Starting phenix.real_space_refine on Mon Mar 25 20:57:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ldw_4040/03_2024/5ldw_4040_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ldw_4040/03_2024/5ldw_4040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ldw_4040/03_2024/5ldw_4040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ldw_4040/03_2024/5ldw_4040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ldw_4040/03_2024/5ldw_4040_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ldw_4040/03_2024/5ldw_4040_updated.pdb" } resolution = 4.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 4 5.49 5 S 325 5.16 5 C 32427 2.51 5 N 9078 2.21 5 O 9318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "N TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 39": "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: 51181 Number of models: 1 Model: "" Number of chains: 52 Chain: "A" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 687 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1159 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 10, 'TRANS': 136} Chain: "C" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1684 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 189} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3229 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 26, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 3, 'HIS:plan': 1, 'GLU:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 84 Chain: "E" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 959 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PTRANS': 17, 'TRANS': 168} Unresolved non-hydrogen bonds: 530 Unresolved non-hydrogen angles: 677 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 5, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 294 Chain: "F" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 2356 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 256} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 957 Unresolved non-hydrogen angles: 1224 Unresolved non-hydrogen dihedrals: 797 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 9, 'ASN:plan1': 12, 'TRP:plan': 6, 'ASP:plan': 17, 'PHE:plan': 13, 'GLU:plan': 26, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 561 Chain: "G" Number of atoms: 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: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2306 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "I" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 165} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "J" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1211 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 3, 'TRANS': 167} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "K" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 720 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "L" Number of atoms: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4538 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 27, 'TRANS': 576} Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 5, 'ASN:plan1': 12, 'HIS:plan': 2, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "M" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3536 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 20, 'TRANS': 436} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "N" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2592 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 21, 'TRANS': 322} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "O" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1851 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 208} Link IDs: {'PTRANS': 10, 'TRANS': 303} Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 882 Unresolved non-hydrogen dihedrals: 498 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 10, 'ASN:plan1': 6, 'ASP:plan': 10, 'TYR:plan': 8, 'UNK:plan-1': 86, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 390 Chain: "P" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 1415 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 283} Link IDs: {'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 566 Unresolved non-hydrogen angles: 849 Unresolved non-hydrogen dihedrals: 283 Planarities with less than four sites: {'UNK:plan-1': 283} Unresolved non-hydrogen planarities: 283 Chain: "Q" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 Chain: "R" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 501 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 1, 'TRANS': 87} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 54, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "S" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 405 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 4, 'TRANS': 75} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 157 Chain: "T" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 378 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 11, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "U" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 432 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 139 Chain: "V" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 685 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 10, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 109 Chain: "W" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 105} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "X" Number of atoms: 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 1419 SG CYS B 119 95.296 89.866 205.246 1.00 29.57 S ATOM 921 SG CYS B 55 89.532 92.524 206.741 1.00 32.08 S ATOM 915 SG CYS B 54 89.601 86.746 204.004 1.00 32.26 S ATOM 1649 SG CYS B 149 91.938 87.493 210.063 1.00 30.40 S ATOM 7257 SG CYS E 103 111.044 42.876 261.793 1.00 99.40 S ATOM 7285 SG CYS E 108 109.250 39.856 263.008 1.00100.21 S ATOM 7466 SG CYS E 144 114.265 40.167 258.861 1.00101.54 S ATOM 7486 SG CYS E 148 112.770 36.921 259.808 1.00 99.96 S ATOM 9514 SG CYS F 362 117.200 47.341 237.285 1.00 66.03 S ATOM 9534 SG CYS F 365 113.373 47.984 242.238 1.00 63.63 S ATOM 9858 SG CYS F 405 117.384 42.759 241.864 1.00 67.04 S ATOM 9495 SG CYS F 359 119.908 48.632 242.942 1.00 65.78 S ATOM 10740 SG CYS G 114 113.979 66.174 228.021 1.00 32.69 S ATOM 10679 SG CYS G 105 108.335 69.209 229.057 1.00 31.43 S ATOM 10700 SG CYS G 108 113.573 71.097 232.269 1.00 31.93 S ATOM 10988 SG CYS G 156 121.458 58.903 233.455 1.00 33.87 S ATOM 10965 SG CYS G 153 119.157 62.858 238.224 1.00 33.69 S ATOM 11012 SG CYS G 159 125.426 62.876 236.425 1.00 33.88 S ATOM 11242 SG CYS G 203 120.918 65.264 232.448 1.00 32.99 S ATOM 10258 SG CYS G 41 121.275 53.753 230.602 1.00 49.30 S ATOM 10335 SG CYS G 52 117.637 52.749 230.715 1.00 49.63 S ATOM 10360 SG CYS G 55 118.961 49.326 226.470 1.00 49.23 S ATOM 10433 SG CYS G 69 122.361 50.606 226.833 1.00 50.26 S ATOM 16900 SG CYS I 119 95.864 82.284 215.164 1.00 23.44 S ATOM 16874 SG CYS I 116 96.862 88.457 216.491 1.00 23.12 S ATOM 16921 SG CYS I 122 97.766 84.053 221.235 1.00 23.28 S ATOM 16648 SG CYS I 87 101.803 84.447 216.027 1.00 23.18 S ATOM 16950 SG CYS I 126 100.323 80.870 228.677 1.00 25.71 S ATOM 16621 SG CYS I 83 103.893 82.841 223.564 1.00 25.04 S ATOM 16579 SG CYS I 77 105.162 85.310 229.284 1.00 26.58 S ATOM 16598 SG CYS I 80 106.409 79.094 228.492 1.00 25.63 S ATOM 34064 SG CYS R 59 102.607 77.022 244.252 1.00 59.19 S ATOM 34215 SG CYS R 84 105.503 77.768 241.702 1.00 58.54 S ATOM 34237 SG CYS R 87 102.705 80.262 242.234 1.00 57.98 S Time building chain proxies: 30.72, per 1000 atoms: 0.60 Number of scatterers: 51181 At special positions: 0 Unit cell: (183.54, 184.87, 292.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 325 16.00 P 4 15.00 O 9318 8.00 N 9078 7.00 C 32427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS X 35 " - pdb=" SG CYS X 65 " distance=2.03 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.03 Simple disulfide: pdb=" SG CYS X 77 " - pdb=" SG CYS X 109 " distance=2.03 Simple disulfide: pdb=" SG CYS X 87 " - pdb=" SG CYS X 99 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 17 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.03 Simple disulfide: pdb=" SG CYS o 58 " - pdb=" SG CYS o 89 " distance=2.03 Simple disulfide: pdb=" SG CYS o 68 " - pdb=" SG CYS o 79 " distance=2.03 Simple disulfide: pdb=" SG CYS p 76 " - pdb=" SG CYS p 83 " distance=2.03 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 21.22 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb=" SF4 B 201 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 54 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 55 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 149 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb=" SF4 G 802 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb=" SF4 I 201 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 87 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 116 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 122 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 119 " pdb="FE2 SF4 I 201 " - pdb=" NE2 HIS I 65 " pdb=" SF4 I 202 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 126 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 80 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 83 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 77 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " Number of angles added : 3 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 277 helices and 19 sheets defined 57.7% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.59 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 removed outlier: 3.560A pdb=" N THR A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 72 removed outlier: 3.730A pdb=" N LEU A 57 " --> pdb=" O LYS A 54 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 61 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 64 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 65 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 67 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.767A pdb=" N ALA A 78 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 103 removed outlier: 4.187A pdb=" N THR A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.657A pdb=" N ASP B 34 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 94 through 106 Proline residue: B 98 - end of helix removed outlier: 3.758A pdb=" N ARG B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS B 102 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 153 through 166 removed outlier: 3.979A pdb=" N TYR B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 32 removed outlier: 3.622A pdb=" N ALA C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA C 30 " --> pdb=" O GLY C 26 " (cutoff:3.500A) removed outlier: 3.932A 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 126 through 137 removed outlier: 3.534A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C 132 " --> pdb=" O TRP C 129 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 134 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET C 137 " --> pdb=" O ILE C 134 " (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: 4.219A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 4.203A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 104' Processing helix chain 'D' and resid 116 through 126 Processing helix chain 'D' and resid 132 through 161 removed outlier: 3.852A pdb=" N TRP D 136 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 154 " --> pdb=" O HIS D 150 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N HIS D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 184 removed outlier: 3.598A pdb=" N MET D 170 " --> pdb=" O PRO D 166 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 226 removed outlier: 4.002A pdb=" N TYR D 212 " --> pdb=" O MET D 208 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU D 225 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) 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: 4.399A pdb=" N ARG D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 351 Processing helix chain 'D' and resid 395 through 405 removed outlier: 3.605A pdb=" N ALA D 400 " --> pdb=" O PHE D 396 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 3.911A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 35 removed outlier: 3.628A pdb=" N VAL E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 4.019A pdb=" N ASP E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 removed outlier: 3.814A pdb=" N ASN E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 72 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU E 73 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 83 Processing helix chain 'E' and resid 106 through 111 removed outlier: 5.049A pdb=" N ARG E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 123 removed outlier: 3.515A pdb=" N LYS E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 177 removed outlier: 4.012A pdb=" N LYS E 177 " --> pdb=" O ILE E 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 38 No H-bonds generated for 'chain 'F' and resid 35 through 38' Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 53 through 63 removed outlier: 4.098A pdb=" N VAL F 60 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 82 removed outlier: 4.281A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 124 removed outlier: 3.752A pdb=" N CYS F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 129 No H-bonds generated for 'chain 'F' and resid 126 through 129' Processing helix chain 'F' and resid 143 through 157 removed outlier: 3.646A pdb=" N ASN F 148 " --> pdb=" O ASN F 144 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG F 154 " --> pdb=" O GLN F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 197 removed outlier: 4.056A pdb=" N ILE F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU F 194 " --> pdb=" O THR F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 236 removed outlier: 3.850A pdb=" N SER F 231 " --> pdb=" O THR F 227 " (cutoff:3.500A) Proline residue: F 232 - end of helix Processing helix chain 'F' and resid 239 through 243 removed outlier: 3.800A pdb=" N ALA F 243 " --> pdb=" O GLY F 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 239 through 243' Processing helix chain 'F' and resid 276 through 283 removed outlier: 3.551A 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 344 through 357 removed outlier: 3.666A pdb=" N TYR F 354 " --> pdb=" O LEU F 350 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 366 No H-bonds generated for 'chain 'F' and resid 363 through 366' Processing helix chain 'F' and resid 369 through 381 removed outlier: 3.538A pdb=" N LYS F 374 " --> pdb=" O ASP F 370 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG F 378 " --> pdb=" O LYS F 374 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE F 379 " --> pdb=" O VAL F 375 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL F 380 " --> pdb=" O MET F 376 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 401 removed outlier: 3.670A pdb=" N TRP F 393 " --> pdb=" O ILE F 389 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU F 394 " --> pdb=" O ASP F 390 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE F 395 " --> pdb=" O SER F 391 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN F 398 " --> pdb=" O GLU F 394 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU F 400 " --> pdb=" O SER F 396 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY F 401 " --> pdb=" O LYS F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 419 Proline residue: F 414 - end of helix removed outlier: 3.785A pdb=" N LEU F 418 " --> pdb=" O PRO F 414 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE F 419 " --> pdb=" O VAL F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 436 removed outlier: 3.847A pdb=" N ARG F 429 " --> pdb=" O GLU F 425 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET F 430 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE F 433 " --> pdb=" O ARG F 429 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN F 435 " --> pdb=" O GLN F 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 30 Processing helix chain 'G' and resid 84 through 97 removed outlier: 3.709A pdb=" N GLY G 92 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET G 94 " --> pdb=" O ARG G 90 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 122 removed outlier: 3.863A pdb=" N MET G 121 " --> pdb=" O GLN G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 164 removed outlier: 3.711A pdb=" N SER G 164 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 202 removed outlier: 4.082A pdb=" N ILE G 200 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 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: 3.540A pdb=" N UNK G 301 " --> pdb=" O UNK G 297 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N UNK G 307 " --> pdb=" O UNK G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 337 removed outlier: 4.062A pdb=" N UNK G 334 " --> pdb=" O UNK G 331 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N UNK G 335 " --> pdb=" O UNK G 332 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N UNK G 336 " --> pdb=" O UNK G 333 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N UNK G 337 " --> pdb=" O UNK G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 373 No H-bonds generated for 'chain 'G' and resid 370 through 373' Processing helix chain 'G' and resid 389 through 401 removed outlier: 3.542A pdb=" N UNK G 395 " --> pdb=" O UNK G 391 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N UNK G 401 " --> pdb=" O UNK G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 433 removed outlier: 3.725A pdb=" N UNK G 433 " --> pdb=" O UNK G 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 429 through 433' Processing helix chain 'G' and resid 440 through 444 Processing helix chain 'G' and resid 461 through 473 removed outlier: 3.589A pdb=" N UNK G 468 " --> pdb=" O UNK G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 503 removed outlier: 3.985A pdb=" N UNK G 501 " --> pdb=" O UNK G 497 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 513 No H-bonds generated for 'chain 'G' and resid 510 through 513' 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: 3.585A pdb=" N UNK G 603 " --> pdb=" O UNK G 599 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N UNK G 604 " --> pdb=" O UNK G 600 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N UNK G 605 " --> pdb=" O UNK G 601 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N UNK G 606 " --> pdb=" O UNK G 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 599 through 606' Processing helix chain 'G' and resid 617 through 622 removed outlier: 4.069A pdb=" N UNK G 621 " --> pdb=" O UNK G 617 " (cutoff:3.500A) Processing helix chain 'G' and resid 646 through 649 No H-bonds generated for 'chain 'G' and resid 646 through 649' Processing helix chain 'G' and resid 682 through 691 removed outlier: 3.552A pdb=" N UNK G 686 " --> pdb=" O UNK G 682 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N UNK G 687 " --> pdb=" O UNK G 683 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N UNK G 688 " --> pdb=" O UNK G 684 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 9 No H-bonds generated for 'chain 'H' and resid 7 through 9' Processing helix chain 'H' and resid 11 through 18 Processing helix chain 'H' and resid 20 through 31 removed outlier: 3.851A pdb=" N ARG H 25 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU H 28 " --> pdb=" O GLU H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 56 removed outlier: 3.952A pdb=" N ALA H 52 " --> pdb=" O PRO H 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE H 53 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 86 removed outlier: 3.596A pdb=" N MET H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 110 removed outlier: 3.579A pdb=" N SER H 109 " --> pdb=" O MET H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 122 removed outlier: 3.916A pdb=" N SER H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY H 120 " --> pdb=" O ILE H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 140 removed outlier: 3.792A pdb=" N ILE H 130 " --> pdb=" O LYS H 126 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY H 131 " --> pdb=" O TYR H 127 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 156 removed outlier: 3.617A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL H 153 " --> pdb=" O ILE H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 167 No H-bonds generated for 'chain 'H' and resid 164 through 167' Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 191 removed outlier: 3.889A pdb=" N MET H 183 " --> pdb=" O TRP H 179 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP H 185 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE H 186 " --> pdb=" O ALA H 182 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE H 187 " --> pdb=" O MET H 183 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR H 189 " --> pdb=" O TRP H 185 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU H 190 " --> pdb=" O PHE H 186 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA H 191 " --> pdb=" O ILE H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 241 removed outlier: 3.922A pdb=" N PHE H 224 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA H 229 " --> pdb=" O MET H 225 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE H 231 " --> pdb=" O GLU H 227 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 276 removed outlier: 3.741A pdb=" N ILE H 257 " --> pdb=" O GLU H 253 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR H 260 " --> pdb=" O THR H 256 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS H 262 " --> pdb=" O ASN H 258 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU H 266 " --> pdb=" O LYS H 262 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER H 269 " --> pdb=" O LEU H 265 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE H 273 " --> pdb=" O SER H 269 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG H 274 " --> pdb=" O PHE H 270 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 275 " --> pdb=" O LEU H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 288 removed outlier: 3.606A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS H 287 " --> pdb=" O ASP H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 310 removed outlier: 3.643A pdb=" N SER H 306 " --> pdb=" O MET H 302 " (cutoff:3.500A) Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 15 through 25 removed outlier: 4.003A pdb=" N ASP I 19 " --> pdb=" O LYS I 15 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG I 20 " --> pdb=" O SER I 16 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 42 removed outlier: 3.635A pdb=" N MET I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR I 37 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR I 40 " --> pdb=" O MET I 36 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE I 42 " --> pdb=" O LEU I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 144 through 147 No H-bonds generated for 'chain 'I' and resid 144 through 147' Processing helix chain 'I' and resid 156 through 171 removed outlier: 3.599A pdb=" N ASP I 159 " --> pdb=" O ASN I 156 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS I 160 " --> pdb=" O ASN I 157 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ALA I 163 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE I 165 " --> pdb=" O GLU I 162 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA I 166 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE I 169 " --> pdb=" O ALA I 166 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN I 170 " --> pdb=" O ALA I 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 21 removed outlier: 3.678A pdb=" N VAL J 11 " --> pdb=" O PHE J 7 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE J 12 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE J 17 " --> pdb=" O PHE J 13 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLY J 19 " --> pdb=" O MET J 15 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER J 21 " --> pdb=" O PHE J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 47 removed outlier: 3.523A pdb=" N GLY J 32 " --> pdb=" O TYR J 28 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU J 33 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE J 43 " --> pdb=" O VAL J 39 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL J 44 " --> pdb=" O GLY J 40 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 58 removed outlier: 3.859A pdb=" N LEU J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE J 57 " --> pdb=" O GLY J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 74 removed outlier: 3.629A pdb=" N TYR J 70 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA J 73 " --> pdb=" O GLY J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 105 removed outlier: 4.158A pdb=" N GLU J 100 " --> pdb=" O GLY J 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE J 102 " --> pdb=" O LEU J 98 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N MET J 103 " --> pdb=" O MET J 99 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR J 105 " --> pdb=" O PHE J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 removed outlier: 3.716A pdb=" N ILE J 155 " --> pdb=" O THR J 151 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL J 165 " --> pdb=" O LEU J 161 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET J 169 " --> pdb=" O VAL J 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 20 removed outlier: 3.669A pdb=" N MET K 10 " --> pdb=" O MET K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 50 removed outlier: 3.718A pdb=" N THR K 47 " --> pdb=" O MET K 43 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE K 48 " --> pdb=" O ALA K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 73 Proline residue: K 60 - end of helix removed outlier: 3.610A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU K 70 " --> pdb=" O ALA K 67 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA K 72 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU K 73 " --> pdb=" O GLU K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 84 removed outlier: 3.848A pdb=" N VAL K 79 " --> pdb=" O LEU K 75 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET K 80 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER K 82 " --> pdb=" O LEU K 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 20 removed outlier: 4.061A pdb=" N LEU L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL L 10 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU L 15 " --> pdb=" O THR L 11 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 56 removed outlier: 3.549A pdb=" N VAL L 36 " --> pdb=" O TYR L 32 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS L 37 " --> pdb=" O PRO L 33 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR L 42 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE L 45 " --> pdb=" O SER L 41 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 85 through 106 removed outlier: 3.811A pdb=" N PHE L 89 " --> pdb=" O PHE L 85 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE L 90 " --> pdb=" O SER L 86 " (cutoff:3.500A) Proline residue: L 91 - end of helix removed outlier: 3.670A pdb=" N SER L 99 " --> pdb=" O PHE L 95 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU L 102 " --> pdb=" O TRP L 98 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 removed outlier: 4.053A pdb=" N PHE L 118 " --> pdb=" O ILE L 114 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS L 119 " --> pdb=" O ASN L 115 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR L 120 " --> pdb=" O LYS L 116 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU L 121 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU L 123 " --> pdb=" O LYS L 119 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 155 removed outlier: 3.725A pdb=" N ILE L 142 " --> pdb=" O PHE L 138 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY L 143 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE L 152 " --> pdb=" O GLY L 148 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU L 153 " --> pdb=" O ILE L 149 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU L 154 " --> pdb=" O MET L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 192 removed outlier: 4.114A pdb=" N ALA L 168 " --> pdb=" O ALA L 164 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE L 172 " --> pdb=" O ALA L 168 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN L 175 " --> pdb=" O ALA L 171 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE L 180 " --> pdb=" O ARG L 176 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE L 189 " --> pdb=" O ALA L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 212 No H-bonds generated for 'chain 'L' and resid 209 through 212' Processing helix chain 'L' and resid 216 through 222 removed outlier: 3.590A pdb=" N GLY L 222 " --> pdb=" O LEU L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 238 removed outlier: 4.199A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 248 removed outlier: 3.874A pdb=" N HIS L 248 " --> pdb=" O SER L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 removed outlier: 4.063A pdb=" N LEU L 259 " --> pdb=" O ALA L 255 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU L 260 " --> pdb=" O GLY L 256 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG L 262 " --> pdb=" O PHE L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 3.502A pdb=" N GLU L 268 " --> pdb=" O TYR L 264 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 264 through 269' Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.576A pdb=" N SER L 275 " --> pdb=" O LYS L 271 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU L 278 " --> pdb=" O GLN L 274 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE L 283 " --> pdb=" O CYS L 279 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR L 284 " --> pdb=" O LEU L 280 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR L 285 " --> pdb=" O GLY L 281 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU L 286 " --> pdb=" O ALA L 282 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE L 287 " --> pdb=" O ILE L 283 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR L 288 " --> pdb=" O THR L 284 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS L 291 " --> pdb=" O PHE L 287 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA L 292 " --> pdb=" O THR L 288 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 removed outlier: 4.263A pdb=" N ILE L 302 " --> pdb=" O ILE L 298 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR L 306 " --> pdb=" O ILE L 302 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER L 307 " --> pdb=" O ALA L 303 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU L 312 " --> pdb=" O SER L 308 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE L 317 " --> pdb=" O MET L 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 349 removed outlier: 4.029A pdb=" N ILE L 329 " --> pdb=" O ALA L 325 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N MET L 338 " --> pdb=" O PHE L 334 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N MET L 341 " --> pdb=" O ALA L 337 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER L 343 " --> pdb=" O LEU L 339 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE L 346 " --> pdb=" O CYS L 342 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE L 347 " --> pdb=" O SER L 343 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS L 348 " --> pdb=" O GLY L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 369 through 380 removed outlier: 3.540A pdb=" N LEU L 373 " --> pdb=" O THR L 369 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU L 380 " --> pdb=" O GLY L 376 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 399 Processing helix chain 'L' and resid 406 through 427 removed outlier: 3.578A pdb=" N LEU L 413 " --> pdb=" O LEU L 409 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE L 414 " --> pdb=" O LEU L 410 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA L 415 " --> pdb=" O MET L 411 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER L 417 " --> pdb=" O LEU L 413 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE L 421 " --> pdb=" O SER L 417 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR L 422 " --> pdb=" O PHE L 418 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER L 423 " --> pdb=" O THR L 419 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE L 426 " --> pdb=" O TYR L 422 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE L 427 " --> pdb=" O SER L 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.724A pdb=" N ASN L 452 " --> pdb=" O PRO L 448 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER L 453 " --> pdb=" O LEU L 449 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG L 456 " --> pdb=" O ASN L 452 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE L 459 " --> pdb=" O LYS L 455 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY L 460 " --> pdb=" O ARG L 456 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA L 464 " --> pdb=" O GLY L 460 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE L 468 " --> pdb=" O ALA L 464 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER L 469 " --> pdb=" O GLY L 465 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN L 470 " --> pdb=" O TYR L 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 489 through 509 removed outlier: 4.343A pdb=" N THR L 494 " --> pdb=" O ALA L 490 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE L 495 " --> pdb=" O LEU L 491 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET L 507 " --> pdb=" O GLU L 503 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 537 through 546 removed outlier: 3.526A pdb=" N ASN L 541 " --> pdb=" O ALA L 537 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET L 544 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER L 545 " --> pdb=" O ASN L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 577 removed outlier: 3.685A pdb=" N LEU L 568 " --> pdb=" O LYS L 564 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA L 569 " --> pdb=" O THR L 565 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET L 571 " --> pdb=" O SER L 567 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR L 575 " --> pdb=" O MET L 571 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU L 576 " --> pdb=" O LYS L 572 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 599 removed outlier: 3.528A pdb=" N PHE L 591 " --> pdb=" O TYR L 587 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU L 592 " --> pdb=" O PHE L 588 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE L 593 " --> pdb=" O LEU L 589 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE L 595 " --> pdb=" O PHE L 591 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 17 Proline residue: M 13 - end of helix removed outlier: 3.732A pdb=" N TRP M 16 " --> pdb=" O PRO M 13 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU M 17 " --> pdb=" O LEU M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 41 removed outlier: 3.984A pdb=" N SER M 31 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE M 34 " --> pdb=" O HIS M 30 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 81 Proline residue: M 74 - end of helix removed outlier: 5.220A pdb=" N LEU M 77 " --> pdb=" O LEU M 73 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET M 78 " --> pdb=" O PRO M 74 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA M 79 " --> pdb=" O LEU M 75 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N SER M 80 " --> pdb=" O MET M 76 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 111 removed outlier: 4.283A pdb=" N LEU M 99 " --> pdb=" O PHE M 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 122 removed outlier: 4.004A pdb=" N ILE M 120 " --> pdb=" O ILE M 116 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU M 121 " --> pdb=" O LEU M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 134 removed outlier: 3.731A pdb=" N THR M 129 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE M 131 " --> pdb=" O VAL M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 150 removed outlier: 4.884A pdb=" N TYR M 148 " --> pdb=" O ASN M 144 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU M 150 " --> pdb=" O GLY M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 170 Proline residue: M 159 - end of helix removed outlier: 4.280A pdb=" N VAL M 162 " --> pdb=" O LEU M 158 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE M 165 " --> pdb=" O LEU M 161 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR M 166 " --> pdb=" O VAL M 162 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR M 170 " --> pdb=" O TYR M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 201 removed outlier: 3.868A pdb=" N CYS M 199 " --> pdb=" O MET M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 206 No H-bonds generated for 'chain 'M' and resid 203 through 206' Processing helix chain 'M' and resid 214 through 221 removed outlier: 3.847A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA M 219 " --> pdb=" O TRP M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 230 through 239 removed outlier: 3.691A pdb=" N LYS M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 249 removed outlier: 3.549A pdb=" N THR M 247 " --> pdb=" O MET M 243 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 267 removed outlier: 3.601A pdb=" N MET M 263 " --> pdb=" O TYR M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 278 removed outlier: 3.575A pdb=" N ILE M 275 " --> pdb=" O MET M 271 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS M 276 " --> pdb=" O THR M 272 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 271 through 278' Processing helix chain 'M' and resid 284 through 287 No H-bonds generated for 'chain 'M' and resid 284 through 287' Processing helix chain 'M' and resid 289 through 303 removed outlier: 4.293A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE M 298 " --> pdb=" O MET M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 334 removed outlier: 3.890A pdb=" N MET M 310 " --> pdb=" O PRO M 306 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY M 311 " --> pdb=" O TRP M 307 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE M 317 " --> pdb=" O THR M 313 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER M 324 " --> pdb=" O GLY M 320 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET M 325 " --> pdb=" O LEU M 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 355 through 366 removed outlier: 3.520A pdb=" N THR M 365 " --> pdb=" O LEU M 361 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN M 366 " --> pdb=" O ALA M 362 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 388 removed outlier: 3.695A pdb=" N LEU M 379 " --> pdb=" O LEU M 375 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE M 380 " --> pdb=" O ILE M 376 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL M 381 " --> pdb=" O GLY M 377 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE M 386 " --> pdb=" O VAL M 382 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER M 387 " --> pdb=" O MET M 383 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP M 388 " --> pdb=" O SER M 384 " (cutoff:3.500A) Processing helix chain 'M' and resid 392 through 412 removed outlier: 3.997A pdb=" N VAL M 398 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN M 399 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA M 404 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU M 405 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER M 407 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR M 409 " --> pdb=" O LEU M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 446 removed outlier: 3.759A pdb=" N MET M 437 " --> pdb=" O GLU M 433 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE M 441 " --> pdb=" O MET M 437 " (cutoff:3.500A) Proline residue: M 443 - end of helix Processing helix chain 'N' and resid 5 through 21 removed outlier: 3.796A pdb=" N ILE N 13 " --> pdb=" O ILE N 9 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE N 18 " --> pdb=" O MET N 14 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL N 20 " --> pdb=" O GLY N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 45 removed outlier: 3.786A pdb=" N TRP N 30 " --> pdb=" O TRP N 26 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN N 36 " --> pdb=" O GLY N 32 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA N 39 " --> pdb=" O MET N 35 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE N 41 " --> pdb=" O MET N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 79 removed outlier: 3.656A pdb=" N GLU N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR N 62 " --> pdb=" O LYS N 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN N 63 " --> pdb=" O TYR N 59 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR N 65 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA N 66 " --> pdb=" O THR N 62 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET N 72 " --> pdb=" O MET N 68 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA N 73 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 103 removed outlier: 3.535A pdb=" N MET N 96 " --> pdb=" O PRO N 92 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU N 97 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET N 100 " --> pdb=" O MET N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 120 removed outlier: 3.734A pdb=" N GLN N 120 " --> pdb=" O PRO N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 142 removed outlier: 3.928A pdb=" N LEU N 130 " --> pdb=" O SER N 126 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU N 131 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR N 132 " --> pdb=" O LEU N 128 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.994A pdb=" N VAL N 141 " --> pdb=" O ALA N 137 " (cutoff:3.500A) 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 167 removed outlier: 4.095A pdb=" N SER N 161 " --> pdb=" O LEU N 157 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE N 162 " --> pdb=" O SER N 158 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU N 163 " --> pdb=" O VAL N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 193 removed outlier: 3.802A pdb=" N ILE N 184 " --> pdb=" O ALA N 180 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA N 192 " --> pdb=" O GLY N 188 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 220 removed outlier: 3.711A pdb=" N LEU N 205 " --> pdb=" O THR N 201 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE N 210 " --> pdb=" O ILE N 206 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET N 220 " --> pdb=" O PHE N 216 " (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: 4.125A pdb=" N ILE N 266 " --> pdb=" O LYS N 263 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE N 267 " --> pdb=" O TRP N 264 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU N 269 " --> pdb=" O ILE N 266 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR N 271 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS N 272 " --> pdb=" O GLU N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 296 removed outlier: 3.859A pdb=" N PHE N 281 " --> pdb=" O ILE N 277 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR N 293 " --> pdb=" O ASN N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 331 Processing helix chain 'N' and resid 341 through 344 No H-bonds generated for 'chain 'N' and resid 341 through 344' Processing helix chain 'O' and resid 36 through 42 removed outlier: 3.757A pdb=" N UNK O 41 " --> pdb=" O UNK O 37 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N UNK O 42 " --> pdb=" O UNK O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 84 removed outlier: 3.778A pdb=" N UNK O 84 " --> pdb=" O UNK O 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 80 through 84' Processing helix chain 'O' and resid 95 through 116 Processing helix chain 'O' and resid 128 through 139 removed outlier: 3.815A pdb=" N ASP O 131 " --> pdb=" O ILE O 128 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE O 132 " --> pdb=" O TYR O 129 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU O 135 " --> pdb=" O PHE O 132 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU O 136 " --> pdb=" O VAL O 133 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA O 137 " --> pdb=" O PHE O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 162 removed outlier: 3.569A pdb=" N ASP O 150 " --> pdb=" O LYS O 146 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL O 155 " --> pdb=" O HIS O 151 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL O 158 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE O 160 " --> pdb=" O LYS O 156 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N CYS O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU O 162 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 184 Processing helix chain 'O' and resid 196 through 215 removed outlier: 3.652A pdb=" N GLY O 208 " --> pdb=" O ASN O 204 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU O 211 " --> pdb=" O LYS O 207 " (cutoff:3.500A) Proline residue: O 212 - end of helix Processing helix chain 'O' and resid 232 through 240 Processing helix chain 'O' and resid 255 through 264 removed outlier: 3.529A pdb=" N MET O 261 " --> pdb=" O HIS O 257 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU O 262 " --> pdb=" O LYS O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 269 No H-bonds generated for 'chain 'O' and resid 266 through 269' Processing helix chain 'O' and resid 280 through 282 No H-bonds generated for 'chain 'O' and resid 280 through 282' Processing helix chain 'O' and resid 286 through 298 removed outlier: 3.737A pdb=" N GLN O 291 " --> pdb=" O HIS O 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 37 Processing helix chain 'P' and resid 53 through 59 removed outlier: 4.809A pdb=" N UNK P 58 " --> pdb=" O UNK P 54 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N UNK P 59 " --> pdb=" O UNK P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 84 Processing helix chain 'P' and resid 112 through 123 removed outlier: 3.672A pdb=" N UNK P 123 " --> pdb=" O UNK P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 157 Processing helix chain 'P' and resid 177 through 184 removed outlier: 3.555A pdb=" N UNK P 181 " --> pdb=" O UNK P 177 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N UNK P 182 " --> pdb=" O UNK P 178 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N UNK P 183 " --> pdb=" O UNK P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 219 removed outlier: 4.232A pdb=" N UNK P 212 " --> pdb=" O UNK P 208 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N UNK P 215 " --> pdb=" O UNK P 211 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 249 removed outlier: 3.528A pdb=" N UNK P 243 " --> pdb=" O UNK P 239 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N UNK P 248 " --> pdb=" O UNK P 244 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N UNK P 249 " --> pdb=" O UNK P 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 289 removed outlier: 3.514A pdb=" N UNK P 286 " --> pdb=" O UNK P 282 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N UNK P 287 " --> pdb=" O UNK P 283 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 98 removed outlier: 3.756A pdb=" N UNK Q 93 " --> pdb=" O UNK Q 89 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N UNK Q 94 " --> pdb=" O UNK Q 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 46 Processing helix chain 'S' and resid 30 through 37 removed outlier: 3.569A pdb=" N ASP S 34 " --> pdb=" O GLN S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 46 removed outlier: 3.582A pdb=" N LYS S 45 " --> pdb=" O VAL S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 94 removed outlier: 3.625A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 21 removed outlier: 3.532A pdb=" N TYR T 17 " --> pdb=" O ASP T 13 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL T 18 " --> pdb=" O ARG T 14 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU T 21 " --> pdb=" O TYR T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 58 removed outlier: 3.705A pdb=" N ILE T 50 " --> pdb=" O ASP T 46 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE T 51 " --> pdb=" O GLN T 47 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA T 53 " --> pdb=" O GLU T 49 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET T 54 " --> pdb=" O ILE T 50 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP T 56 " --> pdb=" O MET T 52 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU T 57 " --> pdb=" O ALA T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 69 removed outlier: 3.893A pdb=" N GLU T 68 " --> pdb=" O ASP T 64 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 64 through 69' Processing helix chain 'T' and resid 73 through 80 removed outlier: 3.967A pdb=" N ASP T 78 " --> pdb=" O GLN T 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 20 removed outlier: 3.668A pdb=" N LYS U 12 " --> pdb=" O LEU U 8 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP U 13 " --> pdb=" O GLU U 9 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL U 18 " --> pdb=" O ARG U 14 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 57 removed outlier: 3.652A pdb=" N GLU U 57 " --> pdb=" O ALA U 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 83 removed outlier: 3.587A pdb=" N ASP U 78 " --> pdb=" O GLN U 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 22 through 34 removed outlier: 3.618A pdb=" N LEU V 26 " --> pdb=" O ARG V 22 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU V 31 " --> pdb=" O TYR V 27 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP V 32 " --> pdb=" O THR V 28 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL V 33 " --> pdb=" O LYS V 29 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 removed outlier: 4.727A pdb=" N GLN V 49 " --> pdb=" O LYS V 45 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE V 50 " --> pdb=" O TYR V 46 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET V 57 " --> pdb=" O GLU V 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL V 58 " --> pdb=" O LYS V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 65 through 69 Processing helix chain 'V' and resid 75 through 84 removed outlier: 3.760A pdb=" N VAL V 79 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU V 81 " --> pdb=" O GLU V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 95 Processing helix chain 'W' and resid 25 through 39 removed outlier: 3.895A pdb=" N ARG W 29 " --> pdb=" O ASN W 25 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL W 31 " --> pdb=" O ALA W 27 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA W 37 " --> pdb=" O GLU W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 47 removed outlier: 4.435A pdb=" N VAL W 46 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS W 47 " --> pdb=" O PRO W 43 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 69 removed outlier: 3.663A pdb=" N VAL W 62 " --> pdb=" O GLY W 58 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG W 63 " --> pdb=" O ARG W 59 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET W 65 " --> pdb=" O LYS W 61 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN W 69 " --> pdb=" O MET W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 85 removed outlier: 3.698A pdb=" N LEU W 80 " --> pdb=" O ARG W 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 123 No H-bonds generated for 'chain 'W' and resid 120 through 123' 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: 3.661A pdb=" N GLU X 48 " --> pdb=" O LEU X 44 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 75 removed outlier: 3.875A pdb=" N LEU X 61 " --> pdb=" O GLU X 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU X 68 " --> pdb=" O GLN X 64 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE X 70 " --> pdb=" O ALA X 66 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN X 72 " --> pdb=" O GLU X 68 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE X 73 " --> pdb=" O PHE X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 90 removed outlier: 3.572A 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: 3.716A pdb=" N TYR Y 8 " --> pdb=" O VAL Y 4 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP Y 9 " --> pdb=" O LEU Y 5 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP Y 10 " --> pdb=" O ARG Y 6 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE Y 11 " --> pdb=" O GLN Y 7 " (cutoff:3.500A) Proline residue: Y 12 - end of helix Processing helix chain 'Y' and resid 20 through 42 removed outlier: 3.894A pdb=" N THR Y 25 " --> pdb=" O THR Y 21 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER Y 26 " --> pdb=" O TYR Y 22 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE Y 27 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL Y 34 " --> pdb=" O ALA Y 30 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL Y 35 " --> pdb=" O ALA Y 31 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL Y 40 " --> pdb=" O SER Y 36 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA Y 41 " --> pdb=" O ALA Y 37 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU Y 42 " --> pdb=" O TYR Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 78 removed outlier: 3.635A pdb=" N THR Y 55 " --> pdb=" O GLY Y 51 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG Y 57 " --> pdb=" O ALA Y 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR Y 58 " --> pdb=" O ARG Y 54 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE Y 60 " --> pdb=" O GLY Y 56 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR Y 61 " --> pdb=" O ARG Y 57 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY Y 66 " --> pdb=" O ALA Y 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS Y 74 " --> pdb=" O GLY Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 101 removed outlier: 3.726A pdb=" N ILE Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY Y 92 " --> pdb=" O ASN Y 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA Y 95 " --> pdb=" O ILE Y 91 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE Y 99 " --> pdb=" O ALA Y 95 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU Y 100 " --> pdb=" O GLY Y 96 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLY Y 101 " --> pdb=" O GLY Y 97 " (cutoff:3.500A) Processing helix chain 'Y' and resid 114 through 124 removed outlier: 3.654A pdb=" N VAL Y 124 " --> pdb=" O THR Y 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 32 through 69 removed outlier: 3.513A pdb=" N ALA Z 36 " --> pdb=" O TYR Z 32 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL Z 37 " --> pdb=" O SER Z 33 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU Z 42 " --> pdb=" O GLY Z 38 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP Z 47 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS Z 51 " --> pdb=" O TRP Z 47 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP Z 52 " --> pdb=" O SER Z 48 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG Z 58 " --> pdb=" O ARG Z 54 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU Z 59 " --> pdb=" O GLU Z 55 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU Z 62 " --> pdb=" O ARG Z 58 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA Z 66 " --> pdb=" O GLU Z 62 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG Z 67 " --> pdb=" O ASP Z 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE Z 68 " --> pdb=" O PHE Z 64 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 95 removed outlier: 3.684A pdb=" N GLU Z 77 " --> pdb=" O LEU Z 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS Z 78 " --> pdb=" O LEU Z 74 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG Z 80 " --> pdb=" O ALA Z 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 128 through 135 removed outlier: 4.039A pdb=" N UNK Z 133 " --> pdb=" O UNK Z 129 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 10 Proline residue: a 7 - end of helix Processing helix chain 'a' and resid 12 through 30 removed outlier: 4.774A pdb=" N PHE a 17 " --> pdb=" O GLY a 13 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.643A pdb=" N THR a 23 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA a 24 " --> pdb=" O GLY a 20 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE a 26 " --> pdb=" O ALA a 22 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N HIS a 27 " --> pdb=" O THR a 23 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE a 29 " --> pdb=" O ARG a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 53 removed outlier: 3.662A pdb=" N LEU a 47 " --> pdb=" O TYR a 43 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG a 52 " --> pdb=" O MET a 48 " (cutoff:3.500A) Processing helix chain 'b' and resid 6 through 13 removed outlier: 4.175A pdb=" N ASN b 10 " --> pdb=" O ALA b 6 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL b 11 " --> pdb=" O PHE b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 34 removed outlier: 3.652A pdb=" N PHE b 22 " --> pdb=" O LEU b 18 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL b 29 " --> pdb=" O ALA b 25 " (cutoff:3.500A) Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 3.621A pdb=" N LEU b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET b 43 " --> pdb=" O LYS b 39 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE b 44 " --> pdb=" O TYR b 40 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN b 45 " --> pdb=" O SER b 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 17 through 45 removed outlier: 3.837A pdb=" N SER c 24 " --> pdb=" O THR c 20 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL c 25 " --> pdb=" O LEU c 21 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR c 30 " --> pdb=" O PHE c 26 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN c 34 " --> pdb=" O TYR c 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 48 removed outlier: 3.514A pdb=" N PHE d 33 " --> pdb=" O PRO d 29 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL d 34 " --> pdb=" O ARG d 30 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY d 42 " --> pdb=" O GLY d 38 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP d 45 " --> pdb=" O SER d 41 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASN d 46 " --> pdb=" O GLY d 42 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA d 47 " --> pdb=" O LEU d 43 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE d 48 " --> pdb=" O ILE d 44 " (cutoff:3.500A) Processing helix chain 'd' and resid 61 through 97 removed outlier: 3.557A pdb=" N PHE d 68 " --> pdb=" O TYR d 64 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET d 90 " --> pdb=" O ARG d 86 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE d 94 " --> pdb=" O MET d 90 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 42 removed outlier: 4.283A pdb=" N GLU e 38 " --> pdb=" O ALA e 34 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP e 39 " --> pdb=" O PHE e 35 " (cutoff:3.500A) Processing helix chain 'e' and resid 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: 3.776A pdb=" N LEU e 66 " --> pdb=" O PHE e 62 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 84 removed outlier: 3.558A pdb=" N ARG e 74 " --> pdb=" O LYS e 70 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE e 78 " --> pdb=" O ARG e 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 4 through 9 removed outlier: 3.512A pdb=" N ARG f 8 " --> pdb=" O LEU f 4 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP f 9 " --> pdb=" O GLN f 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 4 through 9' Processing helix chain 'f' and resid 13 through 32 Proline residue: f 17 - end of helix removed outlier: 3.504A pdb=" N ARG f 28 " --> pdb=" O TYR f 24 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN f 30 " --> pdb=" O LEU f 26 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASP f 31 " --> pdb=" O ASP f 27 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU f 32 " --> pdb=" O ARG f 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 51 through 58 removed outlier: 3.798A pdb=" N TRP g 56 " --> pdb=" O ALA g 52 " (cutoff:3.500A) Processing helix chain 'g' and resid 61 through 68 removed outlier: 3.647A pdb=" N GLY g 65 " --> pdb=" O VAL g 61 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE g 66 " --> pdb=" O PHE g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 88 through 103 removed outlier: 3.766A pdb=" N ARG g 95 " --> pdb=" O ARG g 91 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU g 96 " --> pdb=" O GLU g 92 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA g 102 " --> pdb=" O LYS g 98 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS g 103 " --> pdb=" O TYR g 99 " (cutoff:3.500A) Processing helix chain 'h' and resid 16 through 31 removed outlier: 3.593A pdb=" N ARG h 20 " --> pdb=" O PHE h 16 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE h 21 " --> pdb=" O TYR h 17 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU h 22 " --> pdb=" O ASP h 18 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR h 28 " --> pdb=" O LEU h 24 " (cutoff:3.500A) Processing helix chain 'h' and resid 34 through 44 removed outlier: 3.629A pdb=" N THR h 41 " --> pdb=" O ALA h 37 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE h 43 " --> pdb=" O GLY h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 70 through 78 removed outlier: 3.936A pdb=" N UNK h 78 " --> pdb=" O UNK h 74 " (cutoff:3.500A) Processing helix chain 'h' and resid 82 through 116 removed outlier: 3.979A pdb=" N UNK h 88 " --> pdb=" O UNK h 84 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N UNK h 100 " --> pdb=" O UNK h 96 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N UNK h 116 " --> pdb=" O UNK h 112 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 22 removed outlier: 3.603A pdb=" N ARG i 10 " --> pdb=" O GLU i 7 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN i 12 " --> pdb=" O LEU i 9 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU i 14 " --> pdb=" O LEU i 11 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG i 15 " --> pdb=" O GLN i 12 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU i 16 " --> pdb=" O GLN i 13 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG i 18 " --> pdb=" O ARG i 15 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG i 19 " --> pdb=" O GLU i 16 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG i 20 " --> pdb=" O LEU i 17 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU i 22 " --> pdb=" O ARG i 19 " (cutoff:3.500A) Processing helix chain 'i' and resid 43 through 51 removed outlier: 3.606A pdb=" N UNK i 49 " --> pdb=" O UNK i 45 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N UNK i 50 " --> pdb=" O UNK i 46 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N UNK i 51 " --> pdb=" O UNK i 47 " (cutoff:3.500A) Processing helix chain 'i' and resid 60 through 73 removed outlier: 3.866A pdb=" N UNK i 64 " --> pdb=" O UNK i 60 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N UNK i 65 " --> pdb=" O UNK i 61 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N UNK i 68 " --> pdb=" O UNK i 64 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N UNK i 72 " --> pdb=" O UNK i 68 " (cutoff:3.500A) Processing helix chain 'i' and resid 76 through 86 removed outlier: 3.545A pdb=" N UNK i 80 " --> pdb=" O UNK i 76 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N UNK i 85 " --> pdb=" O UNK i 81 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N UNK i 86 " --> pdb=" O UNK i 82 " (cutoff:3.500A) Processing helix chain 'j' and resid 21 through 38 removed outlier: 3.507A pdb=" N UNK j 26 " --> pdb=" O UNK j 22 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N UNK j 27 " --> pdb=" O UNK j 23 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N UNK j 31 " --> pdb=" O UNK j 27 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N UNK j 32 " --> pdb=" O UNK j 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N UNK j 33 " --> pdb=" O UNK j 29 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N UNK j 36 " --> pdb=" O UNK j 32 " (cutoff:3.500A) Processing helix chain 'k' and resid 17 through 22 Processing helix chain 'k' and resid 41 through 43 No H-bonds generated for 'chain 'k' and resid 41 through 43' Processing helix chain 'k' and resid 45 through 51 removed outlier: 4.041A pdb=" N UNK k 49 " --> pdb=" O UNK k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 69 removed outlier: 3.543A pdb=" N UNK k 65 " --> pdb=" O UNK k 61 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N UNK k 68 " --> pdb=" O UNK k 64 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N UNK k 69 " --> pdb=" O UNK k 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 27 Processing helix chain 'l' and resid 99 through 118 removed outlier: 3.974A pdb=" N UNK l 103 " --> pdb=" O UNK l 99 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N UNK l 107 " --> pdb=" O UNK l 103 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N UNK l 109 " --> pdb=" O UNK l 105 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N UNK l 112 " --> pdb=" O UNK l 108 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N UNK l 115 " --> pdb=" O UNK l 111 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N UNK l 116 " --> pdb=" O UNK l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 27 through 50 removed outlier: 3.749A pdb=" N ALA m 33 " --> pdb=" O UNK m 29 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE m 38 " --> pdb=" O GLU m 34 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG m 41 " --> pdb=" O ALA m 37 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU m 45 " --> pdb=" O ARG m 41 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR m 46 " --> pdb=" O LEU m 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 72 removed outlier: 4.120A pdb=" N ARG m 71 " --> pdb=" O TRP m 67 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 91 Processing helix chain 'm' and resid 95 through 102 removed outlier: 3.621A pdb=" N TRP m 100 " --> pdb=" O PRO m 96 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR m 101 " --> pdb=" O LEU m 97 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR m 102 " --> pdb=" O VAL m 98 " (cutoff:3.500A) Processing helix chain 'm' and resid 104 through 116 removed outlier: 3.561A pdb=" N LYS m 113 " --> pdb=" O ASP m 109 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU m 114 " --> pdb=" O ARG m 110 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN m 116 " --> pdb=" O GLU m 112 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 29 removed outlier: 3.573A pdb=" N VAL n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU n 18 " --> pdb=" O LYS n 14 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG n 24 " --> pdb=" O LYS n 20 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU n 27 " --> pdb=" O LEU n 23 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER n 28 " --> pdb=" O ARG n 24 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP n 29 " --> pdb=" O HIS n 25 " (cutoff:3.500A) Processing helix chain 'n' and resid 33 through 51 removed outlier: 3.585A pdb=" N TYR n 38 " --> pdb=" O ASP n 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS n 41 " --> pdb=" O ARG n 37 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU n 42 " --> pdb=" O TYR n 38 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG n 46 " --> pdb=" O LEU n 42 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE n 47 " --> pdb=" O LEU n 43 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU n 49 " --> pdb=" O ALA n 45 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 58 through 65 removed outlier: 3.503A pdb=" N ARG n 64 " --> pdb=" O THR n 60 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 104 No H-bonds generated for 'chain 'n' and resid 101 through 104' Processing helix chain 'n' and resid 115 through 139 removed outlier: 3.504A pdb=" N LYS n 120 " --> pdb=" O ASP n 116 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N UNK n 137 " --> pdb=" O GLU n 133 " (cutoff:3.500A) Processing helix chain 'o' and resid 60 through 70 removed outlier: 3.799A pdb=" N ARG o 64 " --> pdb=" O HIS o 60 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE o 65 " --> pdb=" O TYR o 61 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU o 66 " --> pdb=" O LEU o 62 " (cutoff:3.500A) Processing helix chain 'o' and resid 81 through 113 removed outlier: 3.827A pdb=" N ASP o 85 " --> pdb=" O HIS o 81 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP o 86 " --> pdb=" O GLU o 82 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP o 87 " --> pdb=" O ARG o 83 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU o 90 " --> pdb=" O TRP o 86 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS o 91 " --> pdb=" O ASP o 87 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN o 109 " --> pdb=" O ARG o 105 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG o 110 " --> pdb=" O ARG o 106 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG o 113 " --> pdb=" O GLN o 109 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 39 removed outlier: 4.115A pdb=" N UNK p 38 " --> pdb=" O UNK p 34 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 52 Processing helix chain 'p' and resid 81 through 116 removed outlier: 3.546A pdb=" N PHE p 85 " --> pdb=" O VAL p 81 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA p 87 " --> pdb=" O CYS p 83 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU p 100 " --> pdb=" O LYS p 96 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL p 102 " --> pdb=" O ASP p 98 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN p 103 " --> pdb=" O GLN p 99 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE p 104 " --> pdb=" O GLU p 100 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN p 114 " --> pdb=" O LYS p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 126 through 141 removed outlier: 3.574A pdb=" N LYS p 136 " --> pdb=" O THR p 132 " (cutoff:3.500A) Processing helix chain 'p' and resid 151 through 171 removed outlier: 3.913A pdb=" N UNK p 155 " --> pdb=" O UNK p 151 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N UNK p 156 " --> pdb=" O UNK p 152 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N UNK p 161 " --> pdb=" O UNK p 157 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N UNK p 164 " --> pdb=" O UNK p 160 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N UNK p 169 " --> pdb=" O UNK p 165 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N UNK p 170 " --> pdb=" O UNK p 166 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N UNK p 171 " --> pdb=" O UNK p 167 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 16 removed outlier: 3.741A pdb=" N LEU q 7 " --> pdb=" O LEU q 3 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY q 10 " --> pdb=" O VAL q 6 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU q 11 " --> pdb=" O LEU q 7 " (cutoff:3.500A) Processing helix chain 'q' and resid 22 through 25 No H-bonds generated for 'chain 'q' and resid 22 through 25' Processing helix chain 'r' and resid 7 through 13 removed outlier: 3.538A pdb=" N UNK r 13 " --> pdb=" O UNK r 9 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 19 removed outlier: 4.298A pdb=" N UNK s 17 " --> pdb=" O UNK s 13 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N UNK s 18 " --> pdb=" O UNK s 14 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 85 through 87 removed outlier: 6.466A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.413A 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: 4.226A pdb=" N VAL C 40 " --> pdb=" O CYS C 51 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 92 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 47 through 49 removed outlier: 3.544A pdb=" N LEU D 49 " --> pdb=" O MET D 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS D 75 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 361 through 365 Processing sheet with id= E, first strand: chain 'E' and resid 137 through 142 removed outlier: 7.552A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N MET E 153 " --> pdb=" O CYS E 103 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 220 through 224 removed outlier: 8.033A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'F' and resid 267 through 270 removed outlier: 3.563A pdb=" N PHE F 256 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU F 270 " --> pdb=" O LYS F 254 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL F 336 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.510A pdb=" N VAL G 20 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL G 11 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL G 18 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 3.554A 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 removed outlier: 4.357A pdb=" N UNK G 249 " --> pdb=" O UNK G 241 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 544 through 546 removed outlier: 6.940A pdb=" N UNK G 559 " --> pdb=" O UNK G 545 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= L, first strand: chain 'I' and resid 92 through 95 Processing sheet with id= M, first strand: chain 'L' and resid 60 through 63 removed outlier: 4.372A pdb=" N GLU L 60 " --> pdb=" O MET L 82 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET L 82 " --> pdb=" O GLU L 60 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'O' and resid 123 through 125 removed outlier: 6.513A pdb=" N UNK O 25 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL O 169 " --> pdb=" O UNK O 26 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU O 219 " --> pdb=" O VAL O 170 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL O 172 " --> pdb=" O GLU O 219 " (cutoff:3.500A) removed outlier: 6.252A 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: 6.789A pdb=" N UNK P 69 " --> pdb=" O UNK P 47 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N UNK P 49 " --> pdb=" O UNK P 69 " (cutoff:3.500A) removed outlier: 6.545A 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 130 through 134 removed outlier: 7.675A pdb=" N UNK P 164 " --> pdb=" O UNK P 131 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N UNK P 133 " --> pdb=" O UNK P 164 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N UNK P 166 " --> pdb=" O UNK P 133 " (cutoff:3.500A) removed outlier: 6.850A 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 34 through 36 removed outlier: 5.843A pdb=" N UNK Q 102 " --> pdb=" O UNK Q 35 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'Q' and resid 55 through 57 removed outlier: 3.573A pdb=" N UNK Q 57 " --> pdb=" O UNK Q 84 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N UNK Q 84 " --> pdb=" O UNK Q 57 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'R' and resid 56 through 59 removed outlier: 4.215A pdb=" N VAL R 71 " --> pdb=" O CYS R 59 " (cutoff:3.500A) 1562 hydrogen bonds defined for protein. 4488 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: 17.29 Time building geometry restraints manager: 22.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 21440 1.43 - 1.65: 30058 1.65 - 1.87: 510 1.87 - 2.09: 0 2.09 - 2.30: 80 Bond restraints: 52088 Sorted by residual: bond pdb=" O2B NAP P 501 " pdb=" P2B NAP P 501 " ideal model delta sigma weight residual 1.736 1.615 0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" C5A FMN F 501 " pdb=" C9A FMN F 501 " ideal model delta sigma weight residual 1.390 1.505 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C7 FMN F 501 " pdb=" C8 FMN F 501 " ideal model delta sigma weight residual 1.390 1.504 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C10 FMN F 501 " pdb=" C4A FMN F 501 " ideal model delta sigma weight residual 1.390 1.490 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C4 FMN F 501 " pdb=" C4A FMN F 501 " ideal model delta sigma weight residual 1.390 1.488 -0.098 2.00e-02 2.50e+03 2.41e+01 ... (remaining 52083 not shown) Histogram of bond angle deviations from ideal: 73.08 - 86.61: 76 86.61 - 100.14: 48 100.14 - 113.66: 29151 113.66 - 127.19: 41802 127.19 - 140.72: 430 Bond angle restraints: 71507 Sorted by residual: angle pdb=" N ILE W 19 " pdb=" CA ILE W 19 " pdb=" C ILE W 19 " ideal model delta sigma weight residual 110.42 121.67 -11.25 9.60e-01 1.09e+00 1.37e+02 angle pdb=" CA PRO G 22 " pdb=" N PRO G 22 " pdb=" CD PRO G 22 " ideal model delta sigma weight residual 112.00 98.56 13.44 1.40e+00 5.10e-01 9.21e+01 angle pdb=" CA PRO F 53 " pdb=" N PRO F 53 " pdb=" CD PRO F 53 " ideal model delta sigma weight residual 112.00 98.71 13.29 1.40e+00 5.10e-01 9.01e+01 angle pdb=" CA PRO E 77 " pdb=" N PRO E 77 " pdb=" CD PRO E 77 " ideal model delta sigma weight residual 112.00 98.74 13.26 1.40e+00 5.10e-01 8.98e+01 angle pdb=" CA PRO E 166 " pdb=" N PRO E 166 " pdb=" CD PRO E 166 " ideal model delta sigma weight residual 112.00 98.83 13.17 1.40e+00 5.10e-01 8.85e+01 ... (remaining 71502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.87: 30389 33.87 - 67.74: 659 67.74 - 101.61: 32 101.61 - 135.48: 0 135.48 - 169.35: 1 Dihedral angle restraints: 31081 sinusoidal: 8273 harmonic: 22808 Sorted by residual: dihedral pdb=" CA CYS B 149 " pdb=" C CYS B 149 " pdb=" N PRO B 150 " pdb=" CA PRO B 150 " ideal model delta harmonic sigma weight residual -180.00 -133.61 -46.39 0 5.00e+00 4.00e-02 8.61e+01 dihedral pdb=" CB CYS X 87 " pdb=" SG CYS X 87 " pdb=" SG CYS X 99 " pdb=" CB CYS X 99 " ideal model delta sinusoidal sigma weight residual 93.00 171.15 -78.15 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 88.25 169.35 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 31078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.260: 8742 4.260 - 8.519: 0 8.519 - 12.779: 0 12.779 - 17.038: 0 17.038 - 21.298: 24 Chirality restraints: 8766 Sorted by residual: chirality pdb="FE4 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S2 SF4 G 801 " pdb=" S3 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.74 21.30 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 G 801 " pdb=" S2 SF4 G 801 " pdb=" S3 SF4 G 801 " pdb=" S4 SF4 G 801 " both_signs ideal model delta sigma weight residual False -10.55 10.74 -21.29 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE3 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S2 SF4 G 801 " pdb=" S4 SF4 G 801 " both_signs ideal model delta sigma weight residual False -10.55 10.72 -21.28 2.00e-01 2.50e+01 1.13e+04 ... (remaining 8763 not shown) Planarity restraints: 9352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 16 " -0.117 5.00e-02 4.00e+02 1.65e-01 4.35e+01 pdb=" N PRO E 17 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO E 17 " -0.091 5.00e-02 4.00e+02 pdb=" CD PRO E 17 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN g 41 " 0.113 5.00e-02 4.00e+02 1.58e-01 3.97e+01 pdb=" N PRO g 42 " -0.272 5.00e-02 4.00e+02 pdb=" CA PRO g 42 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO g 42 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN e 24 " -0.112 5.00e-02 4.00e+02 1.56e-01 3.92e+01 pdb=" N PRO e 25 " 0.270 5.00e-02 4.00e+02 pdb=" CA PRO e 25 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO e 25 " -0.073 5.00e-02 4.00e+02 ... (remaining 9349 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 15 2.27 - 2.92: 18824 2.92 - 3.58: 69657 3.58 - 4.24: 104670 4.24 - 4.90: 177473 Nonbonded interactions: 370639 Sorted by model distance: nonbonded pdb=" CD PRO D 6 " pdb=" OG1 THR N 303 " model vdw 1.608 3.440 nonbonded pdb=" O ALA E 46 " pdb=" CD PRO E 49 " model vdw 1.765 3.440 nonbonded pdb=" CG PRO D 38 " pdb=" CB PRO N 50 " model vdw 1.779 3.840 nonbonded pdb=" CB TYR D 20 " pdb=" OD1 ASN N 171 " model vdw 1.791 3.440 nonbonded pdb=" CG PRO D 38 " pdb=" CG PRO N 50 " model vdw 1.835 3.840 ... (remaining 370634 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: 5.100 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: 0.100 Extract box with map and model: 13.370 Check model and map are aligned: 0.710 Set scattering table: 0.440 Process input model: 144.900 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.530 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.121 52088 Z= 0.556 Angle : 1.418 16.420 71507 Z= 0.894 Chirality : 1.114 21.298 8766 Planarity : 0.009 0.165 9352 Dihedral : 14.777 169.346 16152 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 3.25 % Allowed : 8.51 % Favored : 88.24 % Rotamer: Outliers : 3.32 % Allowed : 9.72 % Favored : 86.96 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (0.08), residues: 5784 helix: -3.34 (0.06), residues: 2920 sheet: -0.57 (0.42), residues: 149 loop : -3.22 (0.10), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 84 HIS 0.005 0.001 HIS R 68 PHE 0.014 0.001 PHE L 124 TYR 0.017 0.001 TYR M 406 ARG 0.005 0.000 ARG D 430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1756 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1637 time to evaluate : 4.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.8197 (p) cc_final: 0.7897 (t) REVERT: A 65 PHE cc_start: 0.8793 (m-10) cc_final: 0.8552 (m-10) REVERT: A 67 LEU cc_start: 0.8828 (mt) cc_final: 0.8542 (mm) REVERT: B 68 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6468 (t70) REVERT: B 83 SER cc_start: 0.9029 (p) cc_final: 0.8157 (t) REVERT: B 107 MET cc_start: 0.8775 (mmm) cc_final: 0.8529 (tpt) REVERT: B 116 MET cc_start: 0.8240 (ttp) cc_final: 0.7886 (ttp) REVERT: B 121 ASN cc_start: 0.7826 (m-40) cc_final: 0.6760 (m110) REVERT: B 131 SER cc_start: 0.8822 (p) cc_final: 0.8591 (m) REVERT: B 156 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8542 (tt) REVERT: C 41 GLN cc_start: 0.8282 (tp-100) cc_final: 0.8082 (tm-30) REVERT: C 58 ILE cc_start: 0.9335 (mt) cc_final: 0.8772 (mp) REVERT: C 90 PHE cc_start: 0.8684 (m-80) cc_final: 0.8465 (m-10) REVERT: C 117 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8490 (mm) REVERT: C 198 ASP cc_start: 0.7052 (t70) cc_final: 0.6714 (t0) REVERT: D 82 LEU cc_start: 0.8844 (mt) cc_final: 0.8554 (mt) REVERT: D 106 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7867 (tp) REVERT: D 111 MET cc_start: 0.8143 (mmt) cc_final: 0.7810 (mmm) REVERT: D 114 ASN cc_start: 0.7278 (m-40) cc_final: 0.7028 (m-40) REVERT: D 135 GLN cc_start: 0.8713 (mt0) cc_final: 0.8482 (mt0) REVERT: D 136 TRP cc_start: 0.8575 (m100) cc_final: 0.8107 (m100) REVERT: D 164 MET cc_start: 0.8079 (mmm) cc_final: 0.7712 (mmt) REVERT: D 167 PHE cc_start: 0.8695 (t80) cc_final: 0.8053 (t80) REVERT: D 169 TRP cc_start: 0.8514 (m-10) cc_final: 0.7716 (m100) REVERT: D 199 VAL cc_start: 0.8149 (t) cc_final: 0.7921 (p) REVERT: D 207 LEU cc_start: 0.8199 (mt) cc_final: 0.7877 (tp) REVERT: D 271 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8392 (pttt) REVERT: D 276 ASP cc_start: 0.7935 (m-30) cc_final: 0.7034 (m-30) REVERT: D 310 ILE cc_start: 0.8990 (mp) cc_final: 0.8496 (mt) REVERT: D 330 VAL cc_start: 0.9212 (t) cc_final: 0.8807 (t) REVERT: F 367 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6587 (mp0) REVERT: F 400 GLU cc_start: 0.7740 (tt0) cc_final: 0.6746 (tp30) REVERT: F 409 ASP cc_start: 0.7408 (m-30) cc_final: 0.5316 (m-30) REVERT: G 45 ARG cc_start: 0.7176 (mtt90) cc_final: 0.6229 (ptm160) REVERT: G 105 CYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8601 (m) REVERT: G 118 ASP cc_start: 0.8549 (m-30) cc_final: 0.8082 (t0) REVERT: G 122 MET cc_start: 0.8749 (mmt) cc_final: 0.8313 (mmt) REVERT: G 160 ILE cc_start: 0.9323 (mm) cc_final: 0.8959 (mm) REVERT: H 31 MET cc_start: 0.9185 (mmm) cc_final: 0.8983 (mmt) REVERT: H 32 GLN cc_start: 0.9299 (mt0) cc_final: 0.8939 (mt0) REVERT: H 51 ASP cc_start: 0.8299 (m-30) cc_final: 0.7632 (t70) REVERT: H 86 TRP cc_start: 0.8843 (m100) cc_final: 0.8616 (m100) REVERT: H 138 GLN cc_start: 0.6971 (mt0) cc_final: 0.6717 (mt0) REVERT: H 142 TYR cc_start: 0.8499 (m-80) cc_final: 0.8291 (m-80) REVERT: H 155 LEU cc_start: 0.9103 (tp) cc_final: 0.8854 (tp) REVERT: H 166 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9081 (mm) REVERT: H 176 LEU cc_start: 0.8592 (mt) cc_final: 0.8309 (tp) REVERT: H 257 ILE cc_start: 0.8425 (mt) cc_final: 0.8170 (tp) REVERT: H 280 PHE cc_start: 0.7085 (m-80) cc_final: 0.6676 (m-80) REVERT: H 282 TYR cc_start: 0.8213 (t80) cc_final: 0.7894 (t80) REVERT: H 290 TRP cc_start: 0.8149 (OUTLIER) cc_final: 0.7778 (m-90) REVERT: H 302 MET cc_start: 0.9009 (mmm) cc_final: 0.8557 (mmp) REVERT: I 15 LYS cc_start: 0.7698 (mtmm) cc_final: 0.7302 (tptp) REVERT: I 34 LEU cc_start: 0.8353 (tt) cc_final: 0.7561 (mt) REVERT: I 40 TYR cc_start: 0.8175 (t80) cc_final: 0.7117 (t80) REVERT: I 54 LYS cc_start: 0.8318 (mmtp) cc_final: 0.7426 (tttt) REVERT: I 90 GLN cc_start: 0.8277 (mt0) cc_final: 0.7663 (mm-40) REVERT: I 110 ASP cc_start: 0.7166 (m-30) cc_final: 0.6063 (m-30) REVERT: J 7 PHE cc_start: 0.7961 (t80) cc_final: 0.7477 (t80) REVERT: J 51 PHE cc_start: 0.7999 (t80) cc_final: 0.7404 (t80) REVERT: J 52 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8647 (mp) REVERT: J 76 THR cc_start: 0.7206 (p) cc_final: 0.6717 (p) REVERT: J 100 GLU cc_start: 0.8704 (tm-30) cc_final: 0.7811 (tp30) REVERT: J 101 PHE cc_start: 0.7671 (m-80) cc_final: 0.7345 (t80) REVERT: J 102 PHE cc_start: 0.7969 (t80) cc_final: 0.6327 (t80) REVERT: J 105 TYR cc_start: 0.6730 (t80) cc_final: 0.6528 (t80) REVERT: K 34 GLU cc_start: 0.8144 (mt-10) cc_final: 0.4725 (mt-10) REVERT: K 55 LEU cc_start: 0.8068 (mt) cc_final: 0.7692 (tp) REVERT: K 59 MET cc_start: 0.8023 (mmp) cc_final: 0.7629 (mmt) REVERT: K 70 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7146 (mt-10) REVERT: L 14 LEU cc_start: 0.9053 (mt) cc_final: 0.8584 (tp) REVERT: L 20 MET cc_start: 0.8581 (mmp) cc_final: 0.7019 (tmm) REVERT: L 48 MET cc_start: 0.8285 (mmm) cc_final: 0.7997 (tpp) REVERT: L 125 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9054 (tt) REVERT: L 138 PHE cc_start: 0.8065 (t80) cc_final: 0.7863 (t80) REVERT: L 179 ASP cc_start: 0.8192 (m-30) cc_final: 0.7766 (m-30) REVERT: L 186 MET cc_start: 0.8277 (mmm) cc_final: 0.7350 (mmt) REVERT: L 223 LYS cc_start: 0.9134 (mmtp) cc_final: 0.8712 (tptt) REVERT: L 252 MET cc_start: 0.8055 (tpt) cc_final: 0.7657 (tpp) REVERT: L 291 CYS cc_start: 0.7713 (m) cc_final: 0.7392 (m) REVERT: L 389 PHE cc_start: 0.6425 (t80) cc_final: 0.5984 (t80) REVERT: L 393 ASP cc_start: 0.7754 (m-30) cc_final: 0.7350 (t0) REVERT: L 454 ILE cc_start: 0.8668 (mt) cc_final: 0.8391 (mm) REVERT: L 459 ILE cc_start: 0.8002 (mt) cc_final: 0.7724 (tt) REVERT: L 532 ILE cc_start: 0.8168 (pt) cc_final: 0.7702 (tt) REVERT: L 535 ARG cc_start: 0.5497 (tpt170) cc_final: 0.3483 (ttt-90) REVERT: L 544 MET cc_start: 0.8594 (mtp) cc_final: 0.8374 (mtt) REVERT: L 571 MET cc_start: 0.7590 (tpt) cc_final: 0.6447 (ttm) REVERT: L 576 LEU cc_start: 0.8314 (mt) cc_final: 0.8011 (mm) REVERT: L 599 MET cc_start: 0.8478 (mmm) cc_final: 0.7157 (tpt) REVERT: M 61 LEU cc_start: 0.8393 (mp) cc_final: 0.8170 (mm) REVERT: M 72 LEU cc_start: 0.9249 (mt) cc_final: 0.9033 (mt) REVERT: M 73 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7952 (tp) REVERT: M 76 MET cc_start: 0.7735 (mtm) cc_final: 0.7346 (mtm) REVERT: M 144 ASN cc_start: 0.7299 (m-40) cc_final: 0.6898 (t0) REVERT: M 200 MET cc_start: 0.8942 (mmp) cc_final: 0.8196 (mmp) REVERT: M 205 VAL cc_start: 0.9073 (t) cc_final: 0.8423 (m) REVERT: M 206 LYS cc_start: 0.7909 (mttm) cc_final: 0.7594 (mmtt) REVERT: M 269 MET cc_start: 0.8431 (mmm) cc_final: 0.7831 (mmm) REVERT: M 276 CYS cc_start: 0.8498 (t) cc_final: 0.8094 (t) REVERT: M 279 GLN cc_start: 0.6372 (mt0) cc_final: 0.5659 (mt0) REVERT: M 281 ASP cc_start: 0.8159 (m-30) cc_final: 0.7574 (m-30) REVERT: M 285 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8502 (mt) REVERT: M 293 HIS cc_start: 0.8566 (m-70) cc_final: 0.8294 (t70) REVERT: M 317 ILE cc_start: 0.9370 (mt) cc_final: 0.9085 (tt) REVERT: M 319 HIS cc_start: 0.7444 (t70) cc_final: 0.6842 (t70) REVERT: M 329 LEU cc_start: 0.9574 (mt) cc_final: 0.9243 (mp) REVERT: M 338 HIS cc_start: 0.8050 (m-70) cc_final: 0.7737 (m170) REVERT: M 401 VAL cc_start: 0.9234 (t) cc_final: 0.8945 (t) REVERT: M 439 LEU cc_start: 0.9171 (mt) cc_final: 0.8948 (tp) REVERT: M 446 LEU cc_start: 0.8395 (mt) cc_final: 0.7968 (tp) REVERT: N 35 MET cc_start: 0.8404 (mmm) cc_final: 0.8068 (ttp) REVERT: N 98 MET cc_start: 0.9107 (tpt) cc_final: 0.8877 (tpp) REVERT: N 112 HIS cc_start: 0.8582 (p-80) cc_final: 0.7847 (p-80) REVERT: N 117 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7637 (mt-10) REVERT: N 164 ILE cc_start: 0.8729 (pt) cc_final: 0.8402 (mt) REVERT: N 175 LEU cc_start: 0.9189 (tp) cc_final: 0.8571 (mt) REVERT: N 193 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8239 (t) REVERT: N 206 ILE cc_start: 0.8993 (mt) cc_final: 0.8773 (mm) REVERT: N 208 TYR cc_start: 0.8802 (t80) cc_final: 0.8102 (t80) REVERT: N 211 MET cc_start: 0.8692 (ttm) cc_final: 0.8338 (ttp) REVERT: N 294 MET cc_start: 0.8674 (mmp) cc_final: 0.8347 (tpp) REVERT: O 100 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9063 (tp) REVERT: O 110 ASP cc_start: 0.7810 (m-30) cc_final: 0.7457 (t70) REVERT: O 160 ILE cc_start: 0.9137 (mt) cc_final: 0.8851 (tt) REVERT: V 26 LEU cc_start: 0.9173 (mt) cc_final: 0.8739 (mm) REVERT: W 32 ARG cc_start: 0.7564 (tpt170) cc_final: 0.6584 (tpt90) REVERT: W 61 LYS cc_start: 0.7047 (ttmt) cc_final: 0.6436 (tptt) REVERT: W 65 MET cc_start: 0.9020 (tpt) cc_final: 0.8735 (tpt) REVERT: W 91 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6650 (tp30) REVERT: X 31 TYR cc_start: 0.8009 (t80) cc_final: 0.7374 (t80) REVERT: X 41 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7094 (tp30) REVERT: X 50 LYS cc_start: 0.6937 (tttt) cc_final: 0.5909 (tptt) REVERT: X 79 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8346 (tp30) REVERT: X 84 TYR cc_start: 0.8234 (t80) cc_final: 0.7343 (t80) REVERT: X 105 GLN cc_start: 0.8125 (mt0) cc_final: 0.7602 (tp40) REVERT: X 107 ASP cc_start: 0.7308 (t70) cc_final: 0.6889 (t0) REVERT: Y 85 ASP cc_start: 0.9080 (m-30) cc_final: 0.8812 (t0) REVERT: Y 91 ILE cc_start: 0.8326 (mt) cc_final: 0.8103 (tp) REVERT: Z 55 GLU cc_start: 0.8137 (tp30) cc_final: 0.7635 (tp30) REVERT: Z 77 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8239 (tt0) REVERT: a 18 ILE cc_start: 0.8223 (mt) cc_final: 0.8016 (mm) REVERT: a 28 ARG cc_start: 0.7874 (mtt180) cc_final: 0.6954 (ptm160) REVERT: b 42 LEU cc_start: 0.9251 (tt) cc_final: 0.9003 (tp) REVERT: d 49 ARG cc_start: 0.8137 (mtt90) cc_final: 0.7550 (tpt-90) REVERT: d 73 TYR cc_start: 0.8476 (t80) cc_final: 0.7995 (t80) REVERT: d 82 MET cc_start: 0.8305 (tpt) cc_final: 0.7885 (tpp) REVERT: d 87 ASP cc_start: 0.7676 (t70) cc_final: 0.6865 (t0) REVERT: d 94 ILE cc_start: 0.8547 (mt) cc_final: 0.8177 (mm) REVERT: e 41 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7721 (tm-30) REVERT: e 83 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7178 (tp30) REVERT: g 80 LEU cc_start: 0.7473 (mt) cc_final: 0.7199 (mt) REVERT: g 92 GLU cc_start: 0.8488 (tp30) cc_final: 0.8142 (mm-30) REVERT: g 96 LEU cc_start: 0.9262 (mt) cc_final: 0.9004 (tp) REVERT: h 43 ILE cc_start: 0.7350 (mt) cc_final: 0.7033 (pt) REVERT: i 9 LEU cc_start: 0.8736 (pp) cc_final: 0.8425 (tt) REVERT: i 20 ARG cc_start: 0.8404 (mtm110) cc_final: 0.7357 (ppt170) REVERT: m 48 LEU cc_start: 0.9468 (mt) cc_final: 0.8834 (tt) REVERT: m 67 TRP cc_start: 0.8389 (t-100) cc_final: 0.8057 (t-100) REVERT: m 80 ARG cc_start: 0.7316 (ptm160) cc_final: 0.7073 (mmt180) REVERT: n 12 GLN cc_start: 0.8520 (mt0) cc_final: 0.8311 (tp-100) REVERT: n 16 LEU cc_start: 0.9092 (mt) cc_final: 0.8455 (pp) REVERT: n 23 LEU cc_start: 0.8653 (mt) cc_final: 0.8174 (tp) REVERT: n 42 LEU cc_start: 0.8734 (tp) cc_final: 0.8519 (tt) REVERT: n 51 LYS cc_start: 0.7908 (tttm) cc_final: 0.7700 (tptt) REVERT: n 57 VAL cc_start: 0.8829 (t) cc_final: 0.8582 (p) REVERT: n 64 ARG cc_start: 0.8042 (ttt180) cc_final: 0.7518 (mmt180) REVERT: p 86 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7770 (mm-30) outliers start: 119 outliers final: 11 residues processed: 1698 average time/residue: 0.5958 time to fit residues: 1675.4812 Evaluate side-chains 986 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 960 time to evaluate : 5.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 460 optimal weight: 20.0000 chunk 413 optimal weight: 20.0000 chunk 229 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 278 optimal weight: 0.6980 chunk 220 optimal weight: 6.9990 chunk 427 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 259 optimal weight: 0.6980 chunk 317 optimal weight: 5.9990 chunk 494 optimal weight: 10.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS D 84 HIS D 114 ASN D 116 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 HIS D 398 HIS ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 HIS G 100 ASN G 155 GLN H 38 ASN H 235 ASN I 136 ASN ** I 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN L 170 GLN ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN L 295 GLN L 320 ASN ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN M 103 GLN M 192 ASN M 213 HIS M 304 GLN N 63 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN N 171 ASN ** N 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 HIS V 36 HIS X 103 GLN Z 89 ASN ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 34 GLN f 30 ASN m 74 ASN m 78 ASN n 50 HIS p 106 GLN ** p 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.280 52088 Z= 0.616 Angle : 1.838 51.586 71507 Z= 1.177 Chirality : 0.328 6.550 8766 Planarity : 0.007 0.171 9352 Dihedral : 6.063 166.080 8196 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 1.68 % Allowed : 7.28 % Favored : 91.04 % Rotamer: Outliers : 0.28 % Allowed : 4.55 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.09), residues: 5784 helix: -1.57 (0.08), residues: 3013 sheet: -0.06 (0.44), residues: 152 loop : -2.95 (0.11), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 413 HIS 0.017 0.002 HIS I 65 PHE 0.039 0.002 PHE D 283 TYR 0.031 0.002 TYR J 79 ARG 0.008 0.001 ARG n 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1136 time to evaluate : 5.823 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: B 62 MET cc_start: 0.8022 (tpp) cc_final: 0.7648 (tmm) REVERT: B 83 SER cc_start: 0.9114 (p) cc_final: 0.8598 (p) REVERT: B 116 MET cc_start: 0.8539 (ttp) cc_final: 0.7685 (tmm) REVERT: B 131 SER cc_start: 0.8795 (p) cc_final: 0.8576 (t) REVERT: B 143 ASP cc_start: 0.8259 (t0) cc_final: 0.7762 (t0) REVERT: D 115 GLU cc_start: 0.8151 (pm20) cc_final: 0.7595 (pm20) REVERT: D 135 GLN cc_start: 0.8762 (mt0) cc_final: 0.8354 (mt0) REVERT: D 136 TRP cc_start: 0.8584 (m100) cc_final: 0.8255 (m100) REVERT: D 164 MET cc_start: 0.8387 (mmm) cc_final: 0.8061 (mmm) REVERT: D 169 TRP cc_start: 0.8580 (m100) cc_final: 0.8325 (m100) REVERT: D 190 HIS cc_start: 0.6861 (m170) cc_final: 0.6626 (m170) REVERT: D 276 ASP cc_start: 0.8046 (m-30) cc_final: 0.7173 (m-30) REVERT: D 301 VAL cc_start: 0.9126 (t) cc_final: 0.8877 (p) REVERT: D 310 ILE cc_start: 0.9167 (mp) cc_final: 0.8703 (mt) REVERT: D 405 MET cc_start: 0.8567 (mmm) cc_final: 0.8295 (mmm) REVERT: F 400 GLU cc_start: 0.8279 (tt0) cc_final: 0.7928 (tp30) REVERT: G 45 ARG cc_start: 0.6781 (mtt90) cc_final: 0.5039 (ptt180) REVERT: G 96 PHE cc_start: 0.8480 (m-80) cc_final: 0.7467 (m-80) REVERT: H 22 LEU cc_start: 0.9217 (mt) cc_final: 0.8835 (tp) REVERT: H 31 MET cc_start: 0.9151 (mmm) cc_final: 0.8900 (mmm) REVERT: H 176 LEU cc_start: 0.8733 (mt) cc_final: 0.8480 (tp) REVERT: H 183 MET cc_start: 0.7892 (tmm) cc_final: 0.7511 (tmm) REVERT: H 248 ASN cc_start: 0.8649 (t0) cc_final: 0.8297 (t0) REVERT: H 268 MET cc_start: 0.8348 (mmp) cc_final: 0.8016 (ttp) REVERT: I 54 LYS cc_start: 0.8312 (mmtp) cc_final: 0.7624 (tttt) REVERT: I 60 ARG cc_start: 0.7639 (tpp-160) cc_final: 0.7327 (mmm160) REVERT: I 90 GLN cc_start: 0.8477 (mt0) cc_final: 0.7904 (mm-40) REVERT: I 110 ASP cc_start: 0.7163 (m-30) cc_final: 0.5902 (m-30) REVERT: I 117 ILE cc_start: 0.9178 (pt) cc_final: 0.8715 (mt) REVERT: J 52 LEU cc_start: 0.9206 (tt) cc_final: 0.8963 (mp) REVERT: J 65 MET cc_start: 0.8772 (mmp) cc_final: 0.8301 (mmp) REVERT: K 34 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7640 (mt-10) REVERT: L 14 LEU cc_start: 0.9144 (mt) cc_final: 0.8828 (tp) REVERT: L 17 MET cc_start: 0.8747 (mmp) cc_final: 0.8469 (ttp) REVERT: L 21 MET cc_start: 0.6533 (ttt) cc_final: 0.6015 (mmp) REVERT: L 103 PHE cc_start: 0.8327 (t80) cc_final: 0.7723 (t80) REVERT: L 138 PHE cc_start: 0.8390 (t80) cc_final: 0.8149 (t80) REVERT: L 179 ASP cc_start: 0.7689 (m-30) cc_final: 0.7415 (m-30) REVERT: L 186 MET cc_start: 0.8128 (mmm) cc_final: 0.7798 (mmt) REVERT: L 268 GLU cc_start: 0.7607 (pp20) cc_final: 0.7389 (pp20) REVERT: L 269 ASN cc_start: 0.8343 (m110) cc_final: 0.7981 (m110) REVERT: L 285 THR cc_start: 0.8623 (p) cc_final: 0.8412 (p) REVERT: L 291 CYS cc_start: 0.8157 (m) cc_final: 0.7739 (m) REVERT: L 373 LEU cc_start: 0.8999 (mt) cc_final: 0.8790 (mt) REVERT: L 389 PHE cc_start: 0.6483 (t80) cc_final: 0.6107 (t80) REVERT: L 393 ASP cc_start: 0.7970 (m-30) cc_final: 0.7576 (m-30) REVERT: L 411 MET cc_start: 0.8828 (ttm) cc_final: 0.8433 (mmt) REVERT: L 458 LEU cc_start: 0.7719 (mt) cc_final: 0.7479 (tp) REVERT: L 524 THR cc_start: 0.8893 (p) cc_final: 0.8621 (t) REVERT: L 535 ARG cc_start: 0.5487 (tpt170) cc_final: 0.4222 (ttt-90) REVERT: L 571 MET cc_start: 0.7682 (tpt) cc_final: 0.6585 (ttm) REVERT: L 576 LEU cc_start: 0.8398 (mt) cc_final: 0.7842 (mm) REVERT: L 581 LYS cc_start: 0.8305 (tttt) cc_final: 0.7276 (mmtt) REVERT: L 599 MET cc_start: 0.8717 (mmm) cc_final: 0.7178 (tpt) REVERT: M 30 HIS cc_start: 0.8405 (m90) cc_final: 0.8046 (m170) REVERT: M 56 PHE cc_start: 0.6066 (t80) cc_final: 0.5802 (t80) REVERT: M 200 MET cc_start: 0.8785 (mmp) cc_final: 0.8477 (mmp) REVERT: M 204 MET cc_start: 0.7855 (mmm) cc_final: 0.7368 (mmt) REVERT: M 249 ILE cc_start: 0.7882 (mm) cc_final: 0.7233 (mm) REVERT: M 271 MET cc_start: 0.7201 (mmm) cc_final: 0.6851 (mmm) REVERT: M 276 CYS cc_start: 0.8756 (t) cc_final: 0.7855 (t) REVERT: M 279 GLN cc_start: 0.6343 (mt0) cc_final: 0.5666 (mt0) REVERT: M 316 MET cc_start: 0.8096 (mmm) cc_final: 0.7634 (mmm) REVERT: M 317 ILE cc_start: 0.9486 (mt) cc_final: 0.9174 (tt) REVERT: M 325 MET cc_start: 0.7613 (tpp) cc_final: 0.6832 (tpp) REVERT: M 338 HIS cc_start: 0.8304 (m-70) cc_final: 0.7985 (m170) REVERT: M 340 ARG cc_start: 0.7415 (mtm110) cc_final: 0.7120 (mtm110) REVERT: M 378 GLU cc_start: 0.7371 (pt0) cc_final: 0.7157 (pp20) REVERT: M 383 MET cc_start: 0.9108 (mmp) cc_final: 0.8594 (mmp) REVERT: M 439 LEU cc_start: 0.9134 (mt) cc_final: 0.8865 (tp) REVERT: M 446 LEU cc_start: 0.8780 (mt) cc_final: 0.8198 (tp) REVERT: N 35 MET cc_start: 0.8178 (mmm) cc_final: 0.7747 (tpt) REVERT: N 38 LEU cc_start: 0.9300 (mt) cc_final: 0.8844 (mt) REVERT: N 61 LEU cc_start: 0.9307 (mt) cc_final: 0.8978 (tp) REVERT: N 79 MET cc_start: 0.8730 (mmm) cc_final: 0.8213 (mmm) REVERT: N 96 MET cc_start: 0.6814 (mmp) cc_final: 0.6432 (mmt) REVERT: N 98 MET cc_start: 0.9247 (tpt) cc_final: 0.8879 (tpp) REVERT: N 133 TRP cc_start: 0.6361 (t60) cc_final: 0.6064 (t-100) REVERT: N 208 TYR cc_start: 0.8762 (t80) cc_final: 0.8062 (t80) REVERT: N 294 MET cc_start: 0.8840 (mmp) cc_final: 0.8582 (tpp) REVERT: O 110 ASP cc_start: 0.7864 (m-30) cc_final: 0.7648 (t70) REVERT: O 147 GLN cc_start: 0.8116 (mp10) cc_final: 0.7690 (mp10) REVERT: O 162 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8058 (tm-30) REVERT: W 33 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8381 (tm-30) REVERT: W 36 ARG cc_start: 0.8399 (tpt170) cc_final: 0.8173 (ttm-80) REVERT: W 41 GLU cc_start: 0.8227 (tp30) cc_final: 0.7976 (tp30) REVERT: W 61 LYS cc_start: 0.6808 (ttmt) cc_final: 0.6367 (tptm) REVERT: W 77 VAL cc_start: 0.9590 (t) cc_final: 0.9188 (t) REVERT: X 31 TYR cc_start: 0.8136 (t80) cc_final: 0.7895 (t80) REVERT: X 50 LYS cc_start: 0.7158 (tttt) cc_final: 0.6519 (mmtp) REVERT: X 51 ASP cc_start: 0.8517 (m-30) cc_final: 0.8057 (t70) REVERT: X 58 GLU cc_start: 0.8658 (mp0) cc_final: 0.8040 (mp0) REVERT: X 107 ASP cc_start: 0.7990 (t70) cc_final: 0.7458 (t0) REVERT: X 109 CYS cc_start: 0.6490 (OUTLIER) cc_final: 0.5797 (p) REVERT: Y 39 SER cc_start: 0.8908 (t) cc_final: 0.8626 (t) REVERT: Z 55 GLU cc_start: 0.8329 (tp30) cc_final: 0.7913 (tp30) REVERT: Z 57 ARG cc_start: 0.8365 (mmm160) cc_final: 0.7273 (mmp80) REVERT: Z 77 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8252 (mt-10) REVERT: Z 91 GLU cc_start: 0.9067 (tp30) cc_final: 0.8694 (tp30) REVERT: a 28 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7173 (ptm160) REVERT: d 33 PHE cc_start: 0.8808 (t80) cc_final: 0.8481 (t80) REVERT: d 49 ARG cc_start: 0.8395 (mtt90) cc_final: 0.7679 (tpt-90) REVERT: d 90 MET cc_start: 0.8669 (ptp) cc_final: 0.8371 (ptm) REVERT: e 41 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7982 (tm-30) REVERT: e 83 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7397 (tp30) REVERT: g 92 GLU cc_start: 0.8735 (tp30) cc_final: 0.8448 (tp30) REVERT: g 101 GLU cc_start: 0.8438 (pt0) cc_final: 0.8155 (pt0) REVERT: i 19 ARG cc_start: 0.8333 (tpt90) cc_final: 0.7289 (tpt90) REVERT: i 20 ARG cc_start: 0.8632 (mtm110) cc_final: 0.7684 (ppt170) REVERT: m 48 LEU cc_start: 0.9588 (mt) cc_final: 0.8983 (tt) REVERT: m 84 LYS cc_start: 0.7124 (mptt) cc_final: 0.5774 (pptt) REVERT: n 16 LEU cc_start: 0.9171 (mt) cc_final: 0.8660 (pp) REVERT: n 20 LYS cc_start: 0.8823 (ttpt) cc_final: 0.8474 (ttpt) REVERT: n 23 LEU cc_start: 0.8609 (mt) cc_final: 0.8185 (tp) REVERT: n 51 LYS cc_start: 0.8144 (tttm) cc_final: 0.7874 (tptt) REVERT: n 64 ARG cc_start: 0.8095 (ttt180) cc_final: 0.7594 (mmt-90) REVERT: n 69 GLU cc_start: 0.8176 (pt0) cc_final: 0.7927 (tm-30) REVERT: p 86 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7769 (mm-30) outliers start: 10 outliers final: 0 residues processed: 1143 average time/residue: 0.5742 time to fit residues: 1111.7067 Evaluate side-chains 843 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 842 time to evaluate : 5.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 275 optimal weight: 0.0770 chunk 153 optimal weight: 7.9990 chunk 411 optimal weight: 0.9990 chunk 337 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 495 optimal weight: 10.0000 chunk 535 optimal weight: 10.0000 chunk 441 optimal weight: 2.9990 chunk 491 optimal weight: 20.0000 chunk 169 optimal weight: 3.9990 chunk 397 optimal weight: 30.0000 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN D 114 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN H 287 HIS H 304 HIS I 144 HIS ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 332 HIS M 81 GLN ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 279 GLN M 293 HIS ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 374 ASN N 36 ASN N 112 HIS N 134 GLN N 144 GLN N 197 ASN N 232 HIS O 151 HIS Z 53 ASN a 44 GLN d 46 ASN m 47 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.270 52088 Z= 0.589 Angle : 1.813 51.208 71507 Z= 1.164 Chirality : 0.331 6.448 8766 Planarity : 0.005 0.152 9352 Dihedral : 5.761 164.825 8196 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 1.38 % Allowed : 8.96 % Favored : 89.66 % Rotamer: Outliers : 0.11 % Allowed : 4.08 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.10), residues: 5784 helix: -0.61 (0.09), residues: 3038 sheet: 0.09 (0.44), residues: 163 loop : -2.82 (0.11), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP N 264 HIS 0.019 0.002 HIS I 65 PHE 0.032 0.002 PHE D 167 TYR 0.056 0.002 TYR Y 89 ARG 0.008 0.001 ARG W 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1038 time to evaluate : 5.187 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 12 THR cc_start: 0.9062 (p) cc_final: 0.8844 (t) REVERT: B 61 HIS cc_start: 0.8180 (m-70) cc_final: 0.7784 (m-70) REVERT: B 69 MET cc_start: 0.5198 (tpt) cc_final: 0.4882 (mmm) REVERT: B 83 SER cc_start: 0.8873 (p) cc_final: 0.8149 (p) REVERT: B 107 MET cc_start: 0.8772 (mmm) cc_final: 0.8424 (mmm) REVERT: B 116 MET cc_start: 0.8459 (ttp) cc_final: 0.8012 (ttp) REVERT: C 172 VAL cc_start: 0.8220 (m) cc_final: 0.7995 (m) REVERT: D 79 HIS cc_start: 0.8103 (m-70) cc_final: 0.7838 (m170) REVERT: D 135 GLN cc_start: 0.8779 (mt0) cc_final: 0.8394 (mt0) REVERT: D 136 TRP cc_start: 0.8787 (m100) cc_final: 0.8479 (m100) REVERT: D 169 TRP cc_start: 0.8669 (m-10) cc_final: 0.7913 (m100) REVERT: D 190 HIS cc_start: 0.6525 (m170) cc_final: 0.5460 (m170) REVERT: D 239 THR cc_start: 0.8269 (p) cc_final: 0.7583 (t) REVERT: D 276 ASP cc_start: 0.8132 (m-30) cc_final: 0.7530 (m-30) REVERT: D 310 ILE cc_start: 0.9246 (mp) cc_final: 0.8810 (mt) REVERT: D 399 LEU cc_start: 0.9449 (mt) cc_final: 0.9229 (mt) REVERT: D 405 MET cc_start: 0.8660 (mmm) cc_final: 0.8274 (tpp) REVERT: F 400 GLU cc_start: 0.8242 (tt0) cc_final: 0.7331 (tp30) REVERT: F 409 ASP cc_start: 0.7950 (m-30) cc_final: 0.6792 (m-30) REVERT: G 116 LEU cc_start: 0.9361 (tp) cc_final: 0.9140 (tp) REVERT: G 119 GLN cc_start: 0.8917 (mm110) cc_final: 0.8628 (mm110) REVERT: H 21 THR cc_start: 0.8141 (m) cc_final: 0.7796 (t) REVERT: H 22 LEU cc_start: 0.9278 (mt) cc_final: 0.9062 (tp) REVERT: H 25 ARG cc_start: 0.7330 (mpt180) cc_final: 0.6457 (mpt180) REVERT: H 31 MET cc_start: 0.9122 (mmm) cc_final: 0.8781 (mmm) REVERT: H 176 LEU cc_start: 0.8840 (mt) cc_final: 0.8617 (tp) REVERT: H 183 MET cc_start: 0.7758 (tmm) cc_final: 0.7298 (tmm) REVERT: H 248 ASN cc_start: 0.8642 (t0) cc_final: 0.8175 (t0) REVERT: H 268 MET cc_start: 0.8581 (mmp) cc_final: 0.8199 (ttp) REVERT: I 54 LYS cc_start: 0.8434 (mmtp) cc_final: 0.7716 (tttt) REVERT: I 60 ARG cc_start: 0.7700 (tpp-160) cc_final: 0.7447 (tpp80) REVERT: I 90 GLN cc_start: 0.8355 (mt0) cc_final: 0.7744 (mm-40) REVERT: I 110 ASP cc_start: 0.7172 (m-30) cc_final: 0.5968 (m-30) REVERT: I 117 ILE cc_start: 0.9229 (pt) cc_final: 0.8819 (mp) REVERT: I 161 TRP cc_start: 0.7665 (m100) cc_final: 0.7347 (m100) REVERT: J 52 LEU cc_start: 0.9128 (tt) cc_final: 0.8738 (mp) REVERT: J 99 MET cc_start: 0.7074 (mmt) cc_final: 0.6698 (tpp) REVERT: J 141 MET cc_start: 0.6375 (ttm) cc_final: 0.5629 (ttm) REVERT: K 6 MET cc_start: 0.7598 (tpp) cc_final: 0.7305 (mtt) REVERT: K 7 ASN cc_start: 0.8936 (p0) cc_final: 0.8672 (p0) REVERT: K 39 SER cc_start: 0.9361 (m) cc_final: 0.9035 (p) REVERT: K 59 MET cc_start: 0.8077 (mtt) cc_final: 0.7405 (mtp) REVERT: L 14 LEU cc_start: 0.9234 (mt) cc_final: 0.8974 (tp) REVERT: L 17 MET cc_start: 0.8619 (mmp) cc_final: 0.8378 (ttp) REVERT: L 186 MET cc_start: 0.8194 (mmm) cc_final: 0.7749 (mmt) REVERT: L 248 HIS cc_start: 0.7843 (m-70) cc_final: 0.7634 (m-70) REVERT: L 268 GLU cc_start: 0.7864 (pp20) cc_final: 0.7613 (pp20) REVERT: L 269 ASN cc_start: 0.8557 (m110) cc_final: 0.8088 (m110) REVERT: L 285 THR cc_start: 0.8792 (p) cc_final: 0.8524 (p) REVERT: L 291 CYS cc_start: 0.8490 (m) cc_final: 0.8156 (m) REVERT: L 352 ASP cc_start: 0.8118 (t70) cc_final: 0.7738 (t0) REVERT: L 373 LEU cc_start: 0.9090 (mt) cc_final: 0.8887 (mt) REVERT: L 389 PHE cc_start: 0.6388 (t80) cc_final: 0.6128 (t80) REVERT: L 393 ASP cc_start: 0.7914 (m-30) cc_final: 0.7495 (m-30) REVERT: L 411 MET cc_start: 0.8847 (ttm) cc_final: 0.8452 (ttm) REVERT: L 524 THR cc_start: 0.8936 (p) cc_final: 0.8555 (t) REVERT: L 535 ARG cc_start: 0.5299 (tpt170) cc_final: 0.4256 (ttt-90) REVERT: L 571 MET cc_start: 0.7477 (tpt) cc_final: 0.6437 (ttm) REVERT: L 599 MET cc_start: 0.8678 (mmm) cc_final: 0.7480 (tpt) REVERT: M 30 HIS cc_start: 0.8430 (m90) cc_final: 0.8200 (m170) REVERT: M 201 MET cc_start: 0.8303 (mmm) cc_final: 0.7966 (mmp) REVERT: M 204 MET cc_start: 0.8014 (mmm) cc_final: 0.7602 (mmt) REVERT: M 269 MET cc_start: 0.7884 (mmm) cc_final: 0.7306 (mmm) REVERT: M 276 CYS cc_start: 0.8378 (t) cc_final: 0.8052 (t) REVERT: M 279 GLN cc_start: 0.6551 (mt0) cc_final: 0.6179 (mt0) REVERT: M 285 LEU cc_start: 0.8877 (mt) cc_final: 0.8664 (mt) REVERT: M 317 ILE cc_start: 0.9478 (mt) cc_final: 0.9169 (tt) REVERT: M 325 MET cc_start: 0.7663 (tpp) cc_final: 0.6586 (tpp) REVERT: M 338 HIS cc_start: 0.8363 (m-70) cc_final: 0.8062 (m170) REVERT: M 383 MET cc_start: 0.9062 (mmp) cc_final: 0.8619 (mmp) REVERT: M 415 GLN cc_start: 0.5158 (tt0) cc_final: 0.4936 (tm-30) REVERT: M 446 LEU cc_start: 0.9004 (mt) cc_final: 0.8514 (tt) REVERT: N 61 LEU cc_start: 0.9390 (mt) cc_final: 0.9094 (tp) REVERT: N 98 MET cc_start: 0.9240 (tpt) cc_final: 0.8929 (tpp) REVERT: N 133 TRP cc_start: 0.6416 (t60) cc_final: 0.6057 (t-100) REVERT: N 208 TYR cc_start: 0.8712 (t80) cc_final: 0.7986 (t80) REVERT: N 211 MET cc_start: 0.8607 (ttm) cc_final: 0.8104 (ttp) REVERT: N 232 HIS cc_start: 0.7301 (OUTLIER) cc_final: 0.6964 (t70) REVERT: N 240 MET cc_start: 0.8506 (ttm) cc_final: 0.7696 (ttm) REVERT: N 281 PHE cc_start: 0.8357 (t80) cc_final: 0.8110 (t80) REVERT: N 294 MET cc_start: 0.8874 (mmp) cc_final: 0.8619 (tpp) REVERT: N 302 LEU cc_start: 0.8258 (mt) cc_final: 0.7898 (mt) REVERT: O 147 GLN cc_start: 0.8401 (mp10) cc_final: 0.7872 (mp10) REVERT: O 162 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8222 (tm-30) REVERT: W 36 ARG cc_start: 0.8377 (tpt170) cc_final: 0.7855 (ttm-80) REVERT: W 41 GLU cc_start: 0.8092 (tp30) cc_final: 0.7565 (tp30) REVERT: W 57 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7938 (tm-30) REVERT: W 61 LYS cc_start: 0.6831 (ttmt) cc_final: 0.6277 (tttt) REVERT: X 50 LYS cc_start: 0.6889 (tttt) cc_final: 0.6385 (mptt) REVERT: X 51 ASP cc_start: 0.8492 (m-30) cc_final: 0.8130 (t70) REVERT: X 108 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8523 (mm-30) REVERT: Y 126 MET cc_start: 0.7937 (tmm) cc_final: 0.7705 (tmm) REVERT: Z 55 GLU cc_start: 0.8358 (tp30) cc_final: 0.7990 (tp30) REVERT: Z 77 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8097 (mt-10) REVERT: Z 85 MET cc_start: 0.8605 (mmp) cc_final: 0.8366 (mmm) REVERT: Z 91 GLU cc_start: 0.9252 (tp30) cc_final: 0.8892 (tp30) REVERT: a 12 MET cc_start: 0.8691 (tpp) cc_final: 0.7980 (mmm) REVERT: d 33 PHE cc_start: 0.8858 (t80) cc_final: 0.8428 (t80) REVERT: d 49 ARG cc_start: 0.8423 (mtt90) cc_final: 0.7669 (tpt-90) REVERT: d 73 TYR cc_start: 0.8776 (t80) cc_final: 0.8451 (t80) REVERT: e 41 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8077 (tm-30) REVERT: e 83 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7301 (tp30) REVERT: g 92 GLU cc_start: 0.8654 (tp30) cc_final: 0.8349 (tp30) REVERT: g 101 GLU cc_start: 0.8571 (pt0) cc_final: 0.8209 (pt0) REVERT: i 16 GLU cc_start: 0.9055 (pt0) cc_final: 0.8854 (pt0) REVERT: i 19 ARG cc_start: 0.8379 (tpt90) cc_final: 0.7176 (tpt90) REVERT: i 20 ARG cc_start: 0.8743 (mtm110) cc_final: 0.7811 (ppt170) REVERT: m 48 LEU cc_start: 0.9665 (mt) cc_final: 0.9140 (tt) REVERT: m 84 LYS cc_start: 0.7276 (mptt) cc_final: 0.6059 (pptt) REVERT: n 16 LEU cc_start: 0.9148 (mt) cc_final: 0.8668 (pp) REVERT: n 20 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8522 (ttpt) REVERT: n 23 LEU cc_start: 0.8673 (mt) cc_final: 0.8080 (tp) REVERT: n 62 LEU cc_start: 0.8352 (tp) cc_final: 0.8145 (tt) REVERT: n 64 ARG cc_start: 0.8072 (ttt180) cc_final: 0.7607 (mmt-90) REVERT: p 86 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7940 (mm-30) outliers start: 4 outliers final: 1 residues processed: 1040 average time/residue: 0.5660 time to fit residues: 1005.7428 Evaluate side-chains 834 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 832 time to evaluate : 5.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 489 optimal weight: 20.0000 chunk 372 optimal weight: 20.0000 chunk 257 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 236 optimal weight: 0.9990 chunk 332 optimal weight: 3.9990 chunk 497 optimal weight: 10.9990 chunk 526 optimal weight: 9.9990 chunk 259 optimal weight: 0.4980 chunk 471 optimal weight: 10.0000 chunk 141 optimal weight: 8.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 HIS H 99 ASN ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN M 213 HIS M 293 HIS ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN N 49 ASN N 134 GLN N 232 HIS O 107 GLN O 167 HIS V 52 ASN X 64 GLN Y 88 ASN ** d 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 133 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.274 52088 Z= 0.585 Angle : 1.811 51.189 71507 Z= 1.162 Chirality : 0.332 6.441 8766 Planarity : 0.005 0.147 9352 Dihedral : 5.661 164.676 8196 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 1.40 % Allowed : 8.25 % Favored : 90.35 % Rotamer: Outliers : 0.11 % Allowed : 4.22 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.11), residues: 5784 helix: -0.19 (0.09), residues: 3032 sheet: 0.13 (0.46), residues: 154 loop : -2.71 (0.11), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 407 HIS 0.022 0.002 HIS O 167 PHE 0.030 0.002 PHE L 522 TYR 0.033 0.002 TYR D 108 ARG 0.010 0.000 ARG M 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 985 time to evaluate : 5.212 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 12 THR cc_start: 0.9093 (p) cc_final: 0.8845 (t) REVERT: B 61 HIS cc_start: 0.8204 (m-70) cc_final: 0.7725 (m90) REVERT: B 83 SER cc_start: 0.9024 (p) cc_final: 0.7636 (p) REVERT: B 84 ASP cc_start: 0.7832 (p0) cc_final: 0.7473 (p0) REVERT: B 107 MET cc_start: 0.8712 (mmm) cc_final: 0.8240 (mmm) REVERT: B 116 MET cc_start: 0.8400 (ttp) cc_final: 0.7669 (ptm) REVERT: D 98 GLN cc_start: 0.9217 (tt0) cc_final: 0.8661 (mt0) REVERT: D 136 TRP cc_start: 0.8752 (m100) cc_final: 0.8515 (m100) REVERT: D 169 TRP cc_start: 0.8773 (m-10) cc_final: 0.7887 (m100) REVERT: D 239 THR cc_start: 0.8354 (p) cc_final: 0.7665 (t) REVERT: D 310 ILE cc_start: 0.9315 (mp) cc_final: 0.8734 (mt) REVERT: D 405 MET cc_start: 0.8665 (mmm) cc_final: 0.8233 (tpp) REVERT: F 389 ILE cc_start: 0.8955 (pt) cc_final: 0.8721 (tp) REVERT: G 122 MET cc_start: 0.8947 (mmm) cc_final: 0.8694 (mmp) REVERT: H 21 THR cc_start: 0.8336 (m) cc_final: 0.8024 (t) REVERT: H 156 MET cc_start: 0.8855 (ttm) cc_final: 0.8631 (ttm) REVERT: H 176 LEU cc_start: 0.9033 (mt) cc_final: 0.8686 (tp) REVERT: H 183 MET cc_start: 0.7797 (tmm) cc_final: 0.7385 (tmm) REVERT: H 248 ASN cc_start: 0.8611 (t0) cc_final: 0.8225 (t0) REVERT: H 268 MET cc_start: 0.8472 (mmp) cc_final: 0.8053 (ttp) REVERT: I 40 TYR cc_start: 0.8265 (t80) cc_final: 0.8020 (t80) REVERT: I 54 LYS cc_start: 0.8546 (mmtp) cc_final: 0.7722 (tttt) REVERT: I 90 GLN cc_start: 0.8258 (mt0) cc_final: 0.7715 (mm-40) REVERT: I 117 ILE cc_start: 0.9061 (pt) cc_final: 0.8610 (mt) REVERT: I 138 GLU cc_start: 0.6804 (tt0) cc_final: 0.6130 (tm-30) REVERT: J 52 LEU cc_start: 0.9319 (tt) cc_final: 0.8924 (mt) REVERT: J 55 MET cc_start: 0.9121 (mmm) cc_final: 0.8536 (mmm) REVERT: K 7 ASN cc_start: 0.8807 (p0) cc_final: 0.8108 (p0) REVERT: K 37 MET cc_start: 0.8659 (mmp) cc_final: 0.7663 (tpp) REVERT: K 55 LEU cc_start: 0.7740 (mp) cc_final: 0.7430 (tp) REVERT: K 59 MET cc_start: 0.8249 (mtt) cc_final: 0.7510 (mtp) REVERT: K 70 GLU cc_start: 0.7506 (pm20) cc_final: 0.7282 (pm20) REVERT: L 14 LEU cc_start: 0.9201 (mt) cc_final: 0.8909 (tp) REVERT: L 21 MET cc_start: 0.7781 (mmp) cc_final: 0.7477 (ttt) REVERT: L 291 CYS cc_start: 0.8629 (m) cc_final: 0.8295 (m) REVERT: L 373 LEU cc_start: 0.9152 (mt) cc_final: 0.8927 (mt) REVERT: L 389 PHE cc_start: 0.6300 (t80) cc_final: 0.6051 (t80) REVERT: L 393 ASP cc_start: 0.8042 (m-30) cc_final: 0.7658 (m-30) REVERT: L 524 THR cc_start: 0.8969 (p) cc_final: 0.8586 (t) REVERT: L 535 ARG cc_start: 0.5255 (tpt170) cc_final: 0.4157 (ttt-90) REVERT: L 571 MET cc_start: 0.7231 (tpt) cc_final: 0.6133 (ttm) REVERT: L 599 MET cc_start: 0.8692 (mmm) cc_final: 0.7581 (tpt) REVERT: M 147 LEU cc_start: 0.9073 (mm) cc_final: 0.8862 (mp) REVERT: M 204 MET cc_start: 0.8220 (mmm) cc_final: 0.7950 (mmt) REVERT: M 250 LEU cc_start: 0.9164 (mm) cc_final: 0.8897 (mm) REVERT: M 276 CYS cc_start: 0.8478 (t) cc_final: 0.8166 (t) REVERT: M 317 ILE cc_start: 0.9476 (mt) cc_final: 0.9080 (tt) REVERT: M 325 MET cc_start: 0.7554 (tpp) cc_final: 0.6382 (tpp) REVERT: M 338 HIS cc_start: 0.8399 (m-70) cc_final: 0.8074 (m170) REVERT: M 437 MET cc_start: 0.8403 (mmp) cc_final: 0.8198 (mmp) REVERT: N 36 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8549 (m-40) REVERT: N 38 LEU cc_start: 0.9363 (mt) cc_final: 0.9148 (mt) REVERT: N 61 LEU cc_start: 0.9485 (mt) cc_final: 0.9197 (tp) REVERT: N 133 TRP cc_start: 0.6291 (t60) cc_final: 0.6029 (t-100) REVERT: N 208 TYR cc_start: 0.8722 (t80) cc_final: 0.8053 (t80) REVERT: N 294 MET cc_start: 0.8814 (mmp) cc_final: 0.8577 (tpp) REVERT: O 162 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8275 (tm-30) REVERT: W 36 ARG cc_start: 0.8429 (tpt170) cc_final: 0.8058 (ttm-80) REVERT: W 41 GLU cc_start: 0.8196 (tp30) cc_final: 0.7701 (tp30) REVERT: W 57 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7884 (tm-30) REVERT: W 61 LYS cc_start: 0.6772 (ttmt) cc_final: 0.6318 (tptt) REVERT: X 50 LYS cc_start: 0.7012 (tttt) cc_final: 0.6227 (mptt) REVERT: X 51 ASP cc_start: 0.8501 (m-30) cc_final: 0.8245 (t70) REVERT: X 108 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8467 (mm-30) REVERT: Y 35 VAL cc_start: 0.8657 (t) cc_final: 0.8435 (t) REVERT: Y 89 TYR cc_start: 0.6269 (m-10) cc_final: 0.6010 (m-10) REVERT: Z 55 GLU cc_start: 0.8395 (tp30) cc_final: 0.8023 (tp30) REVERT: Z 77 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8155 (mt-10) REVERT: Z 85 MET cc_start: 0.8620 (mmp) cc_final: 0.8380 (mmm) REVERT: Z 91 GLU cc_start: 0.9048 (tp30) cc_final: 0.8656 (tp30) REVERT: b 40 TYR cc_start: 0.7755 (m-80) cc_final: 0.7546 (m-80) REVERT: d 33 PHE cc_start: 0.8842 (t80) cc_final: 0.8411 (t80) REVERT: d 49 ARG cc_start: 0.8435 (mtt90) cc_final: 0.7786 (tpt170) REVERT: d 73 TYR cc_start: 0.8727 (t80) cc_final: 0.8457 (t80) REVERT: d 87 ASP cc_start: 0.7914 (t0) cc_final: 0.7285 (t0) REVERT: e 41 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7964 (tm-30) REVERT: e 83 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7486 (tp30) REVERT: g 92 GLU cc_start: 0.8702 (tp30) cc_final: 0.8468 (tp30) REVERT: g 99 TYR cc_start: 0.8673 (t80) cc_final: 0.8282 (t80) REVERT: h 38 ILE cc_start: 0.8327 (mm) cc_final: 0.7835 (tt) REVERT: i 20 ARG cc_start: 0.8833 (mtm110) cc_final: 0.7922 (ppt170) REVERT: m 48 LEU cc_start: 0.9601 (mt) cc_final: 0.9236 (tt) REVERT: m 80 ARG cc_start: 0.7537 (ptm160) cc_final: 0.7110 (mmp-170) REVERT: m 84 LYS cc_start: 0.7402 (mptt) cc_final: 0.6232 (pttp) REVERT: n 20 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8546 (ttpt) REVERT: n 23 LEU cc_start: 0.8696 (mt) cc_final: 0.8132 (tp) REVERT: n 64 ARG cc_start: 0.7954 (ttt180) cc_final: 0.7487 (mmt-90) REVERT: p 86 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7959 (mm-30) outliers start: 4 outliers final: 1 residues processed: 987 average time/residue: 0.5772 time to fit residues: 972.0207 Evaluate side-chains 795 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 793 time to evaluate : 5.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 438 optimal weight: 0.7980 chunk 299 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 392 optimal weight: 20.0000 chunk 217 optimal weight: 0.0570 chunk 449 optimal weight: 8.9990 chunk 364 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 268 optimal weight: 2.9990 chunk 472 optimal weight: 0.7980 chunk 132 optimal weight: 50.0000 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 357 GLN ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 HIS ** G 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN I 123 GLN ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 HIS M 213 HIS M 279 GLN ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN N 232 HIS X 64 GLN ** d 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 133 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.268 52088 Z= 0.571 Angle : 1.793 51.142 71507 Z= 1.154 Chirality : 0.332 6.485 8766 Planarity : 0.005 0.140 9352 Dihedral : 5.356 164.702 8196 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 1.35 % Allowed : 8.09 % Favored : 90.56 % Rotamer: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.11), residues: 5784 helix: 0.07 (0.09), residues: 3036 sheet: 0.21 (0.46), residues: 148 loop : -2.65 (0.11), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP L 66 HIS 0.017 0.001 HIS O 167 PHE 0.031 0.002 PHE d 91 TYR 0.037 0.001 TYR D 108 ARG 0.012 0.000 ARG W 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 998 time to evaluate : 4.968 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 12 THR cc_start: 0.9081 (p) cc_final: 0.8821 (t) REVERT: B 61 HIS cc_start: 0.8222 (m-70) cc_final: 0.7716 (m90) REVERT: B 83 SER cc_start: 0.8880 (p) cc_final: 0.8012 (p) REVERT: B 84 ASP cc_start: 0.7733 (p0) cc_final: 0.7426 (p0) REVERT: B 107 MET cc_start: 0.8613 (mmm) cc_final: 0.8332 (mmm) REVERT: B 116 MET cc_start: 0.8331 (ttp) cc_final: 0.8053 (ttp) REVERT: C 48 LEU cc_start: 0.8241 (tt) cc_final: 0.7861 (mp) REVERT: D 82 LEU cc_start: 0.9112 (mt) cc_final: 0.8899 (mt) REVERT: D 136 TRP cc_start: 0.8706 (m100) cc_final: 0.8427 (m100) REVERT: D 169 TRP cc_start: 0.8737 (m-10) cc_final: 0.7821 (m100) REVERT: D 189 MET cc_start: 0.7467 (ttm) cc_final: 0.6958 (ttm) REVERT: D 190 HIS cc_start: 0.6254 (m-70) cc_final: 0.5975 (m170) REVERT: D 239 THR cc_start: 0.8437 (p) cc_final: 0.7813 (t) REVERT: D 310 ILE cc_start: 0.9348 (mp) cc_final: 0.8955 (mt) REVERT: H 31 MET cc_start: 0.9173 (mmm) cc_final: 0.8878 (mmm) REVERT: H 34 ARG cc_start: 0.7028 (ptm-80) cc_final: 0.6805 (ptm-80) REVERT: H 149 ILE cc_start: 0.9473 (pt) cc_final: 0.9257 (pt) REVERT: H 176 LEU cc_start: 0.9030 (mt) cc_final: 0.8685 (tp) REVERT: H 183 MET cc_start: 0.7787 (tmm) cc_final: 0.7358 (tmm) REVERT: H 248 ASN cc_start: 0.8618 (t0) cc_final: 0.8143 (t0) REVERT: H 268 MET cc_start: 0.8518 (mmp) cc_final: 0.7932 (ttp) REVERT: H 303 TRP cc_start: 0.8763 (t-100) cc_final: 0.8562 (t-100) REVERT: I 34 LEU cc_start: 0.8382 (tt) cc_final: 0.8112 (mt) REVERT: I 54 LYS cc_start: 0.8495 (mmtp) cc_final: 0.7734 (tttt) REVERT: I 90 GLN cc_start: 0.8195 (mt0) cc_final: 0.7605 (mm-40) REVERT: I 117 ILE cc_start: 0.9120 (pt) cc_final: 0.8637 (mt) REVERT: I 138 GLU cc_start: 0.7017 (tt0) cc_final: 0.5874 (tm-30) REVERT: I 150 ASN cc_start: 0.8000 (p0) cc_final: 0.7721 (p0) REVERT: J 74 MET cc_start: 0.8657 (mmp) cc_final: 0.7908 (tpt) REVERT: J 100 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8607 (tm-30) REVERT: K 6 MET cc_start: 0.7394 (mmt) cc_final: 0.6726 (mtt) REVERT: K 7 ASN cc_start: 0.8935 (p0) cc_final: 0.8151 (p0) REVERT: K 55 LEU cc_start: 0.7752 (mp) cc_final: 0.7544 (tp) REVERT: K 59 MET cc_start: 0.8219 (mtt) cc_final: 0.7414 (mtp) REVERT: L 14 LEU cc_start: 0.9234 (mt) cc_final: 0.8890 (tp) REVERT: L 16 THR cc_start: 0.9429 (p) cc_final: 0.9174 (t) REVERT: L 21 MET cc_start: 0.7668 (mmp) cc_final: 0.7215 (ttt) REVERT: L 88 MET cc_start: 0.8599 (tpp) cc_final: 0.8164 (mpp) REVERT: L 285 THR cc_start: 0.8575 (p) cc_final: 0.8308 (p) REVERT: L 291 CYS cc_start: 0.8597 (m) cc_final: 0.8212 (m) REVERT: L 352 ASP cc_start: 0.8211 (t70) cc_final: 0.7359 (t0) REVERT: L 366 MET cc_start: 0.8315 (tpp) cc_final: 0.7944 (tpp) REVERT: L 389 PHE cc_start: 0.6075 (t80) cc_final: 0.5822 (t80) REVERT: L 393 ASP cc_start: 0.7993 (m-30) cc_final: 0.7593 (m-30) REVERT: L 524 THR cc_start: 0.8796 (p) cc_final: 0.8456 (t) REVERT: L 535 ARG cc_start: 0.5029 (tpt170) cc_final: 0.3975 (ttt180) REVERT: L 571 MET cc_start: 0.7109 (tpt) cc_final: 0.6049 (ttm) REVERT: L 599 MET cc_start: 0.8678 (mmm) cc_final: 0.7684 (tpt) REVERT: M 147 LEU cc_start: 0.8963 (mm) cc_final: 0.8760 (mp) REVERT: M 204 MET cc_start: 0.8360 (mmm) cc_final: 0.7679 (ptp) REVERT: M 250 LEU cc_start: 0.9097 (mm) cc_final: 0.8881 (mm) REVERT: M 269 MET cc_start: 0.7427 (tpt) cc_final: 0.7156 (tpt) REVERT: M 317 ILE cc_start: 0.9488 (mt) cc_final: 0.9015 (tt) REVERT: M 325 MET cc_start: 0.7512 (tpp) cc_final: 0.6078 (tpp) REVERT: M 338 HIS cc_start: 0.8387 (m-70) cc_final: 0.8043 (m170) REVERT: M 340 ARG cc_start: 0.7470 (mtm110) cc_final: 0.7076 (mtp180) REVERT: M 383 MET cc_start: 0.9108 (mmp) cc_final: 0.8526 (mmp) REVERT: M 437 MET cc_start: 0.8393 (mmp) cc_final: 0.8049 (mmp) REVERT: M 446 LEU cc_start: 0.9048 (mt) cc_final: 0.7931 (tt) REVERT: N 36 ASN cc_start: 0.8983 (m-40) cc_final: 0.8309 (m-40) REVERT: N 58 LYS cc_start: 0.9211 (ttmt) cc_final: 0.7990 (ttmt) REVERT: N 61 LEU cc_start: 0.9487 (mt) cc_final: 0.9209 (tp) REVERT: N 117 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7875 (pt0) REVERT: N 208 TYR cc_start: 0.8641 (t80) cc_final: 0.7972 (t80) REVERT: N 232 HIS cc_start: 0.7079 (t-90) cc_final: 0.6855 (t70) REVERT: N 282 MET cc_start: 0.8477 (ttm) cc_final: 0.8168 (mtp) REVERT: O 107 GLN cc_start: 0.8875 (pt0) cc_final: 0.7588 (mm-40) REVERT: O 147 GLN cc_start: 0.8344 (mp10) cc_final: 0.8081 (mp10) REVERT: O 162 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8293 (tm-30) REVERT: W 36 ARG cc_start: 0.7900 (tpt170) cc_final: 0.7679 (ttm110) REVERT: W 41 GLU cc_start: 0.7784 (tp30) cc_final: 0.7300 (tp30) REVERT: W 57 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7778 (tm-30) REVERT: W 61 LYS cc_start: 0.6805 (ttmt) cc_final: 0.6363 (tptm) REVERT: X 31 TYR cc_start: 0.8192 (t80) cc_final: 0.7872 (t80) REVERT: X 50 LYS cc_start: 0.7096 (tttt) cc_final: 0.6175 (mptt) REVERT: Y 39 SER cc_start: 0.8740 (m) cc_final: 0.8477 (m) REVERT: Y 89 TYR cc_start: 0.6779 (m-10) cc_final: 0.6232 (m-10) REVERT: Z 55 GLU cc_start: 0.8382 (tp30) cc_final: 0.7968 (tp30) REVERT: Z 77 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8049 (mt-10) REVERT: Z 78 LYS cc_start: 0.8053 (mttt) cc_final: 0.7795 (mmtt) REVERT: Z 85 MET cc_start: 0.8569 (mmp) cc_final: 0.8334 (mmm) REVERT: Z 91 GLU cc_start: 0.9048 (tp30) cc_final: 0.8621 (tp30) REVERT: a 1 MET cc_start: 0.6938 (mpp) cc_final: 0.6552 (tpt) REVERT: b 40 TYR cc_start: 0.7746 (m-80) cc_final: 0.7517 (m-80) REVERT: d 33 PHE cc_start: 0.8904 (t80) cc_final: 0.8371 (t80) REVERT: d 49 ARG cc_start: 0.8412 (mtt90) cc_final: 0.7784 (tpt170) REVERT: d 73 TYR cc_start: 0.8735 (t80) cc_final: 0.8461 (t80) REVERT: e 41 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8046 (tm-30) REVERT: e 83 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7377 (tp30) REVERT: g 92 GLU cc_start: 0.8662 (tp30) cc_final: 0.8440 (tp30) REVERT: g 99 TYR cc_start: 0.8688 (t80) cc_final: 0.8430 (t80) REVERT: h 38 ILE cc_start: 0.8146 (mm) cc_final: 0.7543 (tt) REVERT: i 20 ARG cc_start: 0.8749 (mtm110) cc_final: 0.7754 (ppt170) REVERT: m 48 LEU cc_start: 0.9642 (mt) cc_final: 0.9285 (tt) REVERT: m 80 ARG cc_start: 0.7518 (ptm160) cc_final: 0.7129 (mmp-170) REVERT: m 84 LYS cc_start: 0.7446 (mptt) cc_final: 0.6234 (pttp) REVERT: n 23 LEU cc_start: 0.8615 (mt) cc_final: 0.7712 (tt) REVERT: n 27 GLU cc_start: 0.8546 (tt0) cc_final: 0.8045 (tm-30) REVERT: p 86 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7940 (mm-30) outliers start: 1 outliers final: 0 residues processed: 998 average time/residue: 0.5657 time to fit residues: 963.2681 Evaluate side-chains 790 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 790 time to evaluate : 5.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 177 optimal weight: 6.9990 chunk 474 optimal weight: 0.0570 chunk 104 optimal weight: 6.9990 chunk 309 optimal weight: 0.9980 chunk 130 optimal weight: 30.0000 chunk 527 optimal weight: 20.0000 chunk 437 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 276 optimal weight: 0.0370 overall best weight: 1.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 HIS ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 400 ASN ** M 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 HIS ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 53 ASN ** d 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 133 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.275 52088 Z= 0.573 Angle : 1.799 51.028 71507 Z= 1.157 Chirality : 0.332 6.485 8766 Planarity : 0.005 0.145 9352 Dihedral : 5.251 163.687 8196 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 1.26 % Allowed : 8.06 % Favored : 90.68 % Rotamer: Outliers : 0.03 % Allowed : 2.37 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.11), residues: 5784 helix: 0.16 (0.10), residues: 3032 sheet: 0.29 (0.46), residues: 148 loop : -2.57 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 215 HIS 0.016 0.001 HIS O 167 PHE 0.022 0.002 PHE H 237 TYR 0.026 0.001 TYR M 406 ARG 0.010 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 970 time to evaluate : 4.744 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 12 THR cc_start: 0.9075 (p) cc_final: 0.8818 (t) REVERT: B 83 SER cc_start: 0.8934 (p) cc_final: 0.8533 (p) REVERT: B 84 ASP cc_start: 0.7702 (p0) cc_final: 0.7298 (p0) REVERT: B 86 MET cc_start: 0.8798 (ttp) cc_final: 0.8578 (ttp) REVERT: B 116 MET cc_start: 0.8286 (ttp) cc_final: 0.8008 (ttp) REVERT: B 128 TYR cc_start: 0.8850 (m-80) cc_final: 0.8378 (m-80) REVERT: D 82 LEU cc_start: 0.9131 (mt) cc_final: 0.8866 (mt) REVERT: D 136 TRP cc_start: 0.8760 (m100) cc_final: 0.8460 (m100) REVERT: D 167 PHE cc_start: 0.8491 (t80) cc_final: 0.8186 (t80) REVERT: D 169 TRP cc_start: 0.8852 (m-10) cc_final: 0.7880 (m100) REVERT: D 239 THR cc_start: 0.8556 (p) cc_final: 0.7878 (t) REVERT: D 310 ILE cc_start: 0.9200 (mp) cc_final: 0.8941 (mt) REVERT: D 318 MET cc_start: 0.8615 (tpp) cc_final: 0.8201 (tpp) REVERT: D 405 MET cc_start: 0.8631 (mmm) cc_final: 0.8185 (tpp) REVERT: F 389 ILE cc_start: 0.8967 (pt) cc_final: 0.8679 (tp) REVERT: G 45 ARG cc_start: 0.7438 (mpt90) cc_final: 0.6157 (ptm160) REVERT: H 31 MET cc_start: 0.9148 (mmm) cc_final: 0.8624 (tpp) REVERT: H 46 LEU cc_start: 0.8792 (mt) cc_final: 0.8560 (mt) REVERT: H 141 SER cc_start: 0.8888 (m) cc_final: 0.8023 (t) REVERT: H 176 LEU cc_start: 0.9116 (mt) cc_final: 0.8809 (tp) REVERT: H 183 MET cc_start: 0.7810 (tmm) cc_final: 0.7392 (tmm) REVERT: H 248 ASN cc_start: 0.8624 (t0) cc_final: 0.8117 (t0) REVERT: H 268 MET cc_start: 0.8511 (mmp) cc_final: 0.7936 (ttp) REVERT: H 303 TRP cc_start: 0.8853 (t-100) cc_final: 0.8651 (t-100) REVERT: I 54 LYS cc_start: 0.8347 (mmtp) cc_final: 0.7553 (tttt) REVERT: I 90 GLN cc_start: 0.8314 (mt0) cc_final: 0.7773 (mm-40) REVERT: I 117 ILE cc_start: 0.8958 (pt) cc_final: 0.8432 (mt) REVERT: I 138 GLU cc_start: 0.7123 (tt0) cc_final: 0.5615 (tm-30) REVERT: J 102 PHE cc_start: 0.7485 (t80) cc_final: 0.7193 (t80) REVERT: J 169 MET cc_start: 0.6366 (tmm) cc_final: 0.6128 (tmm) REVERT: K 6 MET cc_start: 0.7405 (mmt) cc_final: 0.6745 (mtt) REVERT: K 7 ASN cc_start: 0.8932 (p0) cc_final: 0.8573 (p0) REVERT: K 59 MET cc_start: 0.8264 (mtt) cc_final: 0.7590 (mtp) REVERT: L 14 LEU cc_start: 0.9170 (mt) cc_final: 0.8898 (tp) REVERT: L 16 THR cc_start: 0.9509 (p) cc_final: 0.8547 (t) REVERT: L 20 MET cc_start: 0.8921 (mmm) cc_final: 0.8047 (mpp) REVERT: L 21 MET cc_start: 0.7696 (mmp) cc_final: 0.7391 (ttt) REVERT: L 88 MET cc_start: 0.8455 (tpp) cc_final: 0.8221 (mpp) REVERT: L 291 CYS cc_start: 0.8634 (m) cc_final: 0.8266 (m) REVERT: L 366 MET cc_start: 0.8342 (tpp) cc_final: 0.7966 (tpp) REVERT: L 389 PHE cc_start: 0.6108 (t80) cc_final: 0.5810 (t80) REVERT: L 393 ASP cc_start: 0.8024 (m-30) cc_final: 0.7520 (m-30) REVERT: L 535 ARG cc_start: 0.5086 (tpt170) cc_final: 0.3995 (ttt-90) REVERT: L 571 MET cc_start: 0.7110 (tpt) cc_final: 0.5972 (ttm) REVERT: L 599 MET cc_start: 0.8683 (mmm) cc_final: 0.7741 (tpt) REVERT: M 147 LEU cc_start: 0.9021 (mm) cc_final: 0.8818 (mp) REVERT: M 200 MET cc_start: 0.8851 (mmp) cc_final: 0.8642 (mmp) REVERT: M 204 MET cc_start: 0.7964 (mmm) cc_final: 0.7563 (mmt) REVERT: M 317 ILE cc_start: 0.9489 (mt) cc_final: 0.8990 (tt) REVERT: M 325 MET cc_start: 0.7511 (tpp) cc_final: 0.6095 (tpp) REVERT: M 338 HIS cc_start: 0.8406 (m-70) cc_final: 0.8054 (m170) REVERT: M 383 MET cc_start: 0.9103 (mmp) cc_final: 0.8518 (mmp) REVERT: M 437 MET cc_start: 0.8424 (mmp) cc_final: 0.7995 (mmp) REVERT: M 446 LEU cc_start: 0.9138 (mt) cc_final: 0.8124 (tt) REVERT: N 14 MET cc_start: 0.7886 (mmt) cc_final: 0.7640 (mmp) REVERT: N 36 ASN cc_start: 0.9023 (m-40) cc_final: 0.8286 (m-40) REVERT: N 38 LEU cc_start: 0.9431 (mt) cc_final: 0.9182 (mt) REVERT: N 58 LYS cc_start: 0.9206 (ttmt) cc_final: 0.8150 (ttmt) REVERT: N 61 LEU cc_start: 0.9523 (mt) cc_final: 0.9211 (tp) REVERT: N 72 MET cc_start: 0.7974 (mmm) cc_final: 0.7523 (mmm) REVERT: N 117 GLU cc_start: 0.8561 (mt-10) cc_final: 0.7959 (pt0) REVERT: O 107 GLN cc_start: 0.8887 (pt0) cc_final: 0.7640 (mm-40) REVERT: O 162 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8274 (tm-30) REVERT: W 36 ARG cc_start: 0.8012 (tpt170) cc_final: 0.7747 (ttm-80) REVERT: W 41 GLU cc_start: 0.8030 (tp30) cc_final: 0.7607 (tp30) REVERT: W 57 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7734 (tm-30) REVERT: W 61 LYS cc_start: 0.7035 (ttmt) cc_final: 0.6619 (tptm) REVERT: X 31 TYR cc_start: 0.8230 (t80) cc_final: 0.7930 (t80) REVERT: X 50 LYS cc_start: 0.7059 (tttt) cc_final: 0.5899 (mptt) REVERT: Y 39 SER cc_start: 0.8747 (m) cc_final: 0.8470 (m) REVERT: Y 89 TYR cc_start: 0.6759 (m-10) cc_final: 0.6078 (m-10) REVERT: Z 55 GLU cc_start: 0.8366 (tp30) cc_final: 0.8001 (tp30) REVERT: Z 77 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8086 (mt-10) REVERT: Z 91 GLU cc_start: 0.9079 (tp30) cc_final: 0.8697 (tp30) REVERT: a 1 MET cc_start: 0.7025 (mpp) cc_final: 0.6407 (tpt) REVERT: b 40 TYR cc_start: 0.7845 (m-80) cc_final: 0.7588 (m-80) REVERT: d 33 PHE cc_start: 0.8832 (t80) cc_final: 0.8430 (t80) REVERT: d 49 ARG cc_start: 0.8474 (mtt90) cc_final: 0.7784 (tpt170) REVERT: d 73 TYR cc_start: 0.8739 (t80) cc_final: 0.8457 (t80) REVERT: d 87 ASP cc_start: 0.7762 (t0) cc_final: 0.7025 (t0) REVERT: e 41 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7969 (tm-30) REVERT: e 67 LEU cc_start: 0.9021 (mm) cc_final: 0.8765 (mp) REVERT: e 83 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7257 (tp30) REVERT: f 22 PHE cc_start: 0.8536 (t80) cc_final: 0.8317 (t80) REVERT: g 99 TYR cc_start: 0.8703 (t80) cc_final: 0.8420 (t80) REVERT: h 38 ILE cc_start: 0.8292 (mm) cc_final: 0.7592 (tt) REVERT: i 16 GLU cc_start: 0.9184 (pt0) cc_final: 0.8970 (pt0) REVERT: i 20 ARG cc_start: 0.8828 (mtm110) cc_final: 0.7868 (ppt170) REVERT: m 48 LEU cc_start: 0.9587 (mt) cc_final: 0.9245 (tt) REVERT: m 80 ARG cc_start: 0.7480 (ptm160) cc_final: 0.7059 (mmp-170) REVERT: m 84 LYS cc_start: 0.7485 (mptt) cc_final: 0.6286 (pttp) REVERT: m 100 TRP cc_start: 0.7721 (m100) cc_final: 0.7405 (m100) REVERT: n 23 LEU cc_start: 0.8596 (mt) cc_final: 0.8132 (tp) REVERT: n 27 GLU cc_start: 0.8565 (tt0) cc_final: 0.8110 (tm-30) REVERT: p 86 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7994 (mm-30) outliers start: 1 outliers final: 0 residues processed: 971 average time/residue: 0.6194 time to fit residues: 1037.4705 Evaluate side-chains 778 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 778 time to evaluate : 4.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 508 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 300 optimal weight: 3.9990 chunk 385 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 chunk 443 optimal weight: 3.9990 chunk 294 optimal weight: 1.9990 chunk 525 optimal weight: 30.0000 chunk 328 optimal weight: 9.9990 chunk 320 optimal weight: 3.9990 chunk 242 optimal weight: 0.8980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN D 79 HIS D 114 ASN D 357 GLN ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 HIS H 235 ASN ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 210 ASN M 81 GLN ** M 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 HIS ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 HIS ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 232 HIS ** O 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 53 ASN ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 12 GLN p 133 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.279 52088 Z= 0.576 Angle : 1.801 50.981 71507 Z= 1.158 Chirality : 0.332 6.454 8766 Planarity : 0.005 0.144 9352 Dihedral : 5.229 163.313 8196 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 1.18 % Allowed : 8.35 % Favored : 90.47 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.11), residues: 5784 helix: 0.28 (0.10), residues: 3034 sheet: 0.31 (0.46), residues: 147 loop : -2.55 (0.12), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 196 HIS 0.016 0.001 HIS O 167 PHE 0.024 0.002 PHE K 66 TYR 0.025 0.001 TYR M 406 ARG 0.010 0.000 ARG M 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 960 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: A 12 THR cc_start: 0.9094 (p) cc_final: 0.8812 (t) REVERT: B 116 MET cc_start: 0.8161 (ttp) cc_final: 0.7900 (tmm) REVERT: D 82 LEU cc_start: 0.9130 (mt) cc_final: 0.8864 (mt) REVERT: D 98 GLN cc_start: 0.9115 (tt0) cc_final: 0.8694 (mt0) REVERT: D 136 TRP cc_start: 0.8804 (m100) cc_final: 0.8447 (m100) REVERT: D 167 PHE cc_start: 0.8631 (t80) cc_final: 0.8213 (t80) REVERT: D 169 TRP cc_start: 0.8937 (m-10) cc_final: 0.7882 (m100) REVERT: D 239 THR cc_start: 0.8335 (p) cc_final: 0.7678 (t) REVERT: D 318 MET cc_start: 0.8617 (tpp) cc_final: 0.8224 (tpp) REVERT: D 405 MET cc_start: 0.8659 (mmm) cc_final: 0.8199 (tpp) REVERT: F 389 ILE cc_start: 0.8938 (pt) cc_final: 0.8685 (tp) REVERT: G 45 ARG cc_start: 0.7657 (mpt90) cc_final: 0.6192 (ttp-170) REVERT: H 24 GLU cc_start: 0.8305 (tt0) cc_final: 0.8055 (tm-30) REVERT: H 25 ARG cc_start: 0.7579 (mmt180) cc_final: 0.7105 (mmt180) REVERT: H 31 MET cc_start: 0.9189 (mmm) cc_final: 0.8897 (mmm) REVERT: H 121 TRP cc_start: 0.8162 (m100) cc_final: 0.7738 (m100) REVERT: H 138 GLN cc_start: 0.7574 (mt0) cc_final: 0.7373 (mt0) REVERT: H 141 SER cc_start: 0.9018 (m) cc_final: 0.8202 (t) REVERT: H 176 LEU cc_start: 0.9130 (mt) cc_final: 0.8835 (tp) REVERT: H 183 MET cc_start: 0.7780 (tmm) cc_final: 0.7379 (tmm) REVERT: H 248 ASN cc_start: 0.8634 (t0) cc_final: 0.8130 (t0) REVERT: H 303 TRP cc_start: 0.8867 (t-100) cc_final: 0.8644 (t-100) REVERT: I 18 THR cc_start: 0.8935 (t) cc_final: 0.8730 (t) REVERT: I 54 LYS cc_start: 0.8460 (mmtp) cc_final: 0.7706 (tttt) REVERT: I 90 GLN cc_start: 0.8209 (mt0) cc_final: 0.7624 (mm-40) REVERT: I 138 GLU cc_start: 0.6900 (tt0) cc_final: 0.5963 (tm-30) REVERT: I 150 ASN cc_start: 0.8210 (p0) cc_final: 0.7995 (p0) REVERT: J 74 MET cc_start: 0.8593 (mmp) cc_final: 0.7854 (tpt) REVERT: J 102 PHE cc_start: 0.7548 (t80) cc_final: 0.7241 (t80) REVERT: K 6 MET cc_start: 0.7400 (mmt) cc_final: 0.6642 (mtt) REVERT: K 7 ASN cc_start: 0.8898 (p0) cc_final: 0.8568 (p0) REVERT: K 59 MET cc_start: 0.8085 (mtt) cc_final: 0.7638 (mtp) REVERT: L 14 LEU cc_start: 0.9189 (mt) cc_final: 0.8888 (tp) REVERT: L 16 THR cc_start: 0.9520 (p) cc_final: 0.8538 (t) REVERT: L 20 MET cc_start: 0.8970 (mmm) cc_final: 0.8225 (mpp) REVERT: L 21 MET cc_start: 0.7736 (mmp) cc_final: 0.7405 (ttt) REVERT: L 88 MET cc_start: 0.8538 (tpp) cc_final: 0.8317 (mpp) REVERT: L 145 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7827 (tm-30) REVERT: L 157 TRP cc_start: 0.9136 (t-100) cc_final: 0.8426 (t60) REVERT: L 279 CYS cc_start: 0.7965 (t) cc_final: 0.7701 (t) REVERT: L 291 CYS cc_start: 0.8619 (m) cc_final: 0.8318 (m) REVERT: L 366 MET cc_start: 0.8374 (tpp) cc_final: 0.8001 (tpp) REVERT: L 389 PHE cc_start: 0.6160 (t80) cc_final: 0.5880 (t80) REVERT: L 393 ASP cc_start: 0.7886 (m-30) cc_final: 0.7474 (m-30) REVERT: L 524 THR cc_start: 0.8840 (p) cc_final: 0.8636 (p) REVERT: L 535 ARG cc_start: 0.5202 (tpt170) cc_final: 0.3987 (ttt-90) REVERT: L 571 MET cc_start: 0.7128 (tpt) cc_final: 0.5883 (ttm) REVERT: L 599 MET cc_start: 0.8671 (mmm) cc_final: 0.7762 (tpt) REVERT: M 317 ILE cc_start: 0.9506 (mt) cc_final: 0.9022 (tt) REVERT: M 325 MET cc_start: 0.7459 (tpp) cc_final: 0.6195 (tpp) REVERT: M 338 HIS cc_start: 0.8353 (m-70) cc_final: 0.8024 (m170) REVERT: M 383 MET cc_start: 0.9200 (mmp) cc_final: 0.8574 (mmp) REVERT: M 437 MET cc_start: 0.8640 (mmp) cc_final: 0.8214 (mmp) REVERT: N 14 MET cc_start: 0.7995 (mmt) cc_final: 0.7645 (mmp) REVERT: N 34 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8389 (mm-30) REVERT: N 36 ASN cc_start: 0.9008 (m-40) cc_final: 0.8430 (m-40) REVERT: N 58 LYS cc_start: 0.9220 (ttmt) cc_final: 0.8156 (ttmt) REVERT: N 61 LEU cc_start: 0.9544 (mt) cc_final: 0.9212 (tp) REVERT: N 72 MET cc_start: 0.8100 (mmm) cc_final: 0.7841 (mmm) REVERT: N 117 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7784 (pt0) REVERT: N 240 MET cc_start: 0.8697 (ttm) cc_final: 0.8483 (ttm) REVERT: N 254 LEU cc_start: 0.8732 (mt) cc_final: 0.8422 (mt) REVERT: O 107 GLN cc_start: 0.8869 (pt0) cc_final: 0.7599 (mm-40) REVERT: O 162 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8183 (tm-30) REVERT: W 36 ARG cc_start: 0.8053 (tpt170) cc_final: 0.7683 (ttm110) REVERT: W 41 GLU cc_start: 0.8058 (tp30) cc_final: 0.7539 (tp30) REVERT: W 57 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7809 (tm-30) REVERT: W 61 LYS cc_start: 0.7049 (ttmt) cc_final: 0.6605 (tptm) REVERT: W 92 THR cc_start: 0.8305 (p) cc_final: 0.8079 (p) REVERT: X 31 TYR cc_start: 0.8276 (t80) cc_final: 0.7869 (t80) REVERT: X 50 LYS cc_start: 0.7038 (tttt) cc_final: 0.5488 (tppt) REVERT: X 71 ARG cc_start: 0.8874 (mtm180) cc_final: 0.8639 (mtm-85) REVERT: X 107 ASP cc_start: 0.7404 (m-30) cc_final: 0.7166 (m-30) REVERT: X 108 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8177 (mm-30) REVERT: Y 89 TYR cc_start: 0.7070 (m-10) cc_final: 0.6312 (m-10) REVERT: Z 55 GLU cc_start: 0.8421 (tp30) cc_final: 0.8056 (tp30) REVERT: Z 77 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8136 (mt-10) REVERT: Z 91 GLU cc_start: 0.8940 (tp30) cc_final: 0.8537 (tp30) REVERT: b 40 TYR cc_start: 0.7885 (m-80) cc_final: 0.7641 (m-80) REVERT: d 33 PHE cc_start: 0.8890 (t80) cc_final: 0.8417 (t80) REVERT: d 49 ARG cc_start: 0.8469 (mtt90) cc_final: 0.7758 (tpt170) REVERT: d 73 TYR cc_start: 0.8814 (t80) cc_final: 0.8514 (t80) REVERT: d 87 ASP cc_start: 0.7881 (t0) cc_final: 0.6970 (t0) REVERT: e 41 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7934 (tm-30) REVERT: e 67 LEU cc_start: 0.8916 (mm) cc_final: 0.8654 (mp) REVERT: e 83 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7268 (tp30) REVERT: g 67 SER cc_start: 0.7401 (p) cc_final: 0.7193 (p) REVERT: g 99 TYR cc_start: 0.8735 (t80) cc_final: 0.8490 (t80) REVERT: h 38 ILE cc_start: 0.8297 (mm) cc_final: 0.7607 (tt) REVERT: i 16 GLU cc_start: 0.9196 (pt0) cc_final: 0.8993 (pt0) REVERT: i 20 ARG cc_start: 0.8898 (mtm110) cc_final: 0.7905 (ppt170) REVERT: m 48 LEU cc_start: 0.9588 (mt) cc_final: 0.9242 (tt) REVERT: m 80 ARG cc_start: 0.7465 (ptm160) cc_final: 0.7063 (mmp-170) REVERT: m 84 LYS cc_start: 0.7484 (mptt) cc_final: 0.6295 (pttp) REVERT: m 100 TRP cc_start: 0.7953 (m100) cc_final: 0.7414 (m100) REVERT: n 23 LEU cc_start: 0.8667 (mt) cc_final: 0.8215 (tp) REVERT: n 27 GLU cc_start: 0.8607 (tt0) cc_final: 0.8179 (tm-30) REVERT: p 86 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8111 (mm-30) outliers start: 0 outliers final: 0 residues processed: 960 average time/residue: 0.5841 time to fit residues: 961.4652 Evaluate side-chains 773 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 773 time to evaluate : 5.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 324 optimal weight: 0.0040 chunk 209 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 101 optimal weight: 50.0000 chunk 333 optimal weight: 0.9990 chunk 357 optimal weight: 10.0000 chunk 259 optimal weight: 0.0470 chunk 48 optimal weight: 5.9990 chunk 412 optimal weight: 9.9990 overall best weight: 1.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 HIS F 421 HIS G 119 GLN ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN ** M 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 HIS ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN N 232 HIS ** O 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 72 GLN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 52 ASN p 133 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.276 52088 Z= 0.571 Angle : 1.800 51.016 71507 Z= 1.156 Chirality : 0.331 6.431 8766 Planarity : 0.004 0.142 9352 Dihedral : 5.161 163.528 8196 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 1.14 % Allowed : 8.02 % Favored : 90.84 % Rotamer: Outliers : 0.03 % Allowed : 1.37 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.11), residues: 5784 helix: 0.35 (0.10), residues: 3034 sheet: 0.15 (0.45), residues: 157 loop : -2.51 (0.12), residues: 2593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP X 47 HIS 0.015 0.001 HIS O 167 PHE 0.019 0.001 PHE J 47 TYR 0.035 0.001 TYR D 108 ARG 0.018 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 964 time to evaluate : 5.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.9087 (p) cc_final: 0.8829 (t) REVERT: A 69 ILE cc_start: 0.9524 (mm) cc_final: 0.8649 (mm) REVERT: B 84 ASP cc_start: 0.7455 (p0) cc_final: 0.6904 (p0) REVERT: B 116 MET cc_start: 0.8026 (ttp) cc_final: 0.7788 (ttp) REVERT: D 82 LEU cc_start: 0.9139 (mt) cc_final: 0.8839 (mt) REVERT: D 98 GLN cc_start: 0.9063 (tt0) cc_final: 0.8612 (mt0) REVERT: D 167 PHE cc_start: 0.8518 (t80) cc_final: 0.8111 (t80) REVERT: D 169 TRP cc_start: 0.8809 (m-10) cc_final: 0.7792 (m100) REVERT: D 189 MET cc_start: 0.7856 (tmm) cc_final: 0.7580 (tmm) REVERT: D 208 MET cc_start: 0.7352 (mtt) cc_final: 0.7147 (mtt) REVERT: D 239 THR cc_start: 0.8314 (p) cc_final: 0.7641 (t) REVERT: D 302 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6893 (mm-30) REVERT: D 318 MET cc_start: 0.8692 (tpp) cc_final: 0.8381 (tpp) REVERT: D 405 MET cc_start: 0.8689 (mmm) cc_final: 0.8409 (tpp) REVERT: F 370 ASP cc_start: 0.7114 (m-30) cc_final: 0.6856 (t0) REVERT: G 45 ARG cc_start: 0.7740 (mpt90) cc_final: 0.7074 (mtp180) REVERT: H 24 GLU cc_start: 0.8255 (tt0) cc_final: 0.7982 (tm-30) REVERT: H 25 ARG cc_start: 0.7574 (mmt180) cc_final: 0.7200 (mmt180) REVERT: H 31 MET cc_start: 0.9137 (mmm) cc_final: 0.8654 (tpp) REVERT: H 46 LEU cc_start: 0.8818 (mt) cc_final: 0.8605 (mt) REVERT: H 121 TRP cc_start: 0.8172 (m100) cc_final: 0.7690 (m100) REVERT: H 141 SER cc_start: 0.8932 (m) cc_final: 0.8291 (t) REVERT: H 176 LEU cc_start: 0.9138 (mt) cc_final: 0.8823 (tp) REVERT: H 268 MET cc_start: 0.8612 (mmp) cc_final: 0.8169 (ttp) REVERT: H 303 TRP cc_start: 0.8850 (t-100) cc_final: 0.8599 (t-100) REVERT: I 54 LYS cc_start: 0.8468 (mmtp) cc_final: 0.7601 (tttt) REVERT: I 90 GLN cc_start: 0.8171 (mt0) cc_final: 0.7557 (mm-40) REVERT: I 138 GLU cc_start: 0.6953 (tt0) cc_final: 0.6450 (tt0) REVERT: J 74 MET cc_start: 0.8658 (mmp) cc_final: 0.7856 (tpt) REVERT: J 102 PHE cc_start: 0.7501 (t80) cc_final: 0.7188 (t80) REVERT: K 6 MET cc_start: 0.7362 (mmt) cc_final: 0.6520 (mtt) REVERT: K 7 ASN cc_start: 0.8954 (p0) cc_final: 0.8497 (p0) REVERT: K 59 MET cc_start: 0.8333 (mtt) cc_final: 0.7820 (mtp) REVERT: L 14 LEU cc_start: 0.9195 (mt) cc_final: 0.8946 (tp) REVERT: L 21 MET cc_start: 0.7649 (mmp) cc_final: 0.7334 (ttt) REVERT: L 88 MET cc_start: 0.8729 (tpp) cc_final: 0.8519 (mpp) REVERT: L 145 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7747 (tm-30) REVERT: L 279 CYS cc_start: 0.7989 (t) cc_final: 0.7680 (t) REVERT: L 291 CYS cc_start: 0.8543 (m) cc_final: 0.8202 (m) REVERT: L 297 ASP cc_start: 0.7041 (t0) cc_final: 0.6760 (m-30) REVERT: L 326 PHE cc_start: 0.8804 (t80) cc_final: 0.8559 (t80) REVERT: L 366 MET cc_start: 0.8359 (tpp) cc_final: 0.8013 (tpp) REVERT: L 389 PHE cc_start: 0.6295 (t80) cc_final: 0.6068 (t80) REVERT: L 393 ASP cc_start: 0.7919 (m-30) cc_final: 0.7473 (m-30) REVERT: L 524 THR cc_start: 0.8872 (p) cc_final: 0.8607 (p) REVERT: L 535 ARG cc_start: 0.5041 (tpt170) cc_final: 0.3962 (ttt-90) REVERT: L 571 MET cc_start: 0.7101 (tpt) cc_final: 0.5837 (ttm) REVERT: L 599 MET cc_start: 0.8646 (mmm) cc_final: 0.7753 (tpt) REVERT: M 76 MET cc_start: 0.7983 (mtt) cc_final: 0.7512 (mtp) REVERT: M 204 MET cc_start: 0.7971 (mmt) cc_final: 0.7609 (mmt) REVERT: M 207 MET cc_start: 0.8699 (mtt) cc_final: 0.8348 (mtt) REVERT: M 250 LEU cc_start: 0.8910 (mm) cc_final: 0.8708 (mm) REVERT: M 269 MET cc_start: 0.7328 (tpt) cc_final: 0.6980 (tpt) REVERT: M 317 ILE cc_start: 0.9482 (mt) cc_final: 0.9062 (tt) REVERT: M 325 MET cc_start: 0.7535 (tpp) cc_final: 0.5902 (tpp) REVERT: M 329 LEU cc_start: 0.9359 (mt) cc_final: 0.9148 (mt) REVERT: M 338 HIS cc_start: 0.8260 (m-70) cc_final: 0.7923 (m170) REVERT: M 383 MET cc_start: 0.9110 (mmp) cc_final: 0.8525 (mmp) REVERT: M 437 MET cc_start: 0.8811 (mmp) cc_final: 0.8383 (mmp) REVERT: N 14 MET cc_start: 0.7907 (mmt) cc_final: 0.7602 (mmp) REVERT: N 36 ASN cc_start: 0.8961 (m-40) cc_final: 0.8416 (m-40) REVERT: N 58 LYS cc_start: 0.9224 (ttmt) cc_final: 0.8991 (ttpt) REVERT: N 61 LEU cc_start: 0.9510 (mt) cc_final: 0.9203 (tp) REVERT: N 112 HIS cc_start: 0.8486 (p90) cc_final: 0.8036 (p-80) REVERT: N 281 PHE cc_start: 0.8616 (t80) cc_final: 0.8287 (t80) REVERT: O 107 GLN cc_start: 0.8865 (pt0) cc_final: 0.7622 (mm-40) REVERT: O 136 GLU cc_start: 0.8830 (tp30) cc_final: 0.8432 (tp30) REVERT: O 162 GLU cc_start: 0.8248 (tm-30) cc_final: 0.8047 (tm-30) REVERT: V 48 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8449 (mm-30) REVERT: W 36 ARG cc_start: 0.8044 (tpt170) cc_final: 0.7726 (ttm-80) REVERT: W 41 GLU cc_start: 0.8003 (tp30) cc_final: 0.7437 (tp30) REVERT: W 57 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7747 (tm-30) REVERT: W 61 LYS cc_start: 0.7212 (ttmt) cc_final: 0.6811 (tptm) REVERT: W 92 THR cc_start: 0.8260 (p) cc_final: 0.8014 (p) REVERT: X 31 TYR cc_start: 0.8294 (t80) cc_final: 0.7832 (t80) REVERT: X 50 LYS cc_start: 0.6988 (tttt) cc_final: 0.6117 (mptt) REVERT: X 81 PHE cc_start: 0.8629 (t80) cc_final: 0.8242 (t80) REVERT: X 95 LEU cc_start: 0.7267 (tt) cc_final: 0.7016 (mt) REVERT: X 108 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8121 (mm-30) REVERT: Z 55 GLU cc_start: 0.8444 (tp30) cc_final: 0.8081 (tp30) REVERT: Z 57 ARG cc_start: 0.8834 (mmm-85) cc_final: 0.8608 (mmm-85) REVERT: Z 75 GLN cc_start: 0.7944 (pp30) cc_final: 0.7677 (pp30) REVERT: Z 77 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8114 (mt-10) REVERT: Z 91 GLU cc_start: 0.8937 (tp30) cc_final: 0.8549 (tp30) REVERT: b 40 TYR cc_start: 0.7879 (m-80) cc_final: 0.7623 (m-80) REVERT: d 33 PHE cc_start: 0.8939 (t80) cc_final: 0.8589 (t80) REVERT: d 49 ARG cc_start: 0.8403 (mtt90) cc_final: 0.7928 (tpt170) REVERT: d 73 TYR cc_start: 0.8807 (t80) cc_final: 0.8517 (t80) REVERT: d 87 ASP cc_start: 0.7833 (t0) cc_final: 0.6939 (t0) REVERT: e 41 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7923 (tm-30) REVERT: e 67 LEU cc_start: 0.8957 (mm) cc_final: 0.8733 (mp) REVERT: e 83 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7215 (tp30) REVERT: g 58 MET cc_start: 0.6148 (mmt) cc_final: 0.5498 (mmm) REVERT: g 67 SER cc_start: 0.7375 (p) cc_final: 0.7160 (p) REVERT: g 99 TYR cc_start: 0.8713 (t80) cc_final: 0.8509 (t80) REVERT: h 38 ILE cc_start: 0.8212 (mm) cc_final: 0.7588 (tt) REVERT: i 16 GLU cc_start: 0.9192 (pt0) cc_final: 0.8992 (pt0) REVERT: i 20 ARG cc_start: 0.8906 (mtm110) cc_final: 0.7924 (ppt170) REVERT: m 48 LEU cc_start: 0.9584 (mt) cc_final: 0.9245 (tt) REVERT: m 80 ARG cc_start: 0.7449 (ptm160) cc_final: 0.7067 (mmp-170) REVERT: m 84 LYS cc_start: 0.7568 (mptt) cc_final: 0.6220 (pttp) REVERT: m 100 TRP cc_start: 0.7983 (m100) cc_final: 0.7337 (m100) REVERT: n 20 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8711 (tppt) REVERT: n 23 LEU cc_start: 0.8651 (mt) cc_final: 0.8199 (tp) REVERT: n 27 GLU cc_start: 0.8636 (tt0) cc_final: 0.8244 (tm-30) REVERT: p 86 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8137 (mm-30) outliers start: 1 outliers final: 0 residues processed: 965 average time/residue: 0.6408 time to fit residues: 1066.5579 Evaluate side-chains 786 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 786 time to evaluate : 5.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 477 optimal weight: 0.9980 chunk 503 optimal weight: 10.0000 chunk 459 optimal weight: 2.9990 chunk 489 optimal weight: 20.0000 chunk 294 optimal weight: 0.0270 chunk 213 optimal weight: 7.9990 chunk 384 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 442 optimal weight: 0.9990 chunk 462 optimal weight: 0.0000 chunk 487 optimal weight: 20.0000 overall best weight: 1.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 HIS ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 HIS L 296 ASN M 81 GLN ** M 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 HIS ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 2 ASN N 232 HIS O 167 HIS ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 72 GLN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 GLN Z 53 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.267 52088 Z= 0.570 Angle : 1.800 50.938 71507 Z= 1.156 Chirality : 0.332 6.519 8766 Planarity : 0.004 0.140 9352 Dihedral : 5.085 163.250 8196 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 1.11 % Allowed : 8.07 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.11), residues: 5784 helix: 0.40 (0.10), residues: 3040 sheet: -0.11 (0.46), residues: 147 loop : -2.48 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 407 HIS 0.015 0.001 HIS D 190 PHE 0.025 0.001 PHE D 167 TYR 0.037 0.001 TYR M 406 ARG 0.009 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 950 time to evaluate : 5.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.9077 (p) cc_final: 0.8789 (t) REVERT: A 69 ILE cc_start: 0.9409 (mm) cc_final: 0.8850 (mm) REVERT: B 84 ASP cc_start: 0.7512 (p0) cc_final: 0.6814 (p0) REVERT: B 116 MET cc_start: 0.8075 (ttp) cc_final: 0.7817 (ttp) REVERT: B 160 ILE cc_start: 0.8457 (mm) cc_final: 0.8245 (mm) REVERT: D 66 MET cc_start: 0.8318 (mmm) cc_final: 0.7806 (mmm) REVERT: D 98 GLN cc_start: 0.9022 (tt0) cc_final: 0.8549 (mt0) REVERT: D 136 TRP cc_start: 0.8776 (m100) cc_final: 0.8521 (m100) REVERT: D 167 PHE cc_start: 0.8368 (t80) cc_final: 0.8062 (t80) REVERT: D 169 TRP cc_start: 0.8773 (m-10) cc_final: 0.7770 (m100) REVERT: D 190 HIS cc_start: 0.6358 (m-70) cc_final: 0.5578 (m-70) REVERT: D 208 MET cc_start: 0.7344 (mtt) cc_final: 0.7139 (mtt) REVERT: D 239 THR cc_start: 0.8377 (p) cc_final: 0.7743 (t) REVERT: D 318 MET cc_start: 0.8713 (tpp) cc_final: 0.8412 (tpp) REVERT: D 405 MET cc_start: 0.8696 (mmm) cc_final: 0.8314 (tpp) REVERT: F 389 ILE cc_start: 0.8918 (pt) cc_final: 0.8667 (tp) REVERT: F 409 ASP cc_start: 0.7881 (m-30) cc_final: 0.7275 (m-30) REVERT: G 45 ARG cc_start: 0.7674 (mpt90) cc_final: 0.6950 (mtp180) REVERT: H 24 GLU cc_start: 0.8209 (tt0) cc_final: 0.7906 (tm-30) REVERT: H 25 ARG cc_start: 0.7574 (mmt180) cc_final: 0.7211 (mmt180) REVERT: H 31 MET cc_start: 0.9154 (mmm) cc_final: 0.8653 (tpp) REVERT: H 121 TRP cc_start: 0.8132 (m100) cc_final: 0.7762 (m100) REVERT: H 141 SER cc_start: 0.9043 (m) cc_final: 0.8429 (t) REVERT: H 176 LEU cc_start: 0.9124 (mt) cc_final: 0.8817 (tp) REVERT: H 248 ASN cc_start: 0.8563 (t0) cc_final: 0.8116 (t0) REVERT: H 268 MET cc_start: 0.8609 (mmp) cc_final: 0.8143 (ttp) REVERT: H 303 TRP cc_start: 0.8784 (t-100) cc_final: 0.8548 (t-100) REVERT: I 54 LYS cc_start: 0.8501 (mmtp) cc_final: 0.7851 (tttt) REVERT: I 90 GLN cc_start: 0.8220 (mt0) cc_final: 0.7550 (mm-40) REVERT: I 138 GLU cc_start: 0.7033 (tt0) cc_final: 0.6756 (tt0) REVERT: J 74 MET cc_start: 0.8580 (mmp) cc_final: 0.7725 (tpt) REVERT: J 102 PHE cc_start: 0.7517 (t80) cc_final: 0.7209 (t80) REVERT: K 6 MET cc_start: 0.7315 (mmt) cc_final: 0.6445 (mtt) REVERT: K 7 ASN cc_start: 0.8927 (p0) cc_final: 0.8500 (p0) REVERT: K 37 MET cc_start: 0.8086 (mmm) cc_final: 0.7627 (mmm) REVERT: K 59 MET cc_start: 0.8286 (mtt) cc_final: 0.7787 (mtp) REVERT: L 14 LEU cc_start: 0.9262 (mt) cc_final: 0.9008 (tp) REVERT: L 21 MET cc_start: 0.7617 (mmp) cc_final: 0.7289 (ttt) REVERT: L 145 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7745 (tm-30) REVERT: L 291 CYS cc_start: 0.8297 (m) cc_final: 0.8089 (m) REVERT: L 352 ASP cc_start: 0.7603 (t70) cc_final: 0.7326 (t0) REVERT: L 366 MET cc_start: 0.8335 (tpp) cc_final: 0.7995 (tpp) REVERT: L 389 PHE cc_start: 0.6334 (t80) cc_final: 0.6075 (t80) REVERT: L 393 ASP cc_start: 0.7867 (m-30) cc_final: 0.7441 (m-30) REVERT: L 524 THR cc_start: 0.9000 (p) cc_final: 0.8754 (p) REVERT: L 535 ARG cc_start: 0.5283 (tpt170) cc_final: 0.4048 (ttt-90) REVERT: L 571 MET cc_start: 0.7072 (tpt) cc_final: 0.5834 (ttm) REVERT: L 599 MET cc_start: 0.8637 (mmm) cc_final: 0.7713 (tpt) REVERT: M 76 MET cc_start: 0.8010 (mtt) cc_final: 0.7599 (mtt) REVERT: M 204 MET cc_start: 0.7857 (mmt) cc_final: 0.7565 (ptp) REVERT: M 207 MET cc_start: 0.8658 (mtt) cc_final: 0.8179 (mtt) REVERT: M 236 LEU cc_start: 0.8434 (mt) cc_final: 0.8219 (mt) REVERT: M 250 LEU cc_start: 0.8897 (mm) cc_final: 0.8640 (mm) REVERT: M 317 ILE cc_start: 0.9538 (mt) cc_final: 0.9026 (tt) REVERT: M 325 MET cc_start: 0.7378 (tpp) cc_final: 0.5893 (tpp) REVERT: M 338 HIS cc_start: 0.8286 (m-70) cc_final: 0.7949 (m170) REVERT: M 383 MET cc_start: 0.9095 (mmp) cc_final: 0.8507 (mmp) REVERT: M 446 LEU cc_start: 0.9150 (mt) cc_final: 0.8103 (tt) REVERT: N 14 MET cc_start: 0.7841 (mmt) cc_final: 0.7578 (mmp) REVERT: N 35 MET cc_start: 0.8232 (mmm) cc_final: 0.7577 (tpp) REVERT: N 36 ASN cc_start: 0.8843 (m-40) cc_final: 0.8363 (m-40) REVERT: N 58 LYS cc_start: 0.9219 (ttmt) cc_final: 0.9001 (ttpt) REVERT: N 61 LEU cc_start: 0.9519 (mt) cc_final: 0.9193 (tp) REVERT: N 96 MET cc_start: 0.4638 (mtt) cc_final: 0.4273 (mmt) REVERT: N 112 HIS cc_start: 0.8290 (p90) cc_final: 0.7850 (p-80) REVERT: N 281 PHE cc_start: 0.8531 (t80) cc_final: 0.8246 (t80) REVERT: N 302 LEU cc_start: 0.8080 (mt) cc_final: 0.7764 (mt) REVERT: O 107 GLN cc_start: 0.8864 (pt0) cc_final: 0.7613 (mm-40) REVERT: O 136 GLU cc_start: 0.8845 (tp30) cc_final: 0.8445 (tp30) REVERT: O 162 GLU cc_start: 0.8222 (tm-30) cc_final: 0.8012 (tm-30) REVERT: W 36 ARG cc_start: 0.8091 (tpt170) cc_final: 0.7762 (ttm110) REVERT: W 41 GLU cc_start: 0.7982 (tp30) cc_final: 0.7424 (tp30) REVERT: W 57 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7710 (tm-30) REVERT: W 61 LYS cc_start: 0.7207 (ttmt) cc_final: 0.6809 (tptm) REVERT: X 31 TYR cc_start: 0.8187 (t80) cc_final: 0.7719 (t80) REVERT: X 50 LYS cc_start: 0.7344 (tttt) cc_final: 0.6060 (mptt) REVERT: X 81 PHE cc_start: 0.8367 (t80) cc_final: 0.8112 (t80) REVERT: X 95 LEU cc_start: 0.7085 (tt) cc_final: 0.6871 (mt) REVERT: X 107 ASP cc_start: 0.7507 (m-30) cc_final: 0.7280 (m-30) REVERT: X 108 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8068 (mm-30) REVERT: Y 73 SER cc_start: 0.7914 (p) cc_final: 0.7115 (p) REVERT: Z 55 GLU cc_start: 0.8530 (tp30) cc_final: 0.8154 (tp30) REVERT: Z 57 ARG cc_start: 0.8843 (mmm-85) cc_final: 0.8574 (mmm-85) REVERT: Z 75 GLN cc_start: 0.7979 (pp30) cc_final: 0.7763 (pp30) REVERT: Z 91 GLU cc_start: 0.8953 (tp30) cc_final: 0.8565 (tp30) REVERT: b 24 ILE cc_start: 0.8879 (tp) cc_final: 0.8496 (tp) REVERT: b 40 TYR cc_start: 0.7902 (m-80) cc_final: 0.7652 (m-80) REVERT: d 33 PHE cc_start: 0.8943 (t80) cc_final: 0.8592 (t80) REVERT: d 49 ARG cc_start: 0.8393 (mtt90) cc_final: 0.7866 (tpt170) REVERT: d 73 TYR cc_start: 0.8789 (t80) cc_final: 0.8543 (t80) REVERT: d 87 ASP cc_start: 0.7648 (t0) cc_final: 0.6785 (t0) REVERT: e 41 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7916 (tm-30) REVERT: e 67 LEU cc_start: 0.8911 (mm) cc_final: 0.8681 (mp) REVERT: e 83 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7217 (tp30) REVERT: g 58 MET cc_start: 0.6256 (mmt) cc_final: 0.5566 (mmm) REVERT: g 67 SER cc_start: 0.7354 (p) cc_final: 0.7147 (p) REVERT: h 38 ILE cc_start: 0.8197 (mm) cc_final: 0.7582 (tt) REVERT: i 20 ARG cc_start: 0.8881 (mtm110) cc_final: 0.7904 (ppt170) REVERT: m 48 LEU cc_start: 0.9579 (mt) cc_final: 0.9245 (tt) REVERT: m 80 ARG cc_start: 0.7438 (ptm160) cc_final: 0.7108 (mmp-170) REVERT: m 84 LYS cc_start: 0.7553 (mptt) cc_final: 0.6192 (pttp) REVERT: n 20 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8687 (tppt) REVERT: n 23 LEU cc_start: 0.8570 (mt) cc_final: 0.8157 (tp) REVERT: n 27 GLU cc_start: 0.8621 (tt0) cc_final: 0.8259 (tm-30) REVERT: p 86 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8207 (mm-30) outliers start: 0 outliers final: 0 residues processed: 950 average time/residue: 0.5628 time to fit residues: 915.5321 Evaluate side-chains 775 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 775 time to evaluate : 5.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 321 optimal weight: 0.0060 chunk 517 optimal weight: 6.9990 chunk 315 optimal weight: 0.7980 chunk 245 optimal weight: 1.9990 chunk 359 optimal weight: 10.0000 chunk 542 optimal weight: 20.0000 chunk 499 optimal weight: 9.9990 chunk 432 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 333 optimal weight: 2.9990 chunk 265 optimal weight: 9.9990 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 GLN F 421 HIS ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN ** M 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 HIS ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN N 232 HIS ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 72 GLN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 133 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.267 52088 Z= 0.576 Angle : 1.806 50.995 71507 Z= 1.158 Chirality : 0.332 6.479 8766 Planarity : 0.004 0.141 9352 Dihedral : 5.143 162.364 8196 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 1.05 % Allowed : 8.49 % Favored : 90.46 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.11), residues: 5784 helix: 0.41 (0.10), residues: 3059 sheet: -0.21 (0.46), residues: 147 loop : -2.45 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 189 HIS 0.011 0.001 HIS D 190 PHE 0.039 0.002 PHE L 85 TYR 0.032 0.001 TYR D 108 ARG 0.019 0.001 ARG H 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 925 time to evaluate : 5.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.9092 (p) cc_final: 0.8829 (t) REVERT: A 69 ILE cc_start: 0.9424 (mm) cc_final: 0.8837 (mm) REVERT: D 66 MET cc_start: 0.8291 (mmm) cc_final: 0.7709 (mmm) REVERT: D 82 LEU cc_start: 0.9229 (mt) cc_final: 0.8878 (mt) REVERT: D 98 GLN cc_start: 0.9055 (tt0) cc_final: 0.8386 (mt0) REVERT: D 136 TRP cc_start: 0.8817 (m100) cc_final: 0.8539 (m100) REVERT: D 167 PHE cc_start: 0.8491 (t80) cc_final: 0.8065 (t80) REVERT: D 169 TRP cc_start: 0.8865 (m-10) cc_final: 0.7678 (m100) REVERT: D 190 HIS cc_start: 0.6644 (m-70) cc_final: 0.5119 (m-70) REVERT: D 239 THR cc_start: 0.8465 (p) cc_final: 0.7840 (t) REVERT: D 318 MET cc_start: 0.8754 (tpp) cc_final: 0.8318 (tpp) REVERT: D 405 MET cc_start: 0.8665 (mmm) cc_final: 0.8402 (tpp) REVERT: F 389 ILE cc_start: 0.8910 (pt) cc_final: 0.8691 (tp) REVERT: F 409 ASP cc_start: 0.7919 (m-30) cc_final: 0.7351 (m-30) REVERT: G 45 ARG cc_start: 0.7495 (mpt90) cc_final: 0.6333 (mtp180) REVERT: H 24 GLU cc_start: 0.8225 (tt0) cc_final: 0.7967 (tm-30) REVERT: H 25 ARG cc_start: 0.7604 (mmt180) cc_final: 0.7222 (mmt180) REVERT: H 46 LEU cc_start: 0.8917 (mt) cc_final: 0.8678 (mt) REVERT: H 121 TRP cc_start: 0.8181 (m100) cc_final: 0.7734 (m100) REVERT: H 141 SER cc_start: 0.9049 (m) cc_final: 0.8435 (t) REVERT: H 151 LEU cc_start: 0.9524 (tt) cc_final: 0.9297 (tp) REVERT: H 176 LEU cc_start: 0.9128 (mt) cc_final: 0.8812 (tp) REVERT: H 248 ASN cc_start: 0.8641 (t0) cc_final: 0.8202 (t0) REVERT: H 282 TYR cc_start: 0.8922 (t80) cc_final: 0.8421 (t80) REVERT: H 303 TRP cc_start: 0.8813 (t-100) cc_final: 0.8586 (t-100) REVERT: I 54 LYS cc_start: 0.8428 (mmtp) cc_final: 0.7728 (tttt) REVERT: I 90 GLN cc_start: 0.8197 (mt0) cc_final: 0.7433 (mm-40) REVERT: I 138 GLU cc_start: 0.6789 (tt0) cc_final: 0.5537 (tm-30) REVERT: J 55 MET cc_start: 0.8802 (tpp) cc_final: 0.8351 (tpp) REVERT: J 74 MET cc_start: 0.8639 (mmp) cc_final: 0.7804 (tpt) REVERT: J 102 PHE cc_start: 0.7552 (t80) cc_final: 0.7200 (t80) REVERT: J 169 MET cc_start: 0.6407 (ppp) cc_final: 0.6076 (ppp) REVERT: K 6 MET cc_start: 0.7329 (mmt) cc_final: 0.6752 (mtt) REVERT: K 7 ASN cc_start: 0.9010 (p0) cc_final: 0.8237 (p0) REVERT: K 37 MET cc_start: 0.8215 (mmm) cc_final: 0.7625 (mmm) REVERT: K 59 MET cc_start: 0.8183 (mtt) cc_final: 0.7581 (mtp) REVERT: L 14 LEU cc_start: 0.9194 (mt) cc_final: 0.8969 (tp) REVERT: L 21 MET cc_start: 0.7690 (mmp) cc_final: 0.7355 (ttt) REVERT: L 88 MET cc_start: 0.7878 (mpp) cc_final: 0.7663 (mpp) REVERT: L 145 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7797 (tm-30) REVERT: L 313 MET cc_start: 0.8010 (mtm) cc_final: 0.7480 (mtp) REVERT: L 352 ASP cc_start: 0.7726 (t70) cc_final: 0.7390 (t0) REVERT: L 366 MET cc_start: 0.8380 (tpp) cc_final: 0.8055 (tpp) REVERT: L 389 PHE cc_start: 0.6326 (t80) cc_final: 0.6092 (t80) REVERT: L 393 ASP cc_start: 0.7877 (m-30) cc_final: 0.7404 (m-30) REVERT: L 571 MET cc_start: 0.7246 (tpt) cc_final: 0.5847 (ttm) REVERT: L 599 MET cc_start: 0.8611 (mmm) cc_final: 0.7767 (tpt) REVERT: M 76 MET cc_start: 0.8048 (mtt) cc_final: 0.7672 (mtt) REVERT: M 200 MET cc_start: 0.8973 (mmp) cc_final: 0.8693 (mmp) REVERT: M 207 MET cc_start: 0.8739 (mtt) cc_final: 0.8287 (mtt) REVERT: M 236 LEU cc_start: 0.8384 (mt) cc_final: 0.8163 (mt) REVERT: M 250 LEU cc_start: 0.8821 (mm) cc_final: 0.8616 (mm) REVERT: M 317 ILE cc_start: 0.9522 (mt) cc_final: 0.9024 (tt) REVERT: M 325 MET cc_start: 0.7374 (tpp) cc_final: 0.6548 (tpp) REVERT: M 338 HIS cc_start: 0.8302 (m-70) cc_final: 0.7967 (m170) REVERT: N 36 ASN cc_start: 0.9130 (m-40) cc_final: 0.8488 (m-40) REVERT: N 58 LYS cc_start: 0.9164 (ttmt) cc_final: 0.8951 (ttpt) REVERT: N 61 LEU cc_start: 0.9553 (mt) cc_final: 0.9220 (tp) REVERT: N 78 LEU cc_start: 0.8638 (mm) cc_final: 0.8399 (mm) REVERT: N 187 MET cc_start: 0.8126 (mmp) cc_final: 0.7507 (mmm) REVERT: N 265 MET cc_start: 0.7891 (mpp) cc_final: 0.7526 (mpp) REVERT: N 281 PHE cc_start: 0.8562 (t80) cc_final: 0.8255 (t80) REVERT: O 107 GLN cc_start: 0.8890 (pt0) cc_final: 0.7636 (mm-40) REVERT: O 136 GLU cc_start: 0.8879 (tp30) cc_final: 0.8491 (tp30) REVERT: O 162 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8036 (tm-30) REVERT: W 36 ARG cc_start: 0.8094 (tpt170) cc_final: 0.7832 (ttm-80) REVERT: W 41 GLU cc_start: 0.8024 (tp30) cc_final: 0.7598 (tp30) REVERT: W 57 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7797 (tm-30) REVERT: W 61 LYS cc_start: 0.7389 (ttmt) cc_final: 0.6983 (tptm) REVERT: X 31 TYR cc_start: 0.8149 (t80) cc_final: 0.7651 (t80) REVERT: X 50 LYS cc_start: 0.7223 (tttt) cc_final: 0.5972 (mptt) REVERT: X 107 ASP cc_start: 0.7551 (m-30) cc_final: 0.7197 (m-30) REVERT: X 108 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8080 (mm-30) REVERT: Z 55 GLU cc_start: 0.8655 (tp30) cc_final: 0.8277 (tp30) REVERT: Z 77 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8419 (mt-10) REVERT: Z 91 GLU cc_start: 0.8970 (tp30) cc_final: 0.8576 (tp30) REVERT: b 24 ILE cc_start: 0.8993 (tp) cc_final: 0.8529 (tp) REVERT: d 33 PHE cc_start: 0.9010 (t80) cc_final: 0.8539 (t80) REVERT: d 49 ARG cc_start: 0.8408 (mtt90) cc_final: 0.7830 (tpt170) REVERT: d 73 TYR cc_start: 0.8828 (t80) cc_final: 0.8552 (t80) REVERT: d 87 ASP cc_start: 0.7890 (t0) cc_final: 0.7005 (t0) REVERT: e 41 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7906 (tm-30) REVERT: e 83 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7269 (tp30) REVERT: g 58 MET cc_start: 0.6205 (mmt) cc_final: 0.5946 (mpp) REVERT: h 38 ILE cc_start: 0.8220 (mm) cc_final: 0.7596 (tt) REVERT: i 20 ARG cc_start: 0.8930 (mtm110) cc_final: 0.7932 (ppt170) REVERT: m 48 LEU cc_start: 0.9590 (mt) cc_final: 0.9262 (tt) REVERT: m 84 LYS cc_start: 0.7624 (mptt) cc_final: 0.6333 (pttp) REVERT: m 100 TRP cc_start: 0.7856 (m100) cc_final: 0.7229 (m100) REVERT: n 20 LYS cc_start: 0.8982 (ttpt) cc_final: 0.8773 (tppt) REVERT: n 23 LEU cc_start: 0.8580 (mt) cc_final: 0.8171 (tp) REVERT: n 27 GLU cc_start: 0.8663 (tt0) cc_final: 0.8301 (tm-30) outliers start: 0 outliers final: 0 residues processed: 925 average time/residue: 0.5641 time to fit residues: 892.0271 Evaluate side-chains 754 residues out of total 5138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 754 time to evaluate : 4.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 343 optimal weight: 20.0000 chunk 460 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 398 optimal weight: 30.0000 chunk 63 optimal weight: 0.6980 chunk 120 optimal weight: 0.4980 chunk 433 optimal weight: 0.1980 chunk 181 optimal weight: 0.0370 chunk 444 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 GLN ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 HIS I 144 HIS ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 HIS L 296 ASN M 81 GLN ** M 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 232 HIS ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 72 GLN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 34 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.076842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.068956 restraints weight = 248250.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.070163 restraints weight = 153822.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.071033 restraints weight = 105405.064| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.269 52088 Z= 0.571 Angle : 1.803 50.978 71507 Z= 1.156 Chirality : 0.332 6.434 8766 Planarity : 0.004 0.140 9352 Dihedral : 5.058 162.457 8196 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 1.04 % Allowed : 8.09 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.11), residues: 5784 helix: 0.46 (0.10), residues: 3047 sheet: 0.02 (0.46), residues: 156 loop : -2.38 (0.12), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 182 HIS 0.013 0.001 HIS N 112 PHE 0.027 0.001 PHE g 64 TYR 0.030 0.001 TYR D 108 ARG 0.008 0.000 ARG H 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15111.05 seconds wall clock time: 267 minutes 39.46 seconds (16059.46 seconds total)