: M 42 MET cc_start: 0.8896 (mmp) cc_final: 0.8593 (mmm) REVERT: M 76 MET cc_start: 0.8087 (mtt) cc_final: 0.7411 (mtm) REVERT: M 113 MET cc_start: 0.7240 (mtt) cc_final: 0.6827 (mtt) REVERT: M 204 MET cc_start: 0.8223 (mmp) cc_final: 0.7927 (ptp) REVERT: M 216 LEU cc_start: 0.9337 (tp) cc_final: 0.9069 (tt) REVERT: M 222 GLU cc_start: 0.8178 (tp30) cc_final: 0.6579 (tp30) REVERT: M 257 MET cc_start: 0.7751 (mtm) cc_final: 0.7252 (mmp) REVERT: M 269 MET cc_start: 0.8861 (mmm) cc_final: 0.8547 (mtt) REVERT: M 310 MET cc_start: 0.7844 (mmt) cc_final: 0.7161 (mmm) REVERT: M 342 MET cc_start: 0.9103 (mmt) cc_final: 0.8483 (mmm) REVERT: M 394 ILE cc_start: 0.8912 (mm) cc_final: 0.8405 (tp) REVERT: M 396 MET cc_start: 0.8893 (mmm) cc_final: 0.8658 (mmm) REVERT: M 410 MET cc_start: 0.9145 (mpp) cc_final: 0.8926 (mpp) REVERT: N 9 ILE cc_start: 0.9388 (mt) cc_final: 0.9051 (tp) REVERT: N 14 MET cc_start: 0.7698 (mmm) cc_final: 0.7341 (mmt) REVERT: N 37 MET cc_start: 0.7997 (mmp) cc_final: 0.6854 (mmp) REVERT: N 63 GLN cc_start: 0.8429 (tt0) cc_final: 0.7797 (tt0) REVERT: N 100 MET cc_start: 0.9033 (ttp) cc_final: 0.8432 (tmm) REVERT: N 144 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8332 (mm110) REVERT: N 211 MET cc_start: 0.8249 (ttm) cc_final: 0.7414 (ttm) REVERT: N 248 LEU cc_start: 0.9039 (mm) cc_final: 0.8497 (mm) REVERT: N 251 MET cc_start: 0.8974 (tpp) cc_final: 0.8138 (tpp) REVERT: N 270 MET cc_start: 0.9050 (mtm) cc_final: 0.8138 (mtt) REVERT: N 304 MET cc_start: 0.8046 (ttm) cc_final: 0.7368 (ttm) REVERT: O 101 TYR cc_start: 0.8606 (t80) cc_final: 0.8067 (t80) REVERT: O 113 GLU cc_start: 0.8778 (pp20) cc_final: 0.8422 (pp20) REVERT: O 114 HIS cc_start: 0.8597 (t70) cc_final: 0.8219 (t70) REVERT: O 131 ASP cc_start: 0.7880 (t0) cc_final: 0.7319 (t0) REVERT: O 134 PHE cc_start: 0.7900 (m-80) cc_final: 0.7326 (m-10) REVERT: O 156 LYS cc_start: 0.9080 (tppt) cc_final: 0.8586 (tptt) REVERT: O 162 GLU cc_start: 0.8610 (mt-10) cc_final: 0.7718 (tp30) REVERT: V 53 GLU cc_start: 0.8542 (pt0) cc_final: 0.8188 (pt0) REVERT: W 33 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: X 48 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7285 (tp30) REVERT: X 67 LEU cc_start: 0.8866 (tt) cc_final: 0.8646 (mt) REVERT: X 68 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8041 (tm-30) REVERT: X 84 TYR cc_start: 0.8641 (t80) cc_final: 0.8423 (t80) REVERT: X 97 ARG cc_start: 0.7478 (ttp-110) cc_final: 0.7250 (ttp-110) REVERT: X 102 GLN cc_start: 0.8373 (mp10) cc_final: 0.8139 (mp10) REVERT: Z 34 MET cc_start: 0.8467 (ttt) cc_final: 0.8135 (tmm) REVERT: Z 48 SER cc_start: 0.9133 (m) cc_final: 0.8771 (t) REVERT: Z 55 GLU cc_start: 0.8766 (mm-30) cc_final: 0.7875 (tm-30) REVERT: Z 87 ARG cc_start: 0.8092 (ptm160) cc_final: 0.7381 (ptm160) REVERT: a 1 MET cc_start: 0.6477 (ppp) cc_final: 0.6257 (ppp) REVERT: a 4 GLU cc_start: 0.8067 (pt0) cc_final: 0.7708 (pt0) REVERT: d 82 MET cc_start: 0.8867 (mmm) cc_final: 0.8629 (mmt) REVERT: g 80 LEU cc_start: 0.9201 (mt) cc_final: 0.8988 (mt) REVERT: h 19 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8115 (mtmt) REVERT: m 45 GLU cc_start: 0.8934 (tp30) cc_final: 0.8292 (tp30) REVERT: m 49 GLN cc_start: 0.9118 (mt0) cc_final: 0.8870 (mt0) REVERT: m 75 ILE cc_start: 0.8866 (mt) cc_final: 0.8525 (mm) REVERT: m 87 LEU cc_start: 0.7837 (mp) cc_final: 0.7407 (tp) REVERT: m 109 ASP cc_start: 0.8512 (m-30) cc_final: 0.8269 (m-30) REVERT: n 27 GLU cc_start: 0.8569 (pp20) cc_final: 0.8281 (pp20) REVERT: n 51 LYS cc_start: 0.8303 (tttm) cc_final: 0.7717 (tptt) outliers start: 3 outliers final: 1 residues processed: 896 average time/residue: 0.5650 time to fit residues: 871.3083 Evaluate side-chains 724 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 721 time to evaluate : 5.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 518 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 306 optimal weight: 7.9990 chunk 392 optimal weight: 20.0000 chunk 304 optimal weight: 1.9990 chunk 452 optimal weight: 0.8980 chunk 300 optimal weight: 5.9990 chunk 535 optimal weight: 4.9990 chunk 335 optimal weight: 0.6980 chunk 326 optimal weight: 8.9990 chunk 247 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 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 98 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** 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 287 HIS J 46 ASN ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN ** M 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN M 169 ASN ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 399 ASN ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 232 HIS ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 GLN b 45 ASN c 9 HIS p 103 ASN ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.267 52638 Z= 0.592 Angle : 1.805 50.989 72283 Z= 1.158 Chirality : 0.330 6.447 8863 Planarity : 0.005 0.147 9468 Dihedral : 5.696 164.926 8303 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 1.04 % Allowed : 9.49 % Favored : 89.47 % Rotamer: Outliers : 0.03 % Allowed : 2.14 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 0.99 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.11), residues: 5840 helix: 0.09 (0.10), residues: 3051 sheet: -0.54 (0.44), residues: 156 loop : -2.51 (0.12), residues: 2633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP L 196 HIS 0.010 0.001 HIS I 65 PHE 0.027 0.002 PHE O 134 TYR 0.054 0.002 TYR G 42 ARG 0.009 0.001 ARG G 53 *********************** 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 878 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 877 time to evaluate : 5.185 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: 0.9103 (tm-30) cc_final: 0.8611 (tm-30) REVERT: A 69 ILE cc_start: 0.8963 (pt) cc_final: 0.8528 (pt) REVERT: B 60 MET cc_start: 0.8030 (mtp) cc_final: 0.7742 (ttm) REVERT: B 94 ASN cc_start: 0.9302 (m110) cc_final: 0.9049 (m110) REVERT: B 137 ASP cc_start: 0.7647 (m-30) cc_final: 0.6844 (m-30) REVERT: C 79 THR cc_start: 0.8963 (t) cc_final: 0.8534 (t) REVERT: C 92 ILE cc_start: 0.8647 (mt) cc_final: 0.8232 (mt) REVERT: C 131 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8309 (mt-10) REVERT: C 133 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8231 (tm-30) REVERT: C 154 ASP cc_start: 0.8217 (t0) cc_final: 0.7896 (t0) REVERT: D 83 LEU cc_start: 0.9336 (tp) cc_final: 0.9018 (tt) REVERT: D 115 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7441 (mt-10) REVERT: D 169 TRP cc_start: 0.8743 (m100) cc_final: 0.7311 (m100) REVERT: D 193 TYR cc_start: 0.8650 (t80) cc_final: 0.8343 (t80) REVERT: D 304 MET cc_start: 0.9070 (tpp) cc_final: 0.8661 (tpp) REVERT: D 338 MET cc_start: 0.9206 (ptm) cc_final: 0.8599 (ppp) REVERT: F 390 ASP cc_start: 0.8939 (t70) cc_final: 0.7994 (t70) REVERT: F 394 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8660 (mt-10) REVERT: G 53 ARG cc_start: 0.8689 (mtt-85) cc_final: 0.8397 (mmt90) REVERT: G 54 MET cc_start: 0.8191 (tpp) cc_final: 0.7797 (tpp) REVERT: G 154 ILE cc_start: 0.8468 (pt) cc_final: 0.7990 (pt) REVERT: G 160 ILE cc_start: 0.9611 (mp) cc_final: 0.9219 (tt) REVERT: H 24 GLU cc_start: 0.8504 (tt0) cc_final: 0.6709 (tt0) REVERT: H 31 MET cc_start: 0.9308 (mmm) cc_final: 0.8893 (mmt) REVERT: H 77 MET cc_start: 0.9123 (mpp) cc_final: 0.8432 (mpp) REVERT: H 230 ASN cc_start: 0.8524 (m110) cc_final: 0.8077 (m110) REVERT: H 251 MET cc_start: 0.8088 (tpt) cc_final: 0.7806 (tpp) REVERT: H 253 GLU cc_start: 0.6803 (mt-10) cc_final: 0.5354 (tt0) REVERT: H 268 MET cc_start: 0.7253 (ttp) cc_final: 0.6949 (tmm) REVERT: H 290 TRP cc_start: 0.8693 (m100) cc_final: 0.8296 (m-10) REVERT: H 305 VAL cc_start: 0.9590 (t) cc_final: 0.9300 (p) REVERT: I 111 ILE cc_start: 0.8846 (mt) cc_final: 0.8509 (mt) REVERT: I 144 HIS cc_start: 0.7172 (m-70) cc_final: 0.6872 (m-70) REVERT: I 164 GLU cc_start: 0.8253 (mp0) cc_final: 0.7209 (mp0) REVERT: J 24 PRO cc_start: 0.8382 (Cg_endo) cc_final: 0.8068 (Cg_exo) REVERT: J 54 LEU cc_start: 0.9242 (mm) cc_final: 0.8966 (mm) REVERT: J 76 THR cc_start: 0.8908 (p) cc_final: 0.8652 (p) REVERT: J 99 MET cc_start: 0.8460 (tpp) cc_final: 0.7834 (tpt) REVERT: J 168 ILE cc_start: 0.9364 (mt) cc_final: 0.9088 (tt) REVERT: K 21 MET cc_start: 0.7421 (mtp) cc_final: 0.7202 (mtm) REVERT: K 25 HIS cc_start: 0.7837 (m-70) cc_final: 0.7407 (m90) REVERT: L 101 MET cc_start: 0.8946 (mmm) cc_final: 0.8655 (mmt) REVERT: L 102 GLU cc_start: 0.8104 (pt0) cc_final: 0.7722 (pt0) REVERT: L 103 PHE cc_start: 0.7851 (m-80) cc_final: 0.7466 (m-80) REVERT: L 104 SER cc_start: 0.9567 (m) cc_final: 0.8615 (t) REVERT: L 237 MET cc_start: 0.8592 (mmp) cc_final: 0.8261 (mmp) REVERT: L 238 GLU cc_start: 0.7339 (tt0) cc_final: 0.6605 (pt0) REVERT: L 279 CYS cc_start: 0.8428 (t) cc_final: 0.8087 (t) REVERT: L 353 GLU cc_start: 0.8024 (tp30) cc_final: 0.7781 (tp30) REVERT: L 393 ASP cc_start: 0.8602 (m-30) cc_final: 0.8329 (m-30) REVERT: L 397 GLU cc_start: 0.7971 (tp30) cc_final: 0.7418 (tp30) REVERT: L 429 PHE cc_start: 0.8054 (t80) cc_final: 0.7532 (t80) REVERT: L 544 MET cc_start: 0.7275 (mtp) cc_final: 0.6530 (tmm) REVERT: M 10 MET cc_start: 0.8739 (ttm) cc_final: 0.8289 (ttm) REVERT: M 12 MET cc_start: 0.7228 (tmm) cc_final: 0.6981 (tmm) REVERT: M 42 MET cc_start: 0.8851 (mmp) cc_final: 0.8474 (mmm) REVERT: M 70 MET cc_start: 0.8989 (mmm) cc_final: 0.8632 (mmm) REVERT: M 76 MET cc_start: 0.8165 (mtt) cc_final: 0.7596 (mtm) REVERT: M 113 MET cc_start: 0.7224 (mtt) cc_final: 0.6800 (mtt) REVERT: M 216 LEU cc_start: 0.9404 (tp) cc_final: 0.9073 (tt) REVERT: M 222 GLU cc_start: 0.8166 (tp30) cc_final: 0.7450 (tp30) REVERT: M 310 MET cc_start: 0.7796 (mmt) cc_final: 0.7205 (mmm) REVERT: M 342 MET cc_start: 0.9072 (mmt) cc_final: 0.8575 (mmm) REVERT: M 394 ILE cc_start: 0.8873 (mm) cc_final: 0.8347 (tp) REVERT: M 410 MET cc_start: 0.9177 (mpp) cc_final: 0.8947 (mpp) REVERT: N 14 MET cc_start: 0.7852 (mmm) cc_final: 0.7405 (mmp) REVERT: N 68 MET cc_start: 0.8899 (mmt) cc_final: 0.8502 (mmt) REVERT: N 96 MET cc_start: 0.8857 (tpp) cc_final: 0.7794 (tmm) REVERT: N 100 MET cc_start: 0.9004 (ttp) cc_final: 0.8629 (tmm) REVERT: N 208 TYR cc_start: 0.8748 (t80) cc_final: 0.8377 (t80) REVERT: N 211 MET cc_start: 0.8359 (ttm) cc_final: 0.7130 (ttm) REVERT: N 248 LEU cc_start: 0.9000 (mm) cc_final: 0.8492 (mm) REVERT: N 251 MET cc_start: 0.8893 (tpp) cc_final: 0.8044 (tpp) REVERT: N 270 MET cc_start: 0.9148 (mtm) cc_final: 0.8142 (mtt) REVERT: N 304 MET cc_start: 0.8031 (ttm) cc_final: 0.7480 (ttm) REVERT: O 101 TYR cc_start: 0.8635 (t80) cc_final: 0.7808 (t80) REVERT: O 113 GLU cc_start: 0.8777 (pp20) cc_final: 0.8394 (pp20) REVERT: O 114 HIS cc_start: 0.8591 (t70) cc_final: 0.8204 (t70) REVERT: O 131 ASP cc_start: 0.7962 (t0) cc_final: 0.7454 (t0) REVERT: O 134 PHE cc_start: 0.7942 (m-80) cc_final: 0.7403 (m-10) REVERT: O 156 LYS cc_start: 0.9117 (tppt) cc_final: 0.8639 (tptt) REVERT: O 162 GLU cc_start: 0.8608 (mt-10) cc_final: 0.7714 (tp30) REVERT: V 53 GLU cc_start: 0.8499 (pt0) cc_final: 0.8182 (pt0) REVERT: X 48 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7247 (tp30) REVERT: X 67 LEU cc_start: 0.8871 (tt) cc_final: 0.8567 (mt) REVERT: X 68 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8048 (tm-30) REVERT: X 84 TYR cc_start: 0.8619 (t80) cc_final: 0.8409 (t80) REVERT: X 102 GLN cc_start: 0.8292 (mp10) cc_final: 0.8069 (mp10) REVERT: Z 48 SER cc_start: 0.9112 (m) cc_final: 0.8748 (t) REVERT: Z 55 GLU cc_start: 0.8767 (mm-30) cc_final: 0.7846 (tm-30) REVERT: Z 87 ARG cc_start: 0.8102 (ptm160) cc_final: 0.7283 (ptm160) REVERT: Z 91 GLU cc_start: 0.9029 (pp20) cc_final: 0.8826 (tp30) REVERT: Z 93 GLU cc_start: 0.8420 (mp0) cc_final: 0.7854 (pm20) REVERT: d 82 MET cc_start: 0.8862 (mmm) cc_final: 0.8631 (tpp) REVERT: g 58 MET cc_start: 0.5794 (mmt) cc_final: 0.4605 (mmm) REVERT: h 19 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8125 (mtmt) REVERT: m 45 GLU cc_start: 0.8884 (tp30) cc_final: 0.8232 (tp30) REVERT: m 49 GLN cc_start: 0.9079 (mt0) cc_final: 0.8750 (mt0) REVERT: m 75 ILE cc_start: 0.8876 (mt) cc_final: 0.8516 (mm) REVERT: m 87 LEU cc_start: 0.7851 (mp) cc_final: 0.7471 (tp) REVERT: m 109 ASP cc_start: 0.8562 (m-30) cc_final: 0.8317 (m-30) REVERT: n 27 GLU cc_start: 0.8567 (pp20) cc_final: 0.8304 (pp20) REVERT: n 68 GLU cc_start: 0.8581 (mp0) cc_final: 0.8246 (mp0) REVERT: p 109 LEU cc_start: 0.9410 (tp) cc_final: 0.9204 (tp) outliers start: 1 outliers final: 0 residues processed: 878 average time/residue: 0.5950 time to fit residues: 907.7936 Evaluate side-chains 712 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 712 time to evaluate : 4.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 331 optimal weight: 0.7980 chunk 214 optimal weight: 6.9990 chunk 320 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 340 optimal weight: 3.9990 chunk 365 optimal weight: 10.0000 chunk 264 optimal weight: 0.0170 chunk 49 optimal weight: 8.9990 chunk 421 optimal weight: 7.9990 overall best weight: 1.9624 ------------------------------------------------------------------------------- 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** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 GLN ** M 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN N 197 ASN N 232 HIS ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 151 HIS O 167 HIS ** W 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 45 ASN ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 103 ASN ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.263 52638 Z= 0.588 Angle : 1.797 51.167 72283 Z= 1.154 Chirality : 0.330 6.489 8863 Planarity : 0.004 0.144 9468 Dihedral : 5.615 165.625 8303 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.99 % Allowed : 9.79 % Favored : 89.21 % Rotamer: Outliers : 0.03 % Allowed : 1.36 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 0.99 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.11), residues: 5840 helix: 0.15 (0.10), residues: 3045 sheet: -0.49 (0.44), residues: 155 loop : -2.49 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 136 HIS 0.008 0.001 HIS I 65 PHE 0.042 0.002 PHE I 137 TYR 0.025 0.002 TYR L 159 ARG 0.012 0.000 ARG Z 67 *********************** 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 885 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 884 time to evaluate : 5.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8712 (tm-30) REVERT: A 69 ILE cc_start: 0.9025 (pt) cc_final: 0.8717 (pt) REVERT: B 43 SER cc_start: 0.9176 (t) cc_final: 0.8764 (m) REVERT: B 94 ASN cc_start: 0.9303 (m110) cc_final: 0.9042 (m110) REVERT: B 137 ASP cc_start: 0.7463 (m-30) cc_final: 0.7000 (m-30) REVERT: C 92 ILE cc_start: 0.8643 (mt) cc_final: 0.8254 (mt) REVERT: C 131 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8213 (mt-10) REVERT: C 154 ASP cc_start: 0.8176 (t0) cc_final: 0.7855 (t0) REVERT: D 76 CYS cc_start: 0.8643 (t) cc_final: 0.8413 (p) REVERT: D 83 LEU cc_start: 0.9294 (tp) cc_final: 0.8958 (tt) REVERT: D 115 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7475 (mt-10) REVERT: D 169 TRP cc_start: 0.8738 (m100) cc_final: 0.7330 (m100) REVERT: D 193 TYR cc_start: 0.8546 (t80) cc_final: 0.8190 (t80) REVERT: D 338 MET cc_start: 0.9202 (ptm) cc_final: 0.8566 (ppp) REVERT: F 355 LYS cc_start: 0.9375 (tptm) cc_final: 0.8872 (tppt) REVERT: F 370 ASP cc_start: 0.8875 (m-30) cc_final: 0.8240 (m-30) REVERT: F 390 ASP cc_start: 0.8931 (t70) cc_final: 0.7745 (t70) REVERT: F 394 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8445 (mt-10) REVERT: G 94 MET cc_start: 0.9072 (mmm) cc_final: 0.8866 (tpp) REVERT: G 154 ILE cc_start: 0.8438 (pt) cc_final: 0.7928 (pt) REVERT: G 160 ILE cc_start: 0.9600 (mp) cc_final: 0.9254 (tt) REVERT: H 31 MET cc_start: 0.9214 (mmm) cc_final: 0.8828 (mmt) REVERT: H 60 PRO cc_start: 0.6765 (Cg_endo) cc_final: 0.6317 (Cg_exo) REVERT: H 77 MET cc_start: 0.9097 (mpp) cc_final: 0.8756 (mpp) REVERT: H 142 TYR cc_start: 0.6823 (m-10) cc_final: 0.6609 (m-10) REVERT: H 172 MET cc_start: 0.5101 (mmp) cc_final: 0.4751 (mmm) REVERT: H 230 ASN cc_start: 0.8500 (m110) cc_final: 0.8057 (m110) REVERT: H 251 MET cc_start: 0.8099 (tpt) cc_final: 0.7837 (tpp) REVERT: H 253 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6044 (tt0) REVERT: H 268 MET cc_start: 0.7187 (ttp) cc_final: 0.6884 (tmm) REVERT: H 290 TRP cc_start: 0.8856 (m100) cc_final: 0.8476 (m-10) REVERT: H 305 VAL cc_start: 0.9576 (t) cc_final: 0.9241 (p) REVERT: I 48 ILE cc_start: 0.9157 (mp) cc_final: 0.8905 (pt) REVERT: I 111 ILE cc_start: 0.8829 (mt) cc_final: 0.8436 (mt) REVERT: I 144 HIS cc_start: 0.7045 (m-70) cc_final: 0.6814 (m170) REVERT: J 24 PRO cc_start: 0.8290 (Cg_endo) cc_final: 0.7870 (Cg_exo) REVERT: J 54 LEU cc_start: 0.9273 (mm) cc_final: 0.9052 (mm) REVERT: J 76 THR cc_start: 0.8865 (p) cc_final: 0.8560 (p) REVERT: J 99 MET cc_start: 0.8448 (tpp) cc_final: 0.8158 (tpt) REVERT: J 168 ILE cc_start: 0.9396 (mt) cc_final: 0.9089 (tt) REVERT: K 25 HIS cc_start: 0.8084 (m-70) cc_final: 0.7446 (m90) REVERT: K 59 MET cc_start: 0.7529 (mmt) cc_final: 0.7265 (mmt) REVERT: L 101 MET cc_start: 0.8955 (mmm) cc_final: 0.8578 (mmt) REVERT: L 102 GLU cc_start: 0.7972 (pt0) cc_final: 0.6602 (tp30) REVERT: L 103 PHE cc_start: 0.7827 (m-80) cc_final: 0.7332 (m-80) REVERT: L 104 SER cc_start: 0.9570 (m) cc_final: 0.8595 (t) REVERT: L 105 MET cc_start: 0.8793 (mmp) cc_final: 0.8331 (mmp) REVERT: L 203 MET cc_start: 0.8512 (ppp) cc_final: 0.8182 (ppp) REVERT: L 237 MET cc_start: 0.8589 (mmp) cc_final: 0.8276 (mmp) REVERT: L 238 GLU cc_start: 0.6927 (tt0) cc_final: 0.6166 (pt0) REVERT: L 249 SER cc_start: 0.8731 (p) cc_final: 0.8348 (t) REVERT: L 279 CYS cc_start: 0.8394 (t) cc_final: 0.8072 (t) REVERT: L 353 GLU cc_start: 0.8018 (tp30) cc_final: 0.7650 (tp30) REVERT: L 393 ASP cc_start: 0.8630 (m-30) cc_final: 0.8358 (m-30) REVERT: L 397 GLU cc_start: 0.7943 (tp30) cc_final: 0.7396 (tp30) REVERT: L 429 PHE cc_start: 0.8065 (t80) cc_final: 0.7532 (t80) REVERT: L 544 MET cc_start: 0.7306 (mtp) cc_final: 0.6485 (tmm) REVERT: M 10 MET cc_start: 0.8749 (ttm) cc_final: 0.7838 (ttm) REVERT: M 12 MET cc_start: 0.7159 (tmm) cc_final: 0.6915 (tmm) REVERT: M 70 MET cc_start: 0.8948 (mmm) cc_final: 0.8745 (tpp) REVERT: M 76 MET cc_start: 0.8035 (mtt) cc_final: 0.7196 (mtm) REVERT: M 113 MET cc_start: 0.7207 (mtt) cc_final: 0.6948 (mtt) REVERT: M 139 GLN cc_start: 0.7300 (pm20) cc_final: 0.7092 (pm20) REVERT: M 216 LEU cc_start: 0.9090 (tp) cc_final: 0.8761 (tt) REVERT: M 222 GLU cc_start: 0.8213 (tp30) cc_final: 0.7292 (tp30) REVERT: M 253 MET cc_start: 0.6426 (mmt) cc_final: 0.6193 (tpt) REVERT: M 269 MET cc_start: 0.8031 (ttp) cc_final: 0.7530 (ttm) REVERT: M 310 MET cc_start: 0.7734 (mmt) cc_final: 0.7145 (mmm) REVERT: M 342 MET cc_start: 0.9120 (mmt) cc_final: 0.8731 (mmm) REVERT: M 394 ILE cc_start: 0.8660 (mm) cc_final: 0.8069 (tp) REVERT: M 410 MET cc_start: 0.9170 (mpp) cc_final: 0.8924 (mpp) REVERT: N 14 MET cc_start: 0.7844 (mmm) cc_final: 0.7390 (mmp) REVERT: N 54 GLU cc_start: 0.8286 (tt0) cc_final: 0.7225 (tt0) REVERT: N 96 MET cc_start: 0.8844 (tpp) cc_final: 0.7822 (tmm) REVERT: N 100 MET cc_start: 0.9004 (ttp) cc_final: 0.8686 (tmm) REVERT: N 144 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8292 (mm110) REVERT: N 211 MET cc_start: 0.8324 (ttm) cc_final: 0.7034 (ttm) REVERT: N 248 LEU cc_start: 0.9008 (mm) cc_final: 0.8467 (mm) REVERT: N 251 MET cc_start: 0.8965 (tpp) cc_final: 0.7843 (tpp) REVERT: N 270 MET cc_start: 0.9158 (mtm) cc_final: 0.8175 (mtt) REVERT: N 304 MET cc_start: 0.8093 (ttm) cc_final: 0.7717 (ttm) REVERT: O 101 TYR cc_start: 0.8644 (t80) cc_final: 0.7843 (t80) REVERT: O 113 GLU cc_start: 0.8795 (pp20) cc_final: 0.8487 (pp20) REVERT: O 114 HIS cc_start: 0.8573 (t70) cc_final: 0.8198 (t70) REVERT: O 131 ASP cc_start: 0.7916 (t0) cc_final: 0.7409 (t0) REVERT: O 134 PHE cc_start: 0.7933 (m-80) cc_final: 0.7372 (m-10) REVERT: O 156 LYS cc_start: 0.9045 (tppt) cc_final: 0.8561 (tptt) REVERT: O 162 GLU cc_start: 0.8600 (mt-10) cc_final: 0.7756 (tp30) REVERT: V 53 GLU cc_start: 0.8555 (pt0) cc_final: 0.8258 (pt0) REVERT: X 43 MET cc_start: 0.7487 (mmm) cc_final: 0.7210 (mmm) REVERT: X 48 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7271 (tp30) REVERT: X 67 LEU cc_start: 0.8915 (tt) cc_final: 0.8676 (mt) REVERT: X 84 TYR cc_start: 0.8625 (t80) cc_final: 0.8417 (t80) REVERT: Z 48 SER cc_start: 0.9106 (m) cc_final: 0.8760 (t) REVERT: Z 55 GLU cc_start: 0.8775 (mm-30) cc_final: 0.7785 (tm-30) REVERT: Z 87 ARG cc_start: 0.8112 (ptm160) cc_final: 0.7291 (ptm160) REVERT: d 82 MET cc_start: 0.8846 (mmm) cc_final: 0.8606 (tpp) REVERT: f 16 VAL cc_start: 0.8675 (t) cc_final: 0.8466 (t) REVERT: g 58 MET cc_start: 0.5399 (mmt) cc_final: 0.4506 (mmm) REVERT: g 60 VAL cc_start: 0.5862 (t) cc_final: 0.5270 (t) REVERT: h 19 LYS cc_start: 0.8652 (mmtt) cc_final: 0.8118 (mtmt) REVERT: m 44 ARG cc_start: 0.8769 (tpp80) cc_final: 0.8550 (tpt-90) REVERT: m 45 GLU cc_start: 0.8844 (tp30) cc_final: 0.8181 (tp30) REVERT: m 49 GLN cc_start: 0.9062 (mt0) cc_final: 0.8690 (mt0) REVERT: m 87 LEU cc_start: 0.7983 (mp) cc_final: 0.7696 (tp) REVERT: m 109 ASP cc_start: 0.8649 (m-30) cc_final: 0.8372 (m-30) REVERT: n 27 GLU cc_start: 0.8609 (pp20) cc_final: 0.8317 (pp20) REVERT: n 68 GLU cc_start: 0.8574 (mp0) cc_final: 0.8241 (mp0) REVERT: p 88 GLU cc_start: 0.9314 (tt0) cc_final: 0.8692 (tp30) REVERT: p 105 ILE cc_start: 0.9347 (tt) cc_final: 0.9131 (tt) outliers start: 1 outliers final: 0 residues processed: 885 average time/residue: 0.5482 time to fit residues: 838.1338 Evaluate side-chains 726 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 725 time to evaluate : 5.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 487 optimal weight: 2.9990 chunk 513 optimal weight: 9.9990 chunk 468 optimal weight: 5.9990 chunk 499 optimal weight: 20.0000 chunk 300 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 392 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 451 optimal weight: 0.9980 chunk 472 optimal weight: 20.0000 chunk 497 optimal weight: 30.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 98 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 GLN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 452 ASN M 81 GLN M 82 HIS M 169 ASN ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 232 HIS ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 103 GLN X 105 GLN b 45 ASN c 9 HIS ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 103 ASN ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.6415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.255 52638 Z= 0.624 Angle : 1.841 50.948 72283 Z= 1.172 Chirality : 0.331 6.486 8863 Planarity : 0.005 0.149 9468 Dihedral : 5.970 165.153 8303 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.99 % Allowed : 11.03 % Favored : 87.98 % Rotamer: Outliers : 0.03 % Allowed : 1.09 % Favored : 98.89 % 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: -1.69 (0.11), residues: 5840 helix: 0.04 (0.09), residues: 3059 sheet: -0.63 (0.43), residues: 158 loop : -2.65 (0.12), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP L 196 HIS 0.011 0.002 HIS M 440 PHE 0.030 0.002 PHE O 134 TYR 0.040 0.002 TYR C 110 ARG 0.013 0.001 ARG H 25 *********************** 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 843 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 842 time to evaluate : 5.505 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: A 68 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8686 (tm-30) REVERT: A 69 ILE cc_start: 0.9064 (pt) cc_final: 0.8719 (pt) REVERT: B 48 MET cc_start: 0.8636 (tpp) cc_final: 0.8283 (tpp) REVERT: B 94 ASN cc_start: 0.9444 (m110) cc_final: 0.9174 (m110) REVERT: B 137 ASP cc_start: 0.7462 (m-30) cc_final: 0.6629 (m-30) REVERT: C 92 ILE cc_start: 0.8784 (mt) cc_final: 0.8439 (mt) REVERT: C 131 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8149 (mt-10) REVERT: C 154 ASP cc_start: 0.8456 (t0) cc_final: 0.8143 (t0) REVERT: D 83 LEU cc_start: 0.9346 (tp) cc_final: 0.9017 (tt) REVERT: D 169 TRP cc_start: 0.8773 (m100) cc_final: 0.7282 (m100) REVERT: D 172 GLU cc_start: 0.7404 (tp30) cc_final: 0.7054 (tp30) REVERT: D 193 TYR cc_start: 0.8714 (t80) cc_final: 0.8340 (t80) REVERT: D 221 ARG cc_start: 0.8409 (mmt180) cc_final: 0.8139 (tpp-160) REVERT: D 338 MET cc_start: 0.9231 (ptm) cc_final: 0.8650 (ppp) REVERT: F 355 LYS cc_start: 0.9399 (tptm) cc_final: 0.8890 (tppt) REVERT: F 370 ASP cc_start: 0.8952 (m-30) cc_final: 0.8338 (m-30) REVERT: F 390 ASP cc_start: 0.9043 (t70) cc_final: 0.7945 (t0) REVERT: F 394 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8523 (mt-10) REVERT: G 154 ILE cc_start: 0.8678 (pt) cc_final: 0.8166 (pt) REVERT: G 160 ILE cc_start: 0.9607 (mp) cc_final: 0.9312 (tt) REVERT: H 21 THR cc_start: 0.9353 (p) cc_final: 0.9113 (t) REVERT: H 25 ARG cc_start: 0.9153 (mtm-85) cc_final: 0.8552 (ttp-110) REVERT: H 31 MET cc_start: 0.9282 (mmm) cc_final: 0.8923 (mmt) REVERT: H 51 ASP cc_start: 0.8404 (m-30) cc_final: 0.8130 (t0) REVERT: H 77 MET cc_start: 0.9084 (mpp) cc_final: 0.8647 (mpp) REVERT: H 91 MET cc_start: 0.8496 (tpp) cc_final: 0.8221 (tpp) REVERT: H 172 MET cc_start: 0.5294 (mmp) cc_final: 0.4847 (mmm) REVERT: H 230 ASN cc_start: 0.8633 (m110) cc_final: 0.8202 (m110) REVERT: H 251 MET cc_start: 0.8281 (tpt) cc_final: 0.7976 (tpp) REVERT: H 253 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6080 (tt0) REVERT: H 268 MET cc_start: 0.7481 (ttp) cc_final: 0.7053 (tmm) REVERT: H 290 TRP cc_start: 0.8876 (m100) cc_final: 0.8491 (m-10) REVERT: I 111 ILE cc_start: 0.8905 (mt) cc_final: 0.8588 (mt) REVERT: I 136 ASN cc_start: 0.8076 (t0) cc_final: 0.7796 (m-40) REVERT: I 144 HIS cc_start: 0.7320 (m-70) cc_final: 0.7061 (m170) REVERT: J 24 PRO cc_start: 0.8574 (Cg_endo) cc_final: 0.8271 (Cg_exo) REVERT: J 76 THR cc_start: 0.8726 (p) cc_final: 0.8352 (p) REVERT: J 99 MET cc_start: 0.8476 (tpp) cc_final: 0.8187 (tpt) REVERT: K 25 HIS cc_start: 0.7909 (m-70) cc_final: 0.7406 (m90) REVERT: L 101 MET cc_start: 0.9067 (mmm) cc_final: 0.8721 (mmm) REVERT: L 102 GLU cc_start: 0.7932 (pt0) cc_final: 0.7678 (pt0) REVERT: L 104 SER cc_start: 0.9566 (m) cc_final: 0.8382 (t) REVERT: L 237 MET cc_start: 0.8650 (mmp) cc_final: 0.7437 (ppp) REVERT: L 238 GLU cc_start: 0.6613 (tt0) cc_final: 0.5558 (pt0) REVERT: L 279 CYS cc_start: 0.8446 (t) cc_final: 0.8109 (t) REVERT: L 330 CYS cc_start: 0.8714 (m) cc_final: 0.8305 (t) REVERT: L 353 GLU cc_start: 0.7960 (tp30) cc_final: 0.7631 (tp30) REVERT: L 393 ASP cc_start: 0.8669 (m-30) cc_final: 0.8384 (m-30) REVERT: L 397 GLU cc_start: 0.8016 (tp30) cc_final: 0.7479 (tp30) REVERT: L 426 ILE cc_start: 0.9449 (mt) cc_final: 0.9234 (tt) REVERT: L 429 PHE cc_start: 0.8095 (t80) cc_final: 0.7638 (t80) REVERT: L 544 MET cc_start: 0.7298 (mtp) cc_final: 0.6342 (tmm) REVERT: M 10 MET cc_start: 0.8756 (ttm) cc_final: 0.7854 (ttm) REVERT: M 76 MET cc_start: 0.8195 (mtt) cc_final: 0.7557 (mtm) REVERT: M 87 GLU cc_start: 0.7870 (pp20) cc_final: 0.7232 (mp0) REVERT: M 139 GLN cc_start: 0.7547 (pm20) cc_final: 0.7304 (pm20) REVERT: M 178 MET cc_start: 0.8045 (pmm) cc_final: 0.7517 (mmp) REVERT: M 216 LEU cc_start: 0.9239 (tp) cc_final: 0.8986 (tt) REVERT: M 222 GLU cc_start: 0.8423 (tp30) cc_final: 0.7382 (tp30) REVERT: M 269 MET cc_start: 0.7925 (ttp) cc_final: 0.7349 (ttm) REVERT: M 276 CYS cc_start: 0.8265 (t) cc_final: 0.8039 (t) REVERT: M 310 MET cc_start: 0.7840 (mmt) cc_final: 0.7266 (mmm) REVERT: M 342 MET cc_start: 0.9157 (mmt) cc_final: 0.8630 (mmm) REVERT: M 394 ILE cc_start: 0.8959 (mm) cc_final: 0.8365 (tp) REVERT: M 410 MET cc_start: 0.9126 (mpp) cc_final: 0.8891 (mpp) REVERT: N 14 MET cc_start: 0.7982 (mmm) cc_final: 0.7581 (mmt) REVERT: N 54 GLU cc_start: 0.8320 (tt0) cc_final: 0.7574 (tt0) REVERT: N 63 GLN cc_start: 0.8018 (tt0) cc_final: 0.7439 (tt0) REVERT: N 96 MET cc_start: 0.8933 (tpp) cc_final: 0.7837 (tmm) REVERT: N 100 MET cc_start: 0.9127 (ttp) cc_final: 0.8923 (tmm) REVERT: N 200 MET cc_start: 0.8849 (ptm) cc_final: 0.8440 (ptp) REVERT: N 208 TYR cc_start: 0.8672 (t80) cc_final: 0.8341 (t80) REVERT: N 211 MET cc_start: 0.8555 (ttm) cc_final: 0.7220 (ttm) REVERT: N 240 MET cc_start: 0.8887 (tpt) cc_final: 0.8663 (tpp) REVERT: N 248 LEU cc_start: 0.8739 (mm) cc_final: 0.8099 (mp) REVERT: N 251 MET cc_start: 0.8700 (tpp) cc_final: 0.8096 (tpp) REVERT: N 270 MET cc_start: 0.9103 (mtm) cc_final: 0.8101 (mtt) REVERT: N 304 MET cc_start: 0.8497 (ttm) cc_final: 0.8016 (ttm) REVERT: O 113 GLU cc_start: 0.8812 (pp20) cc_final: 0.8445 (pp20) REVERT: O 131 ASP cc_start: 0.7878 (t0) cc_final: 0.7457 (t0) REVERT: O 134 PHE cc_start: 0.8102 (m-80) cc_final: 0.7387 (m-10) REVERT: O 162 GLU cc_start: 0.8623 (mt-10) cc_final: 0.7832 (tp30) REVERT: V 48 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8427 (mt-10) REVERT: V 53 GLU cc_start: 0.8529 (pt0) cc_final: 0.8302 (pt0) REVERT: X 48 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7055 (tp30) REVERT: X 84 TYR cc_start: 0.8547 (t80) cc_final: 0.8269 (t80) REVERT: Z 48 SER cc_start: 0.9165 (m) cc_final: 0.8732 (t) REVERT: Z 55 GLU cc_start: 0.8828 (mm-30) cc_final: 0.7759 (tm-30) REVERT: Z 59 LEU cc_start: 0.9105 (mp) cc_final: 0.8866 (mp) REVERT: Z 87 ARG cc_start: 0.8262 (ptm160) cc_final: 0.7452 (ptm160) REVERT: d 82 MET cc_start: 0.8881 (mmm) cc_final: 0.8639 (tpp) REVERT: f 16 VAL cc_start: 0.8922 (t) cc_final: 0.8654 (t) REVERT: g 58 MET cc_start: 0.6544 (mmt) cc_final: 0.5596 (mmm) REVERT: g 60 VAL cc_start: 0.5917 (t) cc_final: 0.5358 (t) REVERT: h 19 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8148 (mtmt) REVERT: m 42 LEU cc_start: 0.8442 (mt) cc_final: 0.8236 (mt) REVERT: m 45 GLU cc_start: 0.8877 (tp30) cc_final: 0.8235 (tp30) REVERT: m 49 GLN cc_start: 0.9076 (mt0) cc_final: 0.8807 (mt0) REVERT: m 87 LEU cc_start: 0.8044 (mp) cc_final: 0.7713 (tp) REVERT: m 109 ASP cc_start: 0.8735 (m-30) cc_final: 0.8488 (m-30) REVERT: n 27 GLU cc_start: 0.8694 (pp20) cc_final: 0.8396 (pp20) REVERT: p 105 ILE cc_start: 0.9346 (tt) cc_final: 0.9121 (tt) outliers start: 1 outliers final: 0 residues processed: 843 average time/residue: 0.5463 time to fit residues: 802.3879 Evaluate side-chains 703 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 703 time to evaluate : 5.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 327 optimal weight: 0.7980 chunk 528 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 chunk 250 optimal weight: 9.9990 chunk 367 optimal weight: 20.0000 chunk 553 optimal weight: 30.0000 chunk 509 optimal weight: 20.0000 chunk 441 optimal weight: 9.9990 chunk 45 optimal weight: 0.2980 chunk 340 optimal weight: 0.4980 chunk 270 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN D 98 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 452 ASN M 169 ASN M 192 ASN ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 434 ASN O 92 ASN ** W 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 45 ASN ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 103 ASN ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.6411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.263 52638 Z= 0.588 Angle : 1.805 50.850 72283 Z= 1.156 Chirality : 0.330 6.459 8863 Planarity : 0.005 0.142 9468 Dihedral : 5.717 166.639 8303 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.99 % Allowed : 9.38 % Favored : 89.62 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 0.99 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.11), residues: 5840 helix: 0.21 (0.10), residues: 3038 sheet: -0.73 (0.44), residues: 161 loop : -2.61 (0.12), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 303 HIS 0.009 0.001 HIS L 248 PHE 0.036 0.002 PHE H 237 TYR 0.027 0.002 TYR L 159 ARG 0.006 0.000 ARG O 126 ********************** 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 879 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 879 time to evaluate : 4.848 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: A 54 LYS cc_start: 0.8182 (mmpt) cc_final: 0.7974 (mmmt) REVERT: A 60 ILE cc_start: 0.9481 (mm) cc_final: 0.9263 (mm) REVERT: A 67 LEU cc_start: 0.9322 (mt) cc_final: 0.9113 (mt) REVERT: A 68 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8672 (tm-30) REVERT: A 69 ILE cc_start: 0.8999 (pt) cc_final: 0.8616 (pt) REVERT: A 83 ASN cc_start: 0.8635 (t0) cc_final: 0.8425 (t0) REVERT: B 137 ASP cc_start: 0.7406 (m-30) cc_final: 0.6824 (m-30) REVERT: C 92 ILE cc_start: 0.8824 (mt) cc_final: 0.8430 (mt) REVERT: C 131 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8362 (mt-10) REVERT: C 151 ILE cc_start: 0.8073 (pt) cc_final: 0.7628 (mm) REVERT: C 154 ASP cc_start: 0.8145 (t0) cc_final: 0.7824 (t0) REVERT: D 83 LEU cc_start: 0.9239 (tp) cc_final: 0.8937 (tt) REVERT: D 169 TRP cc_start: 0.8729 (m100) cc_final: 0.7286 (m100) REVERT: D 193 TYR cc_start: 0.8484 (t80) cc_final: 0.8096 (t80) REVERT: D 220 LEU cc_start: 0.9042 (tp) cc_final: 0.8831 (tp) REVERT: D 318 MET cc_start: 0.8815 (tpp) cc_final: 0.8590 (mmt) REVERT: D 338 MET cc_start: 0.9206 (ptm) cc_final: 0.8550 (ppp) REVERT: D 405 MET cc_start: 0.8920 (mmt) cc_final: 0.8681 (mmm) REVERT: F 355 LYS cc_start: 0.9385 (tptm) cc_final: 0.8812 (tppt) REVERT: F 370 ASP cc_start: 0.8866 (m-30) cc_final: 0.8287 (m-30) REVERT: F 390 ASP cc_start: 0.8953 (t70) cc_final: 0.8102 (t0) REVERT: G 154 ILE cc_start: 0.8521 (pt) cc_final: 0.7982 (pt) REVERT: G 160 ILE cc_start: 0.9571 (mp) cc_final: 0.9267 (tt) REVERT: H 25 ARG cc_start: 0.9025 (mtm-85) cc_final: 0.8616 (ttp-110) REVERT: H 31 MET cc_start: 0.9262 (mmm) cc_final: 0.8677 (tpp) REVERT: H 51 ASP cc_start: 0.8345 (m-30) cc_final: 0.8103 (t0) REVERT: H 60 PRO cc_start: 0.6341 (Cg_endo) cc_final: 0.5939 (Cg_exo) REVERT: H 77 MET cc_start: 0.9219 (mpp) cc_final: 0.8727 (mpp) REVERT: H 172 MET cc_start: 0.5147 (mmp) cc_final: 0.4696 (mmm) REVERT: H 230 ASN cc_start: 0.8526 (m110) cc_final: 0.8272 (m-40) REVERT: H 251 MET cc_start: 0.8187 (tpt) cc_final: 0.7924 (tpp) REVERT: H 253 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6346 (tt0) REVERT: H 268 MET cc_start: 0.7422 (ttp) cc_final: 0.7028 (tmm) REVERT: H 285 LEU cc_start: 0.8854 (tp) cc_final: 0.8591 (tp) REVERT: H 290 TRP cc_start: 0.8851 (m100) cc_final: 0.8606 (m-10) REVERT: I 136 ASN cc_start: 0.8181 (t0) cc_final: 0.7839 (m-40) REVERT: I 144 HIS cc_start: 0.7142 (m-70) cc_final: 0.6875 (m-70) REVERT: I 164 GLU cc_start: 0.8352 (mp0) cc_final: 0.7514 (mp0) REVERT: J 24 PRO cc_start: 0.8374 (Cg_endo) cc_final: 0.7994 (Cg_exo) REVERT: J 54 LEU cc_start: 0.9173 (mm) cc_final: 0.8950 (mm) REVERT: J 76 THR cc_start: 0.8762 (p) cc_final: 0.8366 (p) REVERT: J 99 MET cc_start: 0.8446 (tpp) cc_final: 0.8159 (tpt) REVERT: K 25 HIS cc_start: 0.7820 (m-70) cc_final: 0.7179 (m90) REVERT: K 37 MET cc_start: 0.8253 (tpt) cc_final: 0.7789 (tpp) REVERT: K 59 MET cc_start: 0.7500 (mmt) cc_final: 0.7229 (mmt) REVERT: L 101 MET cc_start: 0.9070 (mmm) cc_final: 0.8773 (mmt) REVERT: L 102 GLU cc_start: 0.7934 (pt0) cc_final: 0.6478 (tp30) REVERT: L 104 SER cc_start: 0.9527 (m) cc_final: 0.8404 (t) REVERT: L 105 MET cc_start: 0.8655 (mmm) cc_final: 0.8108 (mmm) REVERT: L 237 MET cc_start: 0.8570 (mmp) cc_final: 0.8294 (mmp) REVERT: L 238 GLU cc_start: 0.6641 (tt0) cc_final: 0.5858 (pt0) REVERT: L 249 SER cc_start: 0.8828 (p) cc_final: 0.8430 (t) REVERT: L 279 CYS cc_start: 0.8398 (t) cc_final: 0.8065 (t) REVERT: L 313 MET cc_start: 0.8098 (mtp) cc_final: 0.7741 (mtp) REVERT: L 393 ASP cc_start: 0.8637 (m-30) cc_final: 0.8351 (m-30) REVERT: L 397 GLU cc_start: 0.8014 (tp30) cc_final: 0.7456 (tp30) REVERT: L 426 ILE cc_start: 0.9442 (mt) cc_final: 0.9205 (tt) REVERT: L 429 PHE cc_start: 0.7973 (t80) cc_final: 0.7569 (t80) REVERT: L 544 MET cc_start: 0.7406 (mtp) cc_final: 0.6514 (tmm) REVERT: M 10 MET cc_start: 0.8689 (ttm) cc_final: 0.8330 (ttm) REVERT: M 70 MET cc_start: 0.9017 (tpp) cc_final: 0.8790 (mmm) REVERT: M 76 MET cc_start: 0.8142 (mtt) cc_final: 0.7458 (mtm) REVERT: M 87 GLU cc_start: 0.7698 (pp20) cc_final: 0.7194 (mp0) REVERT: M 98 MET cc_start: 0.8813 (mmm) cc_final: 0.8605 (mmt) REVERT: M 216 LEU cc_start: 0.9181 (tp) cc_final: 0.8970 (tt) REVERT: M 222 GLU cc_start: 0.8173 (tp30) cc_final: 0.7232 (tp30) REVERT: M 257 MET cc_start: 0.8099 (pmm) cc_final: 0.6946 (mmm) REVERT: M 269 MET cc_start: 0.7812 (ttp) cc_final: 0.7200 (ttm) REVERT: M 310 MET cc_start: 0.7621 (mmt) cc_final: 0.7270 (mmm) REVERT: M 342 MET cc_start: 0.8997 (mmt) cc_final: 0.8689 (mmm) REVERT: M 394 ILE cc_start: 0.8813 (mm) cc_final: 0.8159 (tp) REVERT: M 410 MET cc_start: 0.9060 (mpp) cc_final: 0.8845 (mpp) REVERT: N 14 MET cc_start: 0.7956 (mmm) cc_final: 0.7542 (mmp) REVERT: N 44 MET cc_start: 0.8892 (mtm) cc_final: 0.8681 (mtp) REVERT: N 54 GLU cc_start: 0.8296 (tt0) cc_final: 0.7365 (tt0) REVERT: N 96 MET cc_start: 0.8836 (tpp) cc_final: 0.7874 (tmm) REVERT: N 100 MET cc_start: 0.9121 (ttp) cc_final: 0.8859 (tmm) REVERT: N 208 TYR cc_start: 0.8641 (t80) cc_final: 0.8358 (t80) REVERT: N 211 MET cc_start: 0.8423 (ttm) cc_final: 0.6929 (ttm) REVERT: N 248 LEU cc_start: 0.8821 (mm) cc_final: 0.8394 (mm) REVERT: N 251 MET cc_start: 0.8983 (tpp) cc_final: 0.7815 (tpp) REVERT: N 268 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7592 (tm-30) REVERT: N 269 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6789 (mm-30) REVERT: N 270 MET cc_start: 0.9096 (mtm) cc_final: 0.8100 (mtt) REVERT: N 304 MET cc_start: 0.8348 (ttm) cc_final: 0.7984 (ttm) REVERT: O 113 GLU cc_start: 0.8811 (pp20) cc_final: 0.8488 (pp20) REVERT: O 131 ASP cc_start: 0.7786 (t0) cc_final: 0.7363 (t0) REVERT: O 134 PHE cc_start: 0.7997 (m-80) cc_final: 0.7493 (m-10) REVERT: O 162 GLU cc_start: 0.8584 (mt-10) cc_final: 0.7773 (tp30) REVERT: V 48 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8336 (mt-10) REVERT: V 53 GLU cc_start: 0.8391 (pt0) cc_final: 0.8087 (pt0) REVERT: X 48 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7173 (tp30) REVERT: X 67 LEU cc_start: 0.8899 (tt) cc_final: 0.8552 (mt) REVERT: X 84 TYR cc_start: 0.8458 (t80) cc_final: 0.8198 (t80) REVERT: Z 48 SER cc_start: 0.9162 (m) cc_final: 0.8715 (t) REVERT: Z 55 GLU cc_start: 0.8787 (mm-30) cc_final: 0.7713 (tm-30) REVERT: Z 87 ARG cc_start: 0.8219 (ptm160) cc_final: 0.7370 (ptm160) REVERT: a 21 MET cc_start: 0.8673 (tpp) cc_final: 0.8466 (tpp) REVERT: b 7 PHE cc_start: 0.7443 (t80) cc_final: 0.6906 (t80) REVERT: d 46 ASN cc_start: 0.8271 (m110) cc_final: 0.7001 (t0) REVERT: d 82 MET cc_start: 0.8836 (mmm) cc_final: 0.8585 (tpp) REVERT: g 60 VAL cc_start: 0.5769 (t) cc_final: 0.5114 (t) REVERT: h 19 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8143 (mtmt) REVERT: i 6 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6896 (tm-30) REVERT: m 44 ARG cc_start: 0.8739 (tpp80) cc_final: 0.8492 (tpt-90) REVERT: m 45 GLU cc_start: 0.8778 (tp30) cc_final: 0.8145 (tp30) REVERT: m 49 GLN cc_start: 0.9051 (mt0) cc_final: 0.8685 (mt0) REVERT: m 87 LEU cc_start: 0.7991 (mp) cc_final: 0.7722 (tp) REVERT: m 109 ASP cc_start: 0.8711 (m-30) cc_final: 0.8464 (m-30) REVERT: n 27 GLU cc_start: 0.8655 (pp20) cc_final: 0.8353 (pp20) REVERT: n 49 GLU cc_start: 0.8680 (pt0) cc_final: 0.8466 (pt0) REVERT: n 68 GLU cc_start: 0.8617 (mp0) cc_final: 0.8303 (mp0) REVERT: p 88 GLU cc_start: 0.9230 (tt0) cc_final: 0.8646 (tp30) REVERT: p 105 ILE cc_start: 0.9362 (tt) cc_final: 0.9085 (tt) outliers start: 0 outliers final: 0 residues processed: 879 average time/residue: 0.5573 time to fit residues: 852.5026 Evaluate side-chains 720 residues out of total 5177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 720 time to evaluate : 5.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 350 optimal weight: 1.9990 chunk 469 optimal weight: 0.2980 chunk 135 optimal weight: 40.0000 chunk 406 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 441 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 453 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN D 98 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS G 119 GLN ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 452 ASN M 83 HIS ** M 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 GLN ** Y 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 45 ASN ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 103 ASN ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.070272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.063472 restraints weight = 285627.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.064868 restraints weight = 177147.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.065655 restraints weight = 111057.346| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.266 52638 Z= 0.587 Angle : 1.797 50.832 72283 Z= 1.153 Chirality : 0.330 6.452 8863 Planarity : 0.005 0.143 9468 Dihedral : 5.508 167.521 8303 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.38 % Favored : 89.69 % Rotamer: Outliers : 0.03 % Allowed : 0.53 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.11), residues: 5840 helix: 0.27 (0.10), residues: 3024 sheet: -0.69 (0.44), residues: 164 loop : -2.57 (0.12), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 303 HIS 0.009 0.001 HIS M 319 PHE 0.025 0.002 PHE D 214 TYR 0.051 0.001 TYR G 42 ARG 0.006 0.000 ARG W 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14330.37 seconds wall clock time: 254 minutes 50.79 seconds (15290.79 seconds total)