Starting phenix.real_space_refine on Fri May 17 06:16:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgp_19145/05_2024/8rgp_19145_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgp_19145/05_2024/8rgp_19145.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgp_19145/05_2024/8rgp_19145_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgp_19145/05_2024/8rgp_19145_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgp_19145/05_2024/8rgp_19145_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgp_19145/05_2024/8rgp_19145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgp_19145/05_2024/8rgp_19145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgp_19145/05_2024/8rgp_19145_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgp_19145/05_2024/8rgp_19145_updated.pdb" } resolution = 3.0 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= 0.003 sd= 0.008 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: 9 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 46 5.49 5 Mg 1 5.21 5 S 493 5.16 5 C 43919 2.51 5 N 11183 2.21 5 O 12196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "6 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "2 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 43": "OD1" <-> "OD2" Residue "k TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 34": "OE1" <-> "OE2" Residue "l TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 67868 Number of models: 1 Model: "" Number of chains: 69 Chain: "6" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 144} Chain: "C" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 15, 'TRANS': 191} Chain: "D" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3464 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 26, 'TRANS': 403} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1660 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 21, 'TRANS': 192} Chain: "1" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3321 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "3" Number of atoms: 5305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5305 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 31, 'TRANS': 658} Chain: "9" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1431 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} Chain: "P" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2748 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain: "Q" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1022 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "7" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "S" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 671 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "q" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "r" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 796 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 11, 'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "A" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 932 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'FME:plan-2': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2540 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1308 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3632 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 20, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2703 Classifications: {'peptide': 345} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 324} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2607 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "U" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 706 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "X" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1396 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 11, 'TRANS': 159} Chain: "Y" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1037 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "Z" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1167 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "a" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 572 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "b" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 398 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "d" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 996 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 12, 'TRANS': 107} Chain: "e" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 877 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "f" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 456 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "g" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 850 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "h" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1166 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain: "i" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 828 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 555 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 6, 'TRANS': 57} Chain: "k" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 626 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "l" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1323 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 18, 'TRANS': 138} Chain: "m" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1050 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 11, 'TRANS': 114} Chain: "n" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1541 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "o" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1014 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 110} Chain: "p" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1438 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 10, 'TRANS': 159} Chain: "6" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "D" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 114 Unusual residues: {' UQ': 1, '3PE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "1" 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: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "9" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "r" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "K" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "L" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 217 Unusual residues: {'3PE': 2, 'CDL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 85 Chain: "M" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 141 Unusual residues: {'3PE': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "N" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 90 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'DGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 179 Unusual residues: {'3PE': 1, 'CDL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 72 Chain: "Z" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "d" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 53 Chain: "h" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 121 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "i" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "m" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "n" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 749 SG CYS 6 129 59.585 133.545 105.412 1.00 60.33 S ATOM 252 SG CYS 6 65 54.344 130.585 102.695 1.00 76.31 S ATOM 246 SG CYS 6 64 56.697 127.884 107.711 1.00 66.32 S ATOM 979 SG CYS 6 159 54.126 133.979 108.313 1.00 58.10 S ATOM 7232 SG CYS 2 103 26.065 172.780 160.272 1.00 70.00 S ATOM 7266 SG CYS 2 108 24.059 171.816 162.782 1.00 74.24 S ATOM 7550 SG CYS 2 144 30.721 172.394 163.414 1.00 67.80 S ATOM 7573 SG CYS 2 148 28.664 171.524 166.316 1.00 81.36 S ATOM 10811 SG CYS 1 365 42.545 164.151 152.894 1.00 60.53 S ATOM 11133 SG CYS 1 405 45.722 166.486 158.058 1.00 78.48 S ATOM 10791 SG CYS 1 362 48.618 164.278 152.616 1.00 90.19 S ATOM 10772 SG CYS 1 359 45.655 170.062 152.625 1.00 66.34 S ATOM 12237 SG CYS 3 114 53.079 158.097 133.020 1.00 58.48 S ATOM 12176 SG CYS 3 105 47.957 155.311 130.090 1.00 67.94 S ATOM 12197 SG CYS 3 108 49.875 161.241 128.312 1.00 68.28 S ATOM 12569 SG CYS 3 156 54.304 166.725 140.718 1.00 70.05 S ATOM 12546 SG CYS 3 153 48.396 168.320 138.297 1.00 60.19 S ATOM 12593 SG CYS 3 159 53.308 172.549 138.026 1.00 58.56 S ATOM 12922 SG CYS 3 203 53.535 167.150 134.402 1.00 66.13 S ATOM 11683 SG CYS 3 41 56.256 164.524 146.587 1.00 60.63 S ATOM 11769 SG CYS 3 52 54.996 161.094 145.847 1.00 56.16 S ATOM 11794 SG CYS 3 55 58.639 159.659 150.226 1.00 75.36 S ATOM 11895 SG CYS 3 69 59.369 163.331 150.222 1.00 75.97 S ATOM 17683 SG CYS 9 121 51.621 139.156 114.665 1.00 83.63 S ATOM 17657 SG CYS 9 118 51.231 141.125 108.366 1.00123.82 S ATOM 17704 SG CYS 9 124 48.136 144.302 113.220 1.00 69.79 S ATOM 17431 SG CYS 9 89 54.660 144.473 112.673 1.00 43.52 S ATOM 17733 SG CYS 9 128 43.815 150.144 117.387 1.00 66.84 S ATOM 17403 SG CYS 9 85 49.758 149.982 115.058 1.00 59.07 S ATOM 17361 SG CYS 9 79 46.092 155.376 114.047 1.00 65.10 S ATOM 17380 SG CYS 9 82 48.326 153.516 120.116 1.00 52.41 S ATOM 22393 SG CYS 7 59 32.957 160.496 123.531 1.00 89.59 S ATOM 22569 SG CYS 7 84 35.678 161.915 121.795 1.00102.82 S ATOM 22591 SG CYS 7 87 34.979 158.872 120.242 1.00 81.97 S Time building chain proxies: 26.76, per 1000 atoms: 0.39 Number of scatterers: 67868 At special positions: 0 Unit cell: (233.2, 218.36, 207.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 493 16.00 P 46 15.00 Mg 1 11.99 O 12196 8.00 N 11183 7.00 C 43919 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS X 35 " - pdb=" SG CYS X 65 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS Y 17 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 94 " - pdb=" SG CYS Y 114 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.04 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.04 Simple disulfide: pdb=" SG CYS o 58 " - pdb=" SG CYS o 89 " distance=2.04 Simple disulfide: pdb=" SG CYS o 68 " - pdb=" SG CYS o 79 " distance=2.04 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=2.04 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: 22.02 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 301 " pdb="FE1 FES 2 301 " - pdb=" SG CYS 2 103 " pdb="FE1 FES 2 301 " - pdb=" SG CYS 2 108 " pdb="FE2 FES 2 301 " - pdb=" SG CYS 2 148 " pdb="FE2 FES 2 301 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 502 " pdb="FE1 SF4 1 502 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 502 " - pdb=" SG CYS 1 362 " pdb="FE4 SF4 1 502 " - pdb=" SG CYS 1 359 " pdb="FE2 SF4 1 502 " - pdb=" SG CYS 1 405 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb=" SF4 3 802 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb=" SF4 6 201 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 129 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 159 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 64 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 65 " pdb=" SF4 9 201 " pdb="FE3 SF4 9 201 " - pdb=" SG CYS 9 124 " pdb="FE2 SF4 9 201 " - pdb=" SG CYS 9 118 " pdb="FE4 SF4 9 201 " - pdb=" SG CYS 9 89 " pdb="FE1 SF4 9 201 " - pdb=" SG CYS 9 121 " pdb=" SF4 9 202 " pdb="FE2 SF4 9 202 " - pdb=" SG CYS 9 85 " pdb="FE4 SF4 9 202 " - pdb=" SG CYS 9 82 " pdb="FE1 SF4 9 202 " - pdb=" SG CYS 9 128 " pdb="FE3 SF4 9 202 " - pdb=" SG CYS 9 79 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN 7 201 " pdb="ZN ZN 7 201 " - pdb=" NE2 HIS 7 68 " pdb="ZN ZN 7 201 " - pdb=" SG CYS 7 84 " pdb="ZN ZN 7 201 " - pdb=" SG CYS 7 87 " pdb="ZN ZN 7 201 " - pdb=" SG CYS 7 59 " Number of angles added : 3 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15478 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 327 helices and 27 sheets defined 51.7% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.86 Creating SS restraints... Processing helix chain '6' and resid 36 through 53 Processing helix chain '6' and resid 64 through 73 Processing helix chain '6' and resid 90 through 92 No H-bonds generated for 'chain '6' and resid 90 through 92' Processing helix chain '6' and resid 104 through 115 Proline residue: 6 108 - end of helix Processing helix chain '6' and resid 127 through 132 Processing helix chain '6' and resid 134 through 136 No H-bonds generated for 'chain '6' and resid 134 through 136' Processing helix chain '6' and resid 146 through 148 No H-bonds generated for 'chain '6' and resid 146 through 148' Processing helix chain '6' and resid 163 through 178 Processing helix chain '6' and resid 182 through 187 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 54 through 65 removed outlier: 3.649A pdb=" N VAL C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.519A pdb=" N LEU C 64 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 8 through 12 Processing helix chain 'D' and resid 87 through 93 Processing helix chain 'D' and resid 96 through 106 Proline residue: D 101 - end of helix removed outlier: 3.905A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 165 through 184 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 218 through 229 Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 259 through 263 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 277 through 279 No H-bonds generated for 'chain 'D' and resid 277 through 279' Processing helix chain 'D' and resid 293 through 316 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 394 through 400 Processing helix chain 'D' and resid 402 through 405 No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'D' and resid 411 through 420 Processing helix chain 'D' and resid 425 through 429 Processing helix chain '2' and resid 13 through 15 No H-bonds generated for 'chain '2' and resid 13 through 15' Processing helix chain '2' and resid 25 through 37 Processing helix chain '2' and resid 43 through 58 removed outlier: 4.396A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix Processing helix chain '2' and resid 63 through 73 Processing helix chain '2' and resid 77 through 86 Processing helix chain '2' and resid 106 through 110 Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 166 through 178 Processing helix chain '1' and resid 33 through 39 Processing helix chain '1' and resid 45 through 51 Processing helix chain '1' and resid 53 through 63 Processing helix chain '1' and resid 75 through 82 removed outlier: 4.631A pdb=" N MET 1 82 " --> pdb=" O LYS 1 78 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 129 Processing helix chain '1' and resid 143 through 159 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 185 through 187 No H-bonds generated for 'chain '1' and resid 185 through 187' Processing helix chain '1' and resid 189 through 197 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 236 Proline residue: 1 232 - end of helix Processing helix chain '1' and resid 240 through 244 Processing helix chain '1' and resid 276 through 283 Processing helix chain '1' and resid 309 through 312 No H-bonds generated for 'chain '1' and resid 309 through 312' Processing helix chain '1' and resid 319 through 324 Processing helix chain '1' and resid 343 through 357 Processing helix chain '1' and resid 363 through 381 Processing helix chain '1' and resid 387 through 399 Processing helix chain '1' and resid 407 through 421 Proline residue: 1 414 - end of helix Processing helix chain '1' and resid 423 through 436 Processing helix chain '3' and resid 26 through 33 Processing helix chain '3' and resid 84 through 100 removed outlier: 4.179A pdb=" N ASN 3 100 " --> pdb=" O PHE 3 96 " (cutoff:3.500A) Processing helix chain '3' and resid 115 through 123 Processing helix chain '3' and resid 150 through 152 No H-bonds generated for 'chain '3' and resid 150 through 152' Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 198 through 202 Processing helix chain '3' and resid 265 through 275 removed outlier: 5.113A pdb=" N TYR 3 271 " --> pdb=" O THR 3 267 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP 3 272 " --> pdb=" O ARG 3 268 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLY 3 273 " --> pdb=" O PHE 3 269 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU 3 274 " --> pdb=" O ALA 3 270 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS 3 275 " --> pdb=" O TYR 3 271 " (cutoff:3.500A) Processing helix chain '3' and resid 296 through 309 Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 359 through 361 No H-bonds generated for 'chain '3' and resid 359 through 361' Processing helix chain '3' and resid 368 through 373 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 434 removed outlier: 3.533A pdb=" N SER 3 434 " --> pdb=" O ASP 3 431 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 445 Processing helix chain '3' and resid 455 through 458 No H-bonds generated for 'chain '3' and resid 455 through 458' Processing helix chain '3' and resid 463 through 480 Processing helix chain '3' and resid 499 through 505 Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 642 through 651 Processing helix chain '3' and resid 668 through 672 Processing helix chain '3' and resid 676 through 680 Processing helix chain '3' and resid 682 through 692 Processing helix chain '9' and resid 16 through 28 Processing helix chain '9' and resid 30 through 44 Processing helix chain '9' and resid 84 through 88 Processing helix chain '9' and resid 123 through 127 Processing helix chain '9' and resid 147 through 149 No H-bonds generated for 'chain '9' and resid 147 through 149' Processing helix chain '9' and resid 153 through 162 Processing helix chain '9' and resid 164 through 174 removed outlier: 4.344A pdb=" N ALA 9 169 " --> pdb=" O ALA 9 165 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 5 No H-bonds generated for 'chain 'P' and resid 3 through 5' Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 57 through 59 No H-bonds generated for 'chain 'P' and resid 57 through 59' Processing helix chain 'P' and resid 78 through 85 Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 124 Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 187 removed outlier: 4.514A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 197 Processing helix chain 'P' and resid 207 through 219 Processing helix chain 'P' and resid 238 through 249 Processing helix chain 'P' and resid 260 through 271 Processing helix chain 'P' and resid 281 through 288 Processing helix chain 'P' and resid 315 through 318 No H-bonds generated for 'chain 'P' and resid 315 through 318' Processing helix chain 'Q' and resid 28 through 31 No H-bonds generated for 'chain 'Q' and resid 28 through 31' Processing helix chain 'Q' and resid 89 through 99 Processing helix chain 'Q' and resid 118 through 122 Processing helix chain '7' and resid 40 through 45 Processing helix chain 'S' and resid 30 through 46 removed outlier: 3.539A pdb=" N TYR S 40 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL S 41 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLU S 42 " --> pdb=" O GLN S 38 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU S 43 " --> pdb=" O ARG S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 8 through 22 Processing helix chain 'T' and resid 44 through 58 Processing helix chain 'T' and resid 64 through 67 No H-bonds generated for 'chain 'T' and resid 64 through 67' Processing helix chain 'T' and resid 73 through 83 Processing helix chain 'V' and resid 19 through 36 removed outlier: 4.182A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 Processing helix chain 'V' and resid 64 through 71 Processing helix chain 'V' and resid 76 through 95 Processing helix chain 'W' and resid 27 through 51 Proline residue: W 46 - end of helix Processing helix chain 'W' and resid 58 through 71 Processing helix chain 'W' and resid 78 through 96 Processing helix chain 'W' and resid 102 through 106 Processing helix chain 'W' and resid 120 through 125 Processing helix chain 'q' and resid 2 through 16 Processing helix chain 'q' and resid 20 through 29 Processing helix chain 'q' and resid 84 through 91 Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 53 through 55 No H-bonds generated for 'chain 'r' and resid 53 through 55' Processing helix chain 'r' and resid 59 through 61 No H-bonds generated for 'chain 'r' and resid 59 through 61' Processing helix chain 's' and resid 35 through 37 No H-bonds generated for 'chain 's' and resid 35 through 37' Processing helix chain 's' and resid 44 through 55 removed outlier: 4.541A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N PHE s 55 " --> pdb=" O ASP s 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 23 Processing helix chain 'A' and resid 31 through 34 No H-bonds generated for 'chain 'A' and resid 31 through 34' Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 56 through 80 Proline residue: A 74 - end of helix removed outlier: 5.745A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 107 Processing helix chain 'H' and resid 3 through 32 Proline residue: H 12 - end of helix Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 87 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 Processing helix chain 'H' and resid 126 through 156 Processing helix chain 'H' and resid 163 through 170 Processing helix chain 'H' and resid 179 through 193 Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 219 through 241 Processing helix chain 'H' and resid 253 through 276 Processing helix chain 'H' and resid 282 through 311 removed outlier: 3.584A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU H 294 " --> pdb=" O TRP H 290 " (cutoff:3.500A) Proline residue: H 295 - end of helix Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 4 through 21 Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 49 through 72 Processing helix chain 'J' and resid 86 through 108 Processing helix chain 'J' and resid 139 through 146 removed outlier: 4.237A pdb=" N TYR J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER J 146 " --> pdb=" O ALA J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 169 Processing helix chain 'K' and resid 3 through 20 Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 58 through 84 Processing helix chain 'L' and resid 3 through 24 Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 27 through 29 No H-bonds generated for 'chain 'L' and resid 27 through 29' Processing helix chain 'L' and resid 32 through 57 Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 107 Processing helix chain 'L' and resid 114 through 133 Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 192 Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 231 through 237 removed outlier: 4.485A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 3.741A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.362A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 293 Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 389 through 401 removed outlier: 3.530A pdb=" N ASP L 393 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 407 through 431 Processing helix chain 'L' and resid 448 through 471 Proline residue: L 453 - end of helix removed outlier: 5.923A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N PHE L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 509 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 549 Proline residue: L 530 - end of helix removed outlier: 3.716A pdb=" N ILE L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS L 534 " --> pdb=" O SER L 531 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.614A pdb=" N LEU L 542 " --> pdb=" O MET L 539 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN L 543 " --> pdb=" O LYS L 540 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU L 544 " --> pdb=" O SER L 541 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU L 546 " --> pdb=" O ASN L 543 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS L 547 " --> pdb=" O LEU L 544 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR L 548 " --> pdb=" O SER L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 553 through 561 removed outlier: 5.707A pdb=" N LEU L 558 " --> pdb=" O ASP L 554 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU L 559 " --> pdb=" O LEU L 555 " (cutoff:3.500A) Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 605 Processing helix chain 'M' and resid 5 through 17 removed outlier: 4.120A pdb=" N LEU M 12 " --> pdb=" O SER M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 4.311A pdb=" N THR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 84 Proline residue: M 74 - end of helix removed outlier: 4.525A pdb=" N ASN M 82 " --> pdb=" O MET M 78 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N HIS M 83 " --> pdb=" O ALA M 79 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU M 84 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 111 Processing helix chain 'M' and resid 115 through 136 Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 171 removed outlier: 3.618A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE M 158 " --> pdb=" O ILE M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.817A pdb=" N VAL M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 181 Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.366A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 222 removed outlier: 3.905A pdb=" N TRP M 215 " --> pdb=" O VAL M 212 " (cutoff:3.500A) Proline residue: M 217 - end of helix removed outlier: 3.516A pdb=" N GLU M 222 " --> pdb=" O ALA M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 249 removed outlier: 5.828A pdb=" N LEU M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE M 248 " --> pdb=" O ILE M 244 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 257 No H-bonds generated for 'chain 'M' and resid 254 through 257' Processing helix chain 'M' and resid 259 through 277 Processing helix chain 'M' and resid 282 through 303 Processing helix chain 'M' and resid 306 through 337 Processing helix chain 'M' and resid 348 through 351 No H-bonds generated for 'chain 'M' and resid 348 through 351' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 414 removed outlier: 3.678A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE M 394 " --> pdb=" O PHE M 391 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET M 408 " --> pdb=" O MET M 405 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR M 414 " --> pdb=" O ILE M 411 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 449 Proline residue: M 443 - end of helix Processing helix chain 'N' and resid 3 through 22 Proline residue: N 17 - end of helix Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 113 through 119 removed outlier: 4.104A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 144 removed outlier: 5.308A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 151 through 171 Processing helix chain 'N' and resid 175 through 194 Processing helix chain 'N' and resid 198 through 222 Proline residue: N 214 - end of helix removed outlier: 4.045A pdb=" N ASN N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 233 removed outlier: 4.484A pdb=" N LEU N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 252 removed outlier: 3.604A pdb=" N LEU N 241 " --> pdb=" O PRO N 238 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR N 242 " --> pdb=" O ALA N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 276 through 300 Processing helix chain 'N' and resid 311 through 316 Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 337 through 343 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 11 Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 58 through 62 Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 93 through 118 Processing helix chain 'O' and resid 128 through 130 No H-bonds generated for 'chain 'O' and resid 128 through 130' Processing helix chain 'O' and resid 132 through 140 Processing helix chain 'O' and resid 146 through 162 Proline residue: O 161 - end of helix Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 196 through 215 removed outlier: 4.720A 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 233 through 239 Processing helix chain 'O' and resid 253 through 264 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 272 through 274 No H-bonds generated for 'chain 'O' and resid 272 through 274' Processing helix chain 'O' and resid 286 through 298 Processing helix chain 'O' and resid 317 through 319 No H-bonds generated for 'chain 'O' and resid 317 through 319' Processing helix chain 'U' and resid 8 through 20 Processing helix chain 'U' and resid 44 through 58 Processing helix chain 'U' and resid 64 through 69 Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'X' and resid 9 through 12 No H-bonds generated for 'chain 'X' and resid 9 through 12' Processing helix chain 'X' and resid 21 through 26 Processing helix chain 'X' and resid 28 through 34 Processing helix chain 'X' and resid 36 through 48 Processing helix chain 'X' and resid 52 through 54 No H-bonds generated for 'chain 'X' and resid 52 through 54' Processing helix chain 'X' and resid 56 through 76 Processing helix chain 'X' and resid 79 through 90 Processing helix chain 'X' and resid 100 through 112 Processing helix chain 'X' and resid 140 through 142 No H-bonds generated for 'chain 'X' and resid 140 through 142' Processing helix chain 'Y' and resid 2 through 7 Processing helix chain 'Y' and resid 17 through 42 Processing helix chain 'Y' and resid 48 through 79 Processing helix chain 'Y' and resid 86 through 104 Processing helix chain 'Y' and resid 107 through 130 Processing helix chain 'Z' and resid 31 through 94 Proline residue: Z 72 - end of helix Processing helix chain 'Z' and resid 120 through 123 No H-bonds generated for 'chain 'Z' and resid 120 through 123' Processing helix chain 'Z' and resid 129 through 141 removed outlier: 6.235A pdb=" N PHE Z 139 " --> pdb=" O ALA Z 135 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR Z 140 " --> pdb=" O ASN Z 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 31 Proline residue: a 7 - end of helix removed outlier: 4.370A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'b' and resid 3 through 14 Processing helix chain 'b' and resid 18 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 4.051A pdb=" N SER b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 81 No H-bonds generated for 'chain 'b' and resid 78 through 81' Processing helix chain 'c' and resid 14 through 45 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 96 Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 33 through 43 Processing helix chain 'e' and resid 49 through 54 Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 through 88 Processing helix chain 'f' and resid 11 through 34 removed outlier: 4.744A pdb=" N VAL f 16 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 17 - end of helix removed outlier: 3.509A pdb=" N LEU f 34 " --> pdb=" O ASP f 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 37 No H-bonds generated for 'chain 'g' and resid 35 through 37' Processing helix chain 'g' and resid 49 through 64 Processing helix chain 'g' and resid 70 through 77 Processing helix chain 'g' and resid 81 through 100 removed outlier: 3.585A pdb=" N GLN g 84 " --> pdb=" O TYR g 81 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU g 85 " --> pdb=" O ARG g 82 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP g 86 " --> pdb=" O MET g 83 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU g 90 " --> pdb=" O ALA g 87 " (cutoff:3.500A) Processing helix chain 'g' and resid 113 through 115 No H-bonds generated for 'chain 'g' and resid 113 through 115' Processing helix chain 'h' and resid 16 through 46 Proline residue: h 35 - end of helix Processing helix chain 'h' and resid 64 through 66 No H-bonds generated for 'chain 'h' and resid 64 through 66' Processing helix chain 'h' and resid 70 through 79 Processing helix chain 'h' and resid 83 through 116 Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 24 Processing helix chain 'i' and resid 69 through 73 Processing helix chain 'i' and resid 75 through 88 Processing helix chain 'j' and resid 19 through 42 Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' Processing helix chain 'j' and resid 61 through 64 No H-bonds generated for 'chain 'j' and resid 61 through 64' Processing helix chain 'k' and resid 24 through 26 No H-bonds generated for 'chain 'k' and resid 24 through 26' Processing helix chain 'k' and resid 33 through 44 removed outlier: 3.906A pdb=" N ARG k 44 " --> pdb=" O LYS k 40 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 51 No H-bonds generated for 'chain 'k' and resid 49 through 51' Processing helix chain 'k' and resid 55 through 58 Processing helix chain 'k' and resid 68 through 72 Processing helix chain 'k' and resid 76 through 93 Processing helix chain 'l' and resid 16 through 25 Processing helix chain 'l' and resid 54 through 56 No H-bonds generated for 'chain 'l' and resid 54 through 56' Processing helix chain 'l' and resid 80 through 83 No H-bonds generated for 'chain 'l' and resid 80 through 83' Processing helix chain 'l' and resid 97 through 120 Processing helix chain 'l' and resid 133 through 141 removed outlier: 6.075A pdb=" N LEU l 139 " --> pdb=" O ASN l 135 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLU l 140 " --> pdb=" O ASN l 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 21 No H-bonds generated for 'chain 'm' and resid 19 through 21' Processing helix chain 'm' and resid 26 through 51 Processing helix chain 'm' and resid 62 through 72 Processing helix chain 'm' and resid 83 through 117 Proline residue: m 96 - end of helix Processing helix chain 'n' and resid 11 through 29 Processing helix chain 'n' and resid 33 through 49 Processing helix chain 'n' and resid 56 through 72 Processing helix chain 'n' and resid 93 through 95 No H-bonds generated for 'chain 'n' and resid 93 through 95' Processing helix chain 'n' and resid 101 through 103 No H-bonds generated for 'chain 'n' and resid 101 through 103' Processing helix chain 'n' and resid 108 through 113 Processing helix chain 'n' and resid 115 through 141 removed outlier: 4.859A pdb=" N ASP n 133 " --> pdb=" O MET n 129 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 167 through 170 No H-bonds generated for 'chain 'n' and resid 167 through 170' Processing helix chain 'o' and resid 2 through 8 Processing helix chain 'o' and resid 18 through 20 No H-bonds generated for 'chain 'o' and resid 18 through 20' Processing helix chain 'o' and resid 42 through 48 Processing helix chain 'o' and resid 59 through 71 Processing helix chain 'o' and resid 80 through 117 Processing helix chain 'p' and resid 28 through 57 removed outlier: 4.900A pdb=" N TRP p 42 " --> pdb=" O LEU p 38 " (cutoff:3.500A) Proline residue: p 43 - end of helix Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 123 removed outlier: 6.538A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ASN p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 142 Processing helix chain 'p' and resid 151 through 170 Processing sheet with id= A, first strand: chain '6' and resid 95 through 99 removed outlier: 6.574A pdb=" N TYR 6 122 " --> pdb=" O MET 6 96 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL 6 98 " --> pdb=" O TYR 6 122 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL 6 124 " --> pdb=" O VAL 6 98 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE 6 154 " --> pdb=" O SER 6 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 74 through 82 removed outlier: 6.496A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU C 48 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LYS C 108 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C 50 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N TYR C 110 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ILE C 52 " --> pdb=" O TYR C 110 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= D, first strand: chain 'D' and resid 47 through 51 Processing sheet with id= E, first strand: chain 'D' and resid 361 through 368 Processing sheet with id= F, first strand: chain '2' and resid 139 through 142 removed outlier: 6.479A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N CYS 2 103 " --> pdb=" O MET 2 153 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N MET 2 153 " --> pdb=" O CYS 2 103 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '1' and resid 219 through 224 removed outlier: 6.158A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '1' and resid 266 through 271 Processing sheet with id= I, first strand: chain '3' and resid 8 through 13 Processing sheet with id= J, first strand: chain '3' and resid 146 through 148 Processing sheet with id= K, first strand: chain '3' and resid 173 through 175 Processing sheet with id= L, first strand: chain '3' and resid 223 through 228 Processing sheet with id= M, first strand: chain '3' and resid 283 through 285 Processing sheet with id= N, first strand: chain '3' and resid 343 through 345 removed outlier: 8.600A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '3' and resid 490 through 493 removed outlier: 8.110A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain '3' and resid 571 through 574 Processing sheet with id= Q, first strand: chain '9' and resid 66 through 69 Processing sheet with id= R, first strand: chain '9' and resid 98 through 100 removed outlier: 3.819A pdb=" N ARG 9 107 " --> pdb=" O GLU 9 99 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.691A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'P' and resid 191 through 193 Processing sheet with id= U, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= V, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= W, first strand: chain '7' and resid 50 through 52 Processing sheet with id= X, first strand: chain '7' and resid 56 through 59 Processing sheet with id= Y, first strand: chain 'S' and resid 51 through 57 removed outlier: 6.566A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS S 63 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 61 through 63 Processing sheet with id= AA, first strand: chain 'O' and resid 219 through 223 removed outlier: 6.578A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N TYR O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) 2949 hydrogen bonds defined for protein. 8364 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: 23.91 Time building geometry restraints manager: 24.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.22: 75 1.22 - 1.49: 39530 1.49 - 1.76: 29074 1.76 - 2.03: 795 2.03 - 2.31: 80 Bond restraints: 69554 Sorted by residual: bond pdb=" C GLY 1 67 " pdb=" N ARG 1 68 " ideal model delta sigma weight residual 1.332 0.942 0.390 1.29e-02 6.01e+03 9.14e+02 bond pdb=" C ALA 1 71 " pdb=" N GLY 1 72 " ideal model delta sigma weight residual 1.331 1.598 -0.267 1.40e-02 5.10e+03 3.64e+02 bond pdb=" C2' DGT O 401 " pdb=" C3' DGT O 401 " ideal model delta sigma weight residual 1.284 1.523 -0.239 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C4' DGT O 401 " pdb=" O4' DGT O 401 " ideal model delta sigma weight residual 1.272 1.446 -0.174 2.00e-02 2.50e+03 7.56e+01 bond pdb=" C4 DGT O 401 " pdb=" N3 DGT O 401 " ideal model delta sigma weight residual 1.502 1.343 0.159 2.00e-02 2.50e+03 6.32e+01 ... (remaining 69549 not shown) Histogram of bond angle deviations from ideal: 70.22 - 83.20: 76 83.20 - 96.18: 0 96.18 - 109.16: 6275 109.16 - 122.14: 76275 122.14 - 135.13: 11448 Bond angle restraints: 94074 Sorted by residual: angle pdb=" O ALA 1 71 " pdb=" C ALA 1 71 " pdb=" N GLY 1 72 " ideal model delta sigma weight residual 122.12 135.13 -13.01 1.06e+00 8.90e-01 1.51e+02 angle pdb=" CA ALA 1 71 " pdb=" C ALA 1 71 " pdb=" N GLY 1 72 " ideal model delta sigma weight residual 117.30 103.87 13.43 1.16e+00 7.43e-01 1.34e+02 angle pdb=" PA NDP P 501 " pdb=" O3 NDP P 501 " pdb=" PN NDP P 501 " ideal model delta sigma weight residual 107.74 129.82 -22.08 1.95e+00 2.62e-01 1.28e+02 angle pdb=" N GLY 1 70 " pdb=" CA GLY 1 70 " pdb=" C GLY 1 70 " ideal model delta sigma weight residual 114.48 104.68 9.80 1.19e+00 7.06e-01 6.79e+01 angle pdb=" N ALA 1 71 " pdb=" CA ALA 1 71 " pdb=" C ALA 1 71 " ideal model delta sigma weight residual 111.28 120.10 -8.82 1.09e+00 8.42e-01 6.55e+01 ... (remaining 94069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 41091 35.74 - 71.48: 1036 71.48 - 107.22: 50 107.22 - 142.96: 4 142.96 - 178.71: 3 Dihedral angle restraints: 42184 sinusoidal: 18196 harmonic: 23988 Sorted by residual: dihedral pdb=" C10 FMN 1 501 " pdb=" C1' FMN 1 501 " pdb=" N10 FMN 1 501 " pdb=" C2' FMN 1 501 " ideal model delta sinusoidal sigma weight residual 257.59 78.89 178.71 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CB CYS X 45 " pdb=" SG CYS X 45 " pdb=" SG CYS X 55 " pdb=" CB CYS X 55 " ideal model delta sinusoidal sigma weight residual 93.00 150.40 -57.40 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CA ASP C 66 " pdb=" C ASP C 66 " pdb=" N HIS C 67 " pdb=" CA HIS C 67 " ideal model delta harmonic sigma weight residual 180.00 152.59 27.41 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 42181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.224: 10181 4.224 - 8.449: 0 8.449 - 12.673: 0 12.673 - 16.897: 0 16.897 - 21.121: 24 Chirality restraints: 10205 Sorted by residual: chirality pdb="FE1 SF4 9 201 " pdb=" S2 SF4 9 201 " pdb=" S3 SF4 9 201 " pdb=" S4 SF4 9 201 " both_signs ideal model delta sigma weight residual False -10.55 10.57 -21.12 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 9 201 " pdb=" S1 SF4 9 201 " pdb=" S2 SF4 9 201 " pdb=" S3 SF4 9 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.57 21.12 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 9 202 " pdb=" S1 SF4 9 202 " pdb=" S2 SF4 9 202 " pdb=" S3 SF4 9 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.56 21.12 2.00e-01 2.50e+01 1.11e+04 ... (remaining 10202 not shown) Planarity restraints: 11741 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN 1 501 " -0.193 2.00e-02 2.50e+03 7.91e-02 2.97e+02 pdb=" C10 FMN 1 501 " -0.041 2.00e-02 2.50e+03 pdb=" C2 FMN 1 501 " 0.077 2.00e-02 2.50e+03 pdb=" C4 FMN 1 501 " -0.022 2.00e-02 2.50e+03 pdb=" C4A FMN 1 501 " -0.057 2.00e-02 2.50e+03 pdb=" C5A FMN 1 501 " -0.045 2.00e-02 2.50e+03 pdb=" C6 FMN 1 501 " -0.011 2.00e-02 2.50e+03 pdb=" C7 FMN 1 501 " 0.037 2.00e-02 2.50e+03 pdb=" C7M FMN 1 501 " 0.082 2.00e-02 2.50e+03 pdb=" C8 FMN 1 501 " 0.046 2.00e-02 2.50e+03 pdb=" C8M FMN 1 501 " 0.086 2.00e-02 2.50e+03 pdb=" C9 FMN 1 501 " 0.010 2.00e-02 2.50e+03 pdb=" C9A FMN 1 501 " -0.035 2.00e-02 2.50e+03 pdb=" N1 FMN 1 501 " 0.015 2.00e-02 2.50e+03 pdb=" N10 FMN 1 501 " -0.053 2.00e-02 2.50e+03 pdb=" N3 FMN 1 501 " 0.050 2.00e-02 2.50e+03 pdb=" N5 FMN 1 501 " -0.068 2.00e-02 2.50e+03 pdb=" O2 FMN 1 501 " 0.187 2.00e-02 2.50e+03 pdb=" O4 FMN 1 501 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ D 501 " -0.032 2.00e-02 2.50e+03 8.62e-02 2.23e+02 pdb=" C2 UQ D 501 " -0.006 2.00e-02 2.50e+03 pdb=" C3 UQ D 501 " -0.032 2.00e-02 2.50e+03 pdb=" C4 UQ D 501 " -0.050 2.00e-02 2.50e+03 pdb=" C5 UQ D 501 " -0.017 2.00e-02 2.50e+03 pdb=" C6 UQ D 501 " -0.042 2.00e-02 2.50e+03 pdb=" C7 UQ D 501 " -0.042 2.00e-02 2.50e+03 pdb=" CM5 UQ D 501 " 0.206 2.00e-02 2.50e+03 pdb=" O1 UQ D 501 " -0.054 2.00e-02 2.50e+03 pdb=" O2 UQ D 501 " 0.164 2.00e-02 2.50e+03 pdb=" O3 UQ D 501 " -0.002 2.00e-02 2.50e+03 pdb=" O4 UQ D 501 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C37 UQ D 501 " -0.109 2.00e-02 2.50e+03 9.25e-02 1.07e+02 pdb=" C38 UQ D 501 " 0.142 2.00e-02 2.50e+03 pdb=" C39 UQ D 501 " 0.050 2.00e-02 2.50e+03 pdb=" C40 UQ D 501 " 0.007 2.00e-02 2.50e+03 pdb=" C41 UQ D 501 " -0.089 2.00e-02 2.50e+03 ... (remaining 11738 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.55: 563 2.55 - 3.19: 59859 3.19 - 3.84: 141545 3.84 - 4.49: 196773 4.49 - 5.14: 312942 Nonbonded interactions: 711682 Sorted by model distance: nonbonded pdb=" OE2 GLU 1 101 " pdb=" N SER 1 302 " model vdw 1.897 2.520 nonbonded pdb=" O GLU 6 119 " pdb=" OH TYR P 54 " model vdw 2.152 2.440 nonbonded pdb=" OH TYR H 114 " pdb=" O LEU J 60 " model vdw 2.159 2.440 nonbonded pdb=" O2B DGT O 401 " pdb="MG MG O 402 " model vdw 2.159 2.170 nonbonded pdb=" O1G DGT O 401 " pdb="MG MG O 402 " model vdw 2.163 2.170 ... (remaining 711677 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 'T' selection = (chain 'U' and resid 6 through 84) } 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 individual isotropic 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 4.950 Check model and map are aligned: 0.390 Set scattering table: 0.470 Process input model: 164.080 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 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 : 0.007 0.390 69554 Z= 0.461 Angle : 0.814 22.078 94074 Z= 0.419 Chirality : 1.023 21.121 10205 Planarity : 0.006 0.092 11741 Dihedral : 14.647 178.705 26670 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.76 % Allowed : 5.81 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.42 (0.09), residues: 8115 helix: 0.61 (0.07), residues: 4502 sheet: -0.84 (0.26), residues: 400 loop : -1.44 (0.11), residues: 3213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP X 85 HIS 0.009 0.001 HIS 7 68 PHE 0.040 0.002 PHE N 292 TYR 0.033 0.002 TYR M 406 ARG 0.006 0.000 ARG d 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1222 time to evaluate : 5.834 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: 6 64 CYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8502 (p) REVERT: D 145 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8828 (p) REVERT: 2 37 ASN cc_start: 0.8022 (m110) cc_final: 0.7710 (m110) REVERT: 2 168 ASP cc_start: 0.8420 (t0) cc_final: 0.7987 (t0) REVERT: 1 312 CYS cc_start: 0.9368 (m) cc_final: 0.8961 (m) REVERT: 3 21 GLU cc_start: 0.9162 (mp0) cc_final: 0.8798 (mp0) REVERT: 3 158 ARG cc_start: 0.9425 (OUTLIER) cc_final: 0.9162 (mmm-85) REVERT: 3 583 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8565 (t) REVERT: 9 17 LYS cc_start: 0.9062 (tttm) cc_final: 0.8800 (tttp) REVERT: P 261 PHE cc_start: 0.7596 (t80) cc_final: 0.6505 (t80) REVERT: Q 14 ASP cc_start: 0.8665 (p0) cc_final: 0.8226 (p0) REVERT: Q 81 ASN cc_start: 0.9299 (OUTLIER) cc_final: 0.8827 (m-40) REVERT: 7 3 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8805 (mm110) REVERT: 7 92 LYS cc_start: 0.9238 (ttpp) cc_final: 0.9029 (ttmm) REVERT: S 92 ASN cc_start: 0.8841 (t0) cc_final: 0.8525 (t0) REVERT: T 52 MET cc_start: 0.9056 (mtm) cc_final: 0.8696 (mtm) REVERT: T 64 ASP cc_start: 0.7772 (t0) cc_final: 0.7084 (t70) REVERT: T 83 LYS cc_start: 0.8868 (tptm) cc_final: 0.8608 (mmmm) REVERT: V 56 ASP cc_start: 0.9139 (m-30) cc_final: 0.8860 (m-30) REVERT: W 44 GLU cc_start: 0.8909 (tp30) cc_final: 0.8418 (tp30) REVERT: W 113 GLU cc_start: 0.8926 (pt0) cc_final: 0.8675 (pp20) REVERT: W 114 THR cc_start: 0.9262 (m) cc_final: 0.8932 (m) REVERT: q 5 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8341 (tm-30) REVERT: q 48 TYR cc_start: 0.9002 (m-80) cc_final: 0.8771 (m-80) REVERT: q 76 ASP cc_start: 0.9309 (m-30) cc_final: 0.8980 (m-30) REVERT: q 127 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.7404 (m-10) REVERT: r 70 SER cc_start: 0.9054 (t) cc_final: 0.8663 (t) REVERT: s 43 TYR cc_start: 0.9350 (m-80) cc_final: 0.9094 (m-80) REVERT: A 23 TRP cc_start: 0.8509 (m100) cc_final: 0.8256 (m100) REVERT: A 32 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8686 (mm-30) REVERT: A 68 GLU cc_start: 0.9415 (OUTLIER) cc_final: 0.9133 (mt-10) REVERT: H 225 MET cc_start: 0.9263 (mtp) cc_final: 0.9061 (mtp) REVERT: J 152 MET cc_start: 0.9587 (tpp) cc_final: 0.8948 (tpp) REVERT: L 60 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8399 (mm-30) REVERT: L 179 ASP cc_start: 0.8899 (m-30) cc_final: 0.8655 (m-30) REVERT: L 539 MET cc_start: 0.9159 (tmm) cc_final: 0.8675 (tmm) REVERT: N 40 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8997 (tt) REVERT: N 117 GLU cc_start: 0.9345 (mm-30) cc_final: 0.9018 (mm-30) REVERT: N 244 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8987 (tp) REVERT: O 44 GLN cc_start: 0.9254 (tp40) cc_final: 0.8991 (tp40) REVERT: O 140 ASN cc_start: 0.9215 (t0) cc_final: 0.9006 (t0) REVERT: O 268 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8716 (mp0) REVERT: O 290 SER cc_start: 0.9451 (OUTLIER) cc_final: 0.9139 (m) REVERT: Y 5 PHE cc_start: 0.8024 (m-10) cc_final: 0.7717 (m-80) REVERT: Y 6 GLU cc_start: 0.9284 (mm-30) cc_final: 0.9016 (mm-30) REVERT: Y 50 GLU cc_start: 0.8918 (mp0) cc_final: 0.8680 (mp0) REVERT: Y 81 GLU cc_start: 0.8585 (mp0) cc_final: 0.8356 (mm-30) REVERT: Z 79 ASP cc_start: 0.8724 (m-30) cc_final: 0.8377 (m-30) REVERT: Z 95 ILE cc_start: 0.6467 (OUTLIER) cc_final: 0.6235 (mm) REVERT: Z 96 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7453 (mp) REVERT: a 18 ILE cc_start: 0.9199 (mt) cc_final: 0.8981 (mp) REVERT: c 13 ASN cc_start: 0.9199 (t0) cc_final: 0.8736 (t0) REVERT: d 25 LYS cc_start: 0.8372 (ptmt) cc_final: 0.7991 (ptpt) REVERT: e 83 GLU cc_start: 0.8759 (tt0) cc_final: 0.8085 (tm-30) REVERT: e 87 LYS cc_start: 0.9144 (mmtp) cc_final: 0.8872 (tppp) REVERT: g 47 SER cc_start: 0.9138 (t) cc_final: 0.8918 (t) REVERT: g 80 ASP cc_start: 0.8776 (t70) cc_final: 0.8198 (t0) REVERT: g 112 ASP cc_start: 0.8989 (t70) cc_final: 0.8721 (t0) REVERT: h 51 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8649 (tm-30) REVERT: i 4 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8628 (p) REVERT: j 43 ASP cc_start: 0.9058 (p0) cc_final: 0.8811 (p0) REVERT: k 39 LYS cc_start: 0.9219 (mttp) cc_final: 0.8979 (mttp) REVERT: l 28 MET cc_start: 0.9028 (mtp) cc_final: 0.8610 (mtm) REVERT: m 61 ASP cc_start: 0.8879 (t0) cc_final: 0.8626 (t70) REVERT: m 105 LYS cc_start: 0.9099 (tptm) cc_final: 0.8462 (tptp) REVERT: m 109 ASP cc_start: 0.9498 (m-30) cc_final: 0.9201 (m-30) REVERT: m 119 LYS cc_start: 0.9007 (mttp) cc_final: 0.8551 (mtmm) REVERT: n 131 SER cc_start: 0.9243 (t) cc_final: 0.8912 (t) REVERT: n 161 ASP cc_start: 0.9001 (p0) cc_final: 0.8779 (p0) REVERT: o 17 ASP cc_start: 0.8971 (t0) cc_final: 0.8745 (t0) REVERT: o 19 GLU cc_start: 0.9211 (mp0) cc_final: 0.8648 (mp0) REVERT: o 45 MET cc_start: 0.9250 (mtm) cc_final: 0.8956 (mtm) REVERT: o 82 GLU cc_start: 0.9193 (mp0) cc_final: 0.8986 (mp0) REVERT: p 33 THR cc_start: 0.9155 (p) cc_final: 0.8920 (m) REVERT: p 37 ASP cc_start: 0.8653 (m-30) cc_final: 0.8150 (m-30) REVERT: p 58 ASN cc_start: 0.8752 (m-40) cc_final: 0.8527 (m110) outliers start: 199 outliers final: 54 residues processed: 1374 average time/residue: 1.4550 time to fit residues: 2624.5678 Evaluate side-chains 1045 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 978 time to evaluate : 5.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain 2 residue 164 LEU Chi-restraints excluded: chain 2 residue 165 THR Chi-restraints excluded: chain 1 residue 45 THR Chi-restraints excluded: chain 1 residue 273 SER Chi-restraints excluded: chain 1 residue 297 VAL Chi-restraints excluded: chain 1 residue 363 THR Chi-restraints excluded: chain 1 residue 365 CYS Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 158 ARG Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 559 VAL Chi-restraints excluded: chain 3 residue 583 THR Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 254 ILE Chi-restraints excluded: chain Q residue 81 ASN Chi-restraints excluded: chain Q residue 105 VAL Chi-restraints excluded: chain 7 residue 87 CYS Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain W residue 75 VAL Chi-restraints excluded: chain q residue 127 TYR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 517 ASN Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 577 THR Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 244 ILE Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Z residue 95 ILE Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain b residue 61 ASN Chi-restraints excluded: chain g residue 105 ILE Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 55 ASP Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain p residue 82 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 677 optimal weight: 10.0000 chunk 607 optimal weight: 10.0000 chunk 337 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 410 optimal weight: 6.9990 chunk 324 optimal weight: 9.9990 chunk 628 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 382 optimal weight: 20.0000 chunk 467 optimal weight: 6.9990 chunk 728 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN D 398 HIS 1 324 GLN 1 431 GLN 1 437 HIS ** 3 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 546 GLN 3 682 GLN P 8 HIS P 203 GLN P 216 ASN Q 44 ASN ** 7 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 95 HIS S 91 GLN W 50 HIS r 50 ASN r 72 GLN s 34 ASN A 10 ASN H 258 ASN L 175 ASN ** L 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 400 ASN M 169 ASN O 19 HIS O 251 GLN X 94 GLN Z 102 ASN i 12 GLN i 73 HIS j 21 GLN m 125 ASN o 54 GLN p 58 ASN p 99 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.259 69554 Z= 0.624 Angle : 1.588 50.864 94074 Z= 1.021 Chirality : 0.313 6.471 10205 Planarity : 0.005 0.059 11741 Dihedral : 12.343 169.526 10507 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.57 % Favored : 94.41 % Rotamer: Outliers : 3.44 % Allowed : 12.33 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.22 (0.09), residues: 8115 helix: 1.19 (0.08), residues: 4482 sheet: -0.66 (0.27), residues: 374 loop : -1.23 (0.11), residues: 3259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 85 HIS 0.011 0.001 HIS O 19 PHE 0.032 0.002 PHE N 292 TYR 0.022 0.002 TYR M 406 ARG 0.008 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1018 time to evaluate : 5.920 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: 6 78 ASP cc_start: 0.8739 (t0) cc_final: 0.8221 (t0) REVERT: 2 37 ASN cc_start: 0.8334 (m110) cc_final: 0.8104 (m110) REVERT: 1 312 CYS cc_start: 0.9459 (m) cc_final: 0.9022 (m) REVERT: 1 436 GLN cc_start: 0.9056 (pt0) cc_final: 0.8713 (pp30) REVERT: 1 437 HIS cc_start: 0.8633 (OUTLIER) cc_final: 0.8386 (m-70) REVERT: 3 21 GLU cc_start: 0.9166 (mp0) cc_final: 0.8850 (mp0) REVERT: 3 52 CYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8685 (p) REVERT: 3 110 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.6991 (mm-40) REVERT: 3 436 ARG cc_start: 0.8459 (mtt90) cc_final: 0.8183 (mtt90) REVERT: 3 583 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8668 (t) REVERT: Q 14 ASP cc_start: 0.8752 (p0) cc_final: 0.8246 (p0) REVERT: S 92 ASN cc_start: 0.8842 (t0) cc_final: 0.8524 (t0) REVERT: T 9 ASP cc_start: 0.8677 (t0) cc_final: 0.8475 (t0) REVERT: T 64 ASP cc_start: 0.7712 (t0) cc_final: 0.7183 (t70) REVERT: T 83 LYS cc_start: 0.8873 (tptm) cc_final: 0.8661 (mmmm) REVERT: V 56 ASP cc_start: 0.9153 (m-30) cc_final: 0.8792 (m-30) REVERT: W 26 ASP cc_start: 0.8593 (p0) cc_final: 0.8280 (p0) REVERT: W 44 GLU cc_start: 0.9060 (tp30) cc_final: 0.8690 (tp30) REVERT: W 53 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7898 (mm-40) REVERT: W 113 GLU cc_start: 0.8981 (pt0) cc_final: 0.8695 (pp20) REVERT: W 114 THR cc_start: 0.9187 (m) cc_final: 0.8874 (m) REVERT: q 5 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8345 (tm-30) REVERT: q 48 TYR cc_start: 0.9117 (m-80) cc_final: 0.8910 (m-80) REVERT: q 76 ASP cc_start: 0.9353 (m-30) cc_final: 0.9036 (m-30) REVERT: s 43 TYR cc_start: 0.9389 (m-80) cc_final: 0.9157 (m-80) REVERT: A 23 TRP cc_start: 0.8569 (m100) cc_final: 0.8351 (m100) REVERT: H 258 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8902 (t160) REVERT: J 152 MET cc_start: 0.9536 (tpp) cc_final: 0.8903 (tpp) REVERT: L 60 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8247 (mm-30) REVERT: L 338 MET cc_start: 0.9467 (OUTLIER) cc_final: 0.9107 (ttp) REVERT: L 539 MET cc_start: 0.9302 (tmm) cc_final: 0.8718 (tmm) REVERT: M 184 HIS cc_start: 0.8879 (OUTLIER) cc_final: 0.8667 (t70) REVERT: M 250 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8657 (mt) REVERT: N 117 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8922 (mm-30) REVERT: O 44 GLN cc_start: 0.9266 (tp40) cc_final: 0.9051 (tp40) REVERT: O 140 ASN cc_start: 0.9249 (t0) cc_final: 0.8959 (t0) REVERT: O 268 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8747 (mp0) REVERT: O 290 SER cc_start: 0.9509 (OUTLIER) cc_final: 0.9170 (m) REVERT: U 28 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7103 (mm-30) REVERT: X 6 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8809 (pp) REVERT: Y 6 GLU cc_start: 0.9347 (mm-30) cc_final: 0.9067 (mm-30) REVERT: Y 10 GLU cc_start: 0.8435 (pm20) cc_final: 0.8225 (pm20) REVERT: Y 42 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9041 (mm) REVERT: Y 50 GLU cc_start: 0.8966 (mp0) cc_final: 0.8749 (mp0) REVERT: Y 80 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8363 (ptm160) REVERT: Y 81 GLU cc_start: 0.8585 (mp0) cc_final: 0.8343 (mm-30) REVERT: Y 82 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8817 (pttp) REVERT: Z 26 ARG cc_start: 0.8885 (mmm160) cc_final: 0.8477 (tmm-80) REVERT: Z 49 MET cc_start: 0.9448 (tpp) cc_final: 0.9059 (tpp) REVERT: Z 79 ASP cc_start: 0.8818 (m-30) cc_final: 0.8471 (m-30) REVERT: a 18 ILE cc_start: 0.9323 (mt) cc_final: 0.9108 (mp) REVERT: c 13 ASN cc_start: 0.9164 (t0) cc_final: 0.8627 (t0) REVERT: d 25 LYS cc_start: 0.8442 (ptmt) cc_final: 0.8062 (ptpt) REVERT: d 111 GLU cc_start: 0.8754 (mp0) cc_final: 0.8408 (mp0) REVERT: e 83 GLU cc_start: 0.8770 (tt0) cc_final: 0.8129 (tm-30) REVERT: e 87 LYS cc_start: 0.9153 (mmtp) cc_final: 0.8941 (tppp) REVERT: f 30 ASP cc_start: 0.9245 (OUTLIER) cc_final: 0.8953 (t0) REVERT: f 45 GLN cc_start: 0.8449 (tt0) cc_final: 0.8099 (tm-30) REVERT: g 33 GLU cc_start: 0.8339 (pm20) cc_final: 0.8080 (pt0) REVERT: g 80 ASP cc_start: 0.8794 (t70) cc_final: 0.8071 (t0) REVERT: g 97 TYR cc_start: 0.9107 (t80) cc_final: 0.8828 (t80) REVERT: g 101 ASN cc_start: 0.9118 (m110) cc_final: 0.8891 (m110) REVERT: g 112 ASP cc_start: 0.9009 (t70) cc_final: 0.8712 (t0) REVERT: h 102 GLU cc_start: 0.9058 (tp30) cc_final: 0.8743 (tp30) REVERT: i 4 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8658 (p) REVERT: j 43 ASP cc_start: 0.9038 (p0) cc_final: 0.8761 (p0) REVERT: j 55 ASP cc_start: 0.8803 (t0) cc_final: 0.8477 (t0) REVERT: j 58 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8647 (mm110) REVERT: l 28 MET cc_start: 0.9064 (mtp) cc_final: 0.8771 (mtm) REVERT: m 61 ASP cc_start: 0.9017 (t0) cc_final: 0.8553 (t70) REVERT: m 109 ASP cc_start: 0.9477 (m-30) cc_final: 0.9264 (m-30) REVERT: m 117 GLU cc_start: 0.8317 (pt0) cc_final: 0.7946 (pt0) REVERT: m 119 LYS cc_start: 0.8998 (mttp) cc_final: 0.8671 (mtmm) REVERT: n 131 SER cc_start: 0.9162 (t) cc_final: 0.8847 (t) REVERT: o 104 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: p 37 ASP cc_start: 0.8657 (m-30) cc_final: 0.8285 (m-30) outliers start: 248 outliers final: 120 residues processed: 1169 average time/residue: 1.5164 time to fit residues: 2329.2644 Evaluate side-chains 1091 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 954 time to evaluate : 5.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 164 LEU Chi-restraints excluded: chain 2 residue 165 THR Chi-restraints excluded: chain 2 residue 201 SER Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 363 THR Chi-restraints excluded: chain 1 residue 437 HIS Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 52 CYS Chi-restraints excluded: chain 3 residue 110 GLN Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 540 ASP Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 559 VAL Chi-restraints excluded: chain 3 residue 583 THR Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 254 ILE Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 81 ASN Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 105 VAL Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain 7 residue 17 VAL Chi-restraints excluded: chain 7 residue 87 CYS Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 75 VAL Chi-restraints excluded: chain q residue 62 VAL Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 127 TYR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 496 LEU Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 517 ASN Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 577 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 184 HIS Chi-restraints excluded: chain M residue 205 ILE Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 68 ASN Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 80 ARG Chi-restraints excluded: chain Y residue 82 LYS Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain d residue 3 ASN Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain e residue 49 THR Chi-restraints excluded: chain e residue 54 GLU Chi-restraints excluded: chain f residue 30 ASP Chi-restraints excluded: chain g residue 105 ILE Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 18 THR Chi-restraints excluded: chain j residue 60 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 144 ASP Chi-restraints excluded: chain m residue 49 GLN Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain m residue 110 ARG Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 116 ASP Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 20 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 23 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 404 optimal weight: 7.9990 chunk 226 optimal weight: 8.9990 chunk 606 optimal weight: 9.9990 chunk 495 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 729 optimal weight: 5.9990 chunk 788 optimal weight: 6.9990 chunk 649 optimal weight: 9.9990 chunk 723 optimal weight: 0.0870 chunk 248 optimal weight: 8.9990 chunk 585 optimal weight: 0.4980 overall best weight: 4.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 3 GLN D 421 GLN 1 437 HIS 3 402 ASN P 8 HIS Q 44 ASN 7 16 GLN 7 95 HIS S 91 GLN A 10 ASN H 163 GLN L 295 GLN ** L 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 HIS X 76 HIS X 94 GLN Z 102 ASN b 68 HIS i 12 GLN i 73 HIS m 125 ASN o 54 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 69554 Z= 0.577 Angle : 1.562 50.617 94074 Z= 1.010 Chirality : 0.309 6.387 10205 Planarity : 0.005 0.056 11741 Dihedral : 11.796 169.048 10471 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.30 % Allowed : 13.79 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.44 (0.10), residues: 8115 helix: 1.40 (0.08), residues: 4461 sheet: -0.63 (0.26), residues: 386 loop : -1.15 (0.11), residues: 3268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 144 HIS 0.008 0.001 HIS O 19 PHE 0.031 0.001 PHE N 292 TYR 0.022 0.001 TYR M 406 ARG 0.009 0.000 ARG k 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1000 time to evaluate : 5.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 78 ASP cc_start: 0.8772 (t0) cc_final: 0.8276 (t0) REVERT: 6 164 GLU cc_start: 0.9288 (tp30) cc_final: 0.8967 (tm-30) REVERT: D 227 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.9086 (tm-30) REVERT: D 259 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7961 (mmm) REVERT: 1 312 CYS cc_start: 0.9438 (m) cc_final: 0.9052 (m) REVERT: 1 436 GLN cc_start: 0.9026 (pt0) cc_final: 0.8527 (pp30) REVERT: 1 437 HIS cc_start: 0.8557 (OUTLIER) cc_final: 0.7568 (m90) REVERT: 3 21 GLU cc_start: 0.9146 (mp0) cc_final: 0.8826 (mp0) REVERT: 3 52 CYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8691 (p) REVERT: 3 436 ARG cc_start: 0.8524 (mtt90) cc_final: 0.8309 (mtt90) REVERT: 3 583 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8665 (t) REVERT: P 139 MET cc_start: 0.7173 (mmm) cc_final: 0.6964 (mmt) REVERT: Q 14 ASP cc_start: 0.8731 (p0) cc_final: 0.8231 (p0) REVERT: S 92 ASN cc_start: 0.8786 (t0) cc_final: 0.8469 (t0) REVERT: T 83 LYS cc_start: 0.8854 (tptm) cc_final: 0.8587 (mmmm) REVERT: V 56 ASP cc_start: 0.9165 (m-30) cc_final: 0.8816 (m-30) REVERT: W 44 GLU cc_start: 0.9138 (tp30) cc_final: 0.8771 (tp30) REVERT: W 53 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7868 (mm-40) REVERT: W 113 GLU cc_start: 0.8954 (pt0) cc_final: 0.8686 (pp20) REVERT: W 114 THR cc_start: 0.9192 (m) cc_final: 0.8870 (m) REVERT: q 5 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8384 (tm-30) REVERT: q 48 TYR cc_start: 0.9089 (m-80) cc_final: 0.8879 (m-80) REVERT: q 76 ASP cc_start: 0.9326 (m-30) cc_final: 0.9029 (m-30) REVERT: s 43 TYR cc_start: 0.9357 (m-80) cc_final: 0.9136 (m-80) REVERT: A 23 TRP cc_start: 0.8565 (m100) cc_final: 0.8314 (m100) REVERT: J 152 MET cc_start: 0.9517 (tpp) cc_final: 0.8930 (tpp) REVERT: L 60 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8270 (mm-30) REVERT: L 179 ASP cc_start: 0.8819 (m-30) cc_final: 0.8537 (m-30) REVERT: L 295 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8360 (tp40) REVERT: L 539 MET cc_start: 0.9302 (tmm) cc_final: 0.8711 (tmm) REVERT: M 250 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8564 (mt) REVERT: N 117 GLU cc_start: 0.9300 (mm-30) cc_final: 0.9001 (mm-30) REVERT: N 220 MET cc_start: 0.9182 (mtm) cc_final: 0.8929 (mtm) REVERT: O 140 ASN cc_start: 0.9234 (t0) cc_final: 0.8955 (t0) REVERT: O 268 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8674 (mm-30) REVERT: O 290 SER cc_start: 0.9488 (OUTLIER) cc_final: 0.9121 (m) REVERT: Y 1 VAL cc_start: 0.7113 (m) cc_final: 0.6840 (t) REVERT: Y 6 GLU cc_start: 0.9333 (mm-30) cc_final: 0.9050 (mm-30) REVERT: Y 42 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8981 (mm) REVERT: Y 50 GLU cc_start: 0.8994 (mp0) cc_final: 0.8755 (mp0) REVERT: Y 81 GLU cc_start: 0.8525 (mp0) cc_final: 0.8305 (mm-30) REVERT: Y 82 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8789 (ptmm) REVERT: Y 85 ASP cc_start: 0.9231 (t70) cc_final: 0.8656 (t0) REVERT: Y 130 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.9053 (mt-10) REVERT: Z 26 ARG cc_start: 0.8882 (mmm160) cc_final: 0.8522 (tmm-80) REVERT: Z 49 MET cc_start: 0.9438 (tpp) cc_final: 0.8964 (tpp) REVERT: Z 79 ASP cc_start: 0.8822 (m-30) cc_final: 0.8474 (m-30) REVERT: a 18 ILE cc_start: 0.9275 (mt) cc_final: 0.9052 (mp) REVERT: c 29 ILE cc_start: 0.9708 (mt) cc_final: 0.9457 (mp) REVERT: d 25 LYS cc_start: 0.8321 (ptmt) cc_final: 0.7912 (ptpt) REVERT: d 111 GLU cc_start: 0.8759 (mp0) cc_final: 0.8334 (mp0) REVERT: e 83 GLU cc_start: 0.8766 (tt0) cc_final: 0.8122 (tm-30) REVERT: e 87 LYS cc_start: 0.9147 (mmtp) cc_final: 0.8928 (tppp) REVERT: f 30 ASP cc_start: 0.9224 (OUTLIER) cc_final: 0.8932 (t0) REVERT: f 45 GLN cc_start: 0.8448 (tt0) cc_final: 0.8063 (tm-30) REVERT: g 80 ASP cc_start: 0.8715 (t70) cc_final: 0.8016 (t0) REVERT: g 97 TYR cc_start: 0.9064 (t80) cc_final: 0.8830 (t80) REVERT: g 112 ASP cc_start: 0.9004 (t70) cc_final: 0.8749 (t0) REVERT: h 102 GLU cc_start: 0.9053 (tp30) cc_final: 0.8813 (tp30) REVERT: h 117 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7774 (pmt100) REVERT: j 43 ASP cc_start: 0.9019 (p0) cc_final: 0.8716 (p0) REVERT: j 55 ASP cc_start: 0.8798 (t0) cc_final: 0.8413 (t0) REVERT: j 58 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8614 (mm110) REVERT: l 3 MET cc_start: 0.9035 (mmp) cc_final: 0.8618 (mmt) REVERT: l 7 MET cc_start: 0.8935 (ptt) cc_final: 0.8663 (pmt) REVERT: l 28 MET cc_start: 0.9066 (mtp) cc_final: 0.8718 (mtm) REVERT: m 61 ASP cc_start: 0.9008 (t0) cc_final: 0.8597 (t70) REVERT: m 109 ASP cc_start: 0.9475 (m-30) cc_final: 0.9264 (m-30) REVERT: m 119 LYS cc_start: 0.8993 (mttp) cc_final: 0.8618 (mtmm) REVERT: n 131 SER cc_start: 0.9119 (t) cc_final: 0.8792 (t) REVERT: o 104 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8361 (tm-30) REVERT: p 37 ASP cc_start: 0.8598 (m-30) cc_final: 0.8241 (m-30) outliers start: 238 outliers final: 128 residues processed: 1152 average time/residue: 1.4653 time to fit residues: 2210.9461 Evaluate side-chains 1097 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 954 time to evaluate : 5.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 164 LEU Chi-restraints excluded: chain 2 residue 201 SER Chi-restraints excluded: chain 1 residue 273 SER Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 363 THR Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 437 HIS Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 52 CYS Chi-restraints excluded: chain 3 residue 103 LEU Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 366 THR Chi-restraints excluded: chain 3 residue 540 ASP Chi-restraints excluded: chain 3 residue 559 VAL Chi-restraints excluded: chain 3 residue 583 THR Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 254 ILE Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 81 ASN Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 105 VAL Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain 7 residue 17 VAL Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 118 LYS Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 127 TYR Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 70 SER Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 295 GLN Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 577 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 205 ILE Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain Y residue 41 SER Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 82 LYS Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain d residue 3 ASN Chi-restraints excluded: chain d residue 47 MET Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain e residue 54 GLU Chi-restraints excluded: chain f residue 30 ASP Chi-restraints excluded: chain g residue 105 ILE Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 117 ARG Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 60 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 144 ASP Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 110 ARG Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 116 ASP Chi-restraints excluded: chain o residue 20 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 16 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 720 optimal weight: 9.9990 chunk 548 optimal weight: 6.9990 chunk 378 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 348 optimal weight: 10.0000 chunk 489 optimal weight: 2.9990 chunk 732 optimal weight: 10.0000 chunk 775 optimal weight: 30.0000 chunk 382 optimal weight: 8.9990 chunk 693 optimal weight: 0.7980 chunk 208 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 121 GLN 1 324 GLN 1 437 HIS ** 3 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 HIS Q 44 ASN ** 7 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 36 ASN 7 95 HIS S 91 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 295 GLN ** O 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 72 GLN X 94 GLN Z 102 ASN g 84 GLN i 12 GLN i 73 HIS m 125 ASN ** n 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 90 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.242 69554 Z= 0.589 Angle : 1.565 50.658 94074 Z= 1.012 Chirality : 0.309 6.395 10205 Planarity : 0.004 0.054 11741 Dihedral : 11.416 168.072 10455 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.62 % Allowed : 14.26 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.55 (0.10), residues: 8115 helix: 1.48 (0.08), residues: 4454 sheet: -0.70 (0.26), residues: 401 loop : -1.08 (0.11), residues: 3260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP X 85 HIS 0.006 0.001 HIS T 35 PHE 0.030 0.001 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.009 0.000 ARG O 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1255 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 994 time to evaluate : 6.062 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: 6 78 ASP cc_start: 0.8824 (t0) cc_final: 0.8334 (t0) REVERT: D 227 GLU cc_start: 0.9374 (OUTLIER) cc_final: 0.9110 (tm-30) REVERT: D 259 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7898 (mmm) REVERT: 1 312 CYS cc_start: 0.9445 (m) cc_final: 0.9062 (m) REVERT: 1 436 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8589 (pp30) REVERT: 1 437 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.7554 (m90) REVERT: 3 21 GLU cc_start: 0.9081 (mp0) cc_final: 0.8806 (mp0) REVERT: 3 52 CYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8673 (p) REVERT: 3 272 ASP cc_start: 0.9122 (t70) cc_final: 0.8882 (t0) REVERT: 3 436 ARG cc_start: 0.8571 (mtt90) cc_final: 0.8339 (mtt90) REVERT: 3 583 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8677 (t) REVERT: Q 14 ASP cc_start: 0.8764 (p0) cc_final: 0.8250 (p0) REVERT: S 92 ASN cc_start: 0.8759 (t0) cc_final: 0.8458 (t0) REVERT: T 64 ASP cc_start: 0.7739 (t0) cc_final: 0.7196 (t70) REVERT: T 71 MET cc_start: 0.8359 (mmp) cc_final: 0.8004 (mmp) REVERT: T 72 CYS cc_start: 0.8613 (m) cc_final: 0.7609 (t) REVERT: T 83 LYS cc_start: 0.8842 (tptm) cc_final: 0.8575 (mmmm) REVERT: W 44 GLU cc_start: 0.9172 (tp30) cc_final: 0.8734 (tp30) REVERT: W 53 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7881 (mm-40) REVERT: W 113 GLU cc_start: 0.8969 (pt0) cc_final: 0.8688 (pp20) REVERT: W 114 THR cc_start: 0.9223 (m) cc_final: 0.8890 (m) REVERT: q 5 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8380 (tm-30) REVERT: q 48 TYR cc_start: 0.9095 (m-80) cc_final: 0.8860 (m-80) REVERT: q 76 ASP cc_start: 0.9337 (m-30) cc_final: 0.9030 (m-30) REVERT: r 59 ARG cc_start: 0.9350 (OUTLIER) cc_final: 0.8983 (ttp-110) REVERT: s 43 TYR cc_start: 0.9355 (m-80) cc_final: 0.9136 (m-80) REVERT: A 23 TRP cc_start: 0.8603 (m100) cc_final: 0.8363 (m100) REVERT: J 152 MET cc_start: 0.9513 (tpp) cc_final: 0.8935 (tpp) REVERT: L 179 ASP cc_start: 0.8816 (m-30) cc_final: 0.8542 (m-30) REVERT: L 539 MET cc_start: 0.9334 (tmm) cc_final: 0.8641 (tmm) REVERT: L 589 MET cc_start: 0.9323 (tpt) cc_final: 0.9069 (tpt) REVERT: M 245 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8617 (mpt90) REVERT: M 250 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8561 (mt) REVERT: N 117 GLU cc_start: 0.9306 (mm-30) cc_final: 0.9090 (mm-30) REVERT: O 140 ASN cc_start: 0.9227 (t0) cc_final: 0.8975 (t0) REVERT: O 195 THR cc_start: 0.9543 (OUTLIER) cc_final: 0.9054 (p) REVERT: O 268 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8676 (mm-30) REVERT: O 290 SER cc_start: 0.9509 (OUTLIER) cc_final: 0.9114 (m) REVERT: U 28 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7052 (mm-30) REVERT: X 6 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8816 (pp) REVERT: Y 6 GLU cc_start: 0.9330 (mm-30) cc_final: 0.9032 (mm-30) REVERT: Y 42 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8985 (mm) REVERT: Y 50 GLU cc_start: 0.9010 (mp0) cc_final: 0.8752 (mp0) REVERT: Y 81 GLU cc_start: 0.8569 (mp0) cc_final: 0.8103 (tp30) REVERT: Y 82 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8784 (ptmm) REVERT: Y 85 ASP cc_start: 0.9232 (t70) cc_final: 0.8611 (t0) REVERT: Y 130 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.8986 (mt-10) REVERT: Z 26 ARG cc_start: 0.8916 (mmm160) cc_final: 0.8589 (tmm-80) REVERT: Z 49 MET cc_start: 0.9428 (tpp) cc_final: 0.9028 (tpp) REVERT: Z 79 ASP cc_start: 0.8834 (m-30) cc_final: 0.8483 (m-30) REVERT: a 18 ILE cc_start: 0.9278 (mt) cc_final: 0.9062 (mp) REVERT: c 29 ILE cc_start: 0.9712 (mt) cc_final: 0.9460 (mp) REVERT: d 25 LYS cc_start: 0.8307 (ptmt) cc_final: 0.7871 (ptpt) REVERT: d 105 GLU cc_start: 0.8957 (pp20) cc_final: 0.8601 (pp20) REVERT: d 111 GLU cc_start: 0.8834 (mp0) cc_final: 0.8497 (mp0) REVERT: e 83 GLU cc_start: 0.8772 (tt0) cc_final: 0.8130 (tm-30) REVERT: e 87 LYS cc_start: 0.9192 (mmtp) cc_final: 0.8950 (tppp) REVERT: f 45 GLN cc_start: 0.8486 (tt0) cc_final: 0.8109 (tm-30) REVERT: g 80 ASP cc_start: 0.8699 (t70) cc_final: 0.7997 (t0) REVERT: g 112 ASP cc_start: 0.8994 (t70) cc_final: 0.8767 (t0) REVERT: h 102 GLU cc_start: 0.9077 (tp30) cc_final: 0.8791 (tp30) REVERT: j 43 ASP cc_start: 0.9012 (p0) cc_final: 0.8686 (p0) REVERT: j 55 ASP cc_start: 0.8839 (t0) cc_final: 0.8474 (t0) REVERT: j 58 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8684 (mm-40) REVERT: k 52 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8768 (mtm-85) REVERT: l 28 MET cc_start: 0.9113 (mtp) cc_final: 0.8787 (mtm) REVERT: m 61 ASP cc_start: 0.9048 (t0) cc_final: 0.8723 (t70) REVERT: m 109 ASP cc_start: 0.9477 (m-30) cc_final: 0.9271 (m-30) REVERT: m 117 GLU cc_start: 0.8268 (pt0) cc_final: 0.7874 (pt0) REVERT: m 119 LYS cc_start: 0.8985 (mttp) cc_final: 0.8628 (mtmm) REVERT: n 131 SER cc_start: 0.9103 (t) cc_final: 0.8774 (t) REVERT: o 104 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: p 37 ASP cc_start: 0.8547 (m-30) cc_final: 0.8109 (m-30) outliers start: 261 outliers final: 155 residues processed: 1161 average time/residue: 1.4664 time to fit residues: 2236.2646 Evaluate side-chains 1135 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 962 time to evaluate : 5.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 164 LEU Chi-restraints excluded: chain 2 residue 201 SER Chi-restraints excluded: chain 1 residue 45 THR Chi-restraints excluded: chain 1 residue 273 SER Chi-restraints excluded: chain 1 residue 323 VAL Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 363 THR Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 436 GLN Chi-restraints excluded: chain 1 residue 437 HIS Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 52 CYS Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 366 THR Chi-restraints excluded: chain 3 residue 441 GLU Chi-restraints excluded: chain 3 residue 540 ASP Chi-restraints excluded: chain 3 residue 559 VAL Chi-restraints excluded: chain 3 residue 583 THR Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 254 ILE Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 81 ASN Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 105 VAL Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain 7 residue 17 VAL Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 75 VAL Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 127 TYR Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 59 ARG Chi-restraints excluded: chain r residue 70 SER Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 295 GLN Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 577 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 205 ILE Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 274 SER Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain O residue 19 HIS Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 195 THR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 68 ASN Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 82 LYS Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Z residue 50 MET Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain c residue 9 ASN Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain d residue 3 ASN Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain e residue 54 GLU Chi-restraints excluded: chain g residue 105 ILE Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 112 THR Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 18 THR Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain j residue 60 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 52 ARG Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 14 ARG Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 144 ASP Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 110 ARG Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 116 ASP Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 20 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 150 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 645 optimal weight: 10.0000 chunk 440 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 577 optimal weight: 8.9990 chunk 319 optimal weight: 7.9990 chunk 661 optimal weight: 8.9990 chunk 535 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 395 optimal weight: 10.0000 chunk 695 optimal weight: 0.0040 chunk 195 optimal weight: 7.9990 overall best weight: 4.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 437 HIS P 8 HIS P 203 GLN ** 7 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 95 HIS S 91 GLN K 91 GLN L 295 GLN X 76 HIS Z 102 ASN i 12 GLN m 125 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 69554 Z= 0.580 Angle : 1.563 50.628 94074 Z= 1.010 Chirality : 0.309 6.379 10205 Planarity : 0.004 0.074 11741 Dihedral : 11.148 167.872 10453 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.76 % Allowed : 14.76 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.62 (0.10), residues: 8115 helix: 1.54 (0.08), residues: 4445 sheet: -0.67 (0.27), residues: 389 loop : -1.03 (0.11), residues: 3281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 85 HIS 0.010 0.001 HIS 1 437 PHE 0.030 0.001 PHE N 292 TYR 0.021 0.001 TYR M 406 ARG 0.010 0.000 ARG Y 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 993 time to evaluate : 6.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 78 ASP cc_start: 0.8841 (t0) cc_final: 0.8395 (t0) REVERT: 6 164 GLU cc_start: 0.9313 (tp30) cc_final: 0.8999 (tm-30) REVERT: D 227 GLU cc_start: 0.9420 (OUTLIER) cc_final: 0.9126 (tm-30) REVERT: D 259 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7889 (mmm) REVERT: 1 312 CYS cc_start: 0.9436 (m) cc_final: 0.9055 (m) REVERT: 1 436 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8609 (pp30) REVERT: 1 437 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.7366 (m170) REVERT: 3 21 GLU cc_start: 0.9078 (mp0) cc_final: 0.8801 (mp0) REVERT: 3 52 CYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8659 (p) REVERT: 3 272 ASP cc_start: 0.9141 (t70) cc_final: 0.8922 (t0) REVERT: 3 436 ARG cc_start: 0.8604 (mtt90) cc_final: 0.8397 (mtt90) REVERT: 3 437 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7654 (m-70) REVERT: 3 583 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8648 (t) REVERT: P 57 MET cc_start: 0.9528 (mmp) cc_final: 0.9245 (mmm) REVERT: Q 14 ASP cc_start: 0.8751 (p0) cc_final: 0.8241 (p0) REVERT: 7 34 GLU cc_start: 0.8840 (pt0) cc_final: 0.8556 (pt0) REVERT: S 92 ASN cc_start: 0.8746 (t0) cc_final: 0.8459 (t0) REVERT: T 64 ASP cc_start: 0.7755 (t0) cc_final: 0.7211 (t70) REVERT: T 83 LYS cc_start: 0.8849 (tptm) cc_final: 0.8596 (mmmm) REVERT: W 44 GLU cc_start: 0.9177 (tp30) cc_final: 0.8745 (tp30) REVERT: W 53 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7877 (mm-40) REVERT: W 113 GLU cc_start: 0.8969 (pt0) cc_final: 0.8692 (pp20) REVERT: W 114 THR cc_start: 0.9228 (m) cc_final: 0.8883 (m) REVERT: q 5 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8365 (tm-30) REVERT: q 48 TYR cc_start: 0.9093 (m-80) cc_final: 0.8865 (m-80) REVERT: q 76 ASP cc_start: 0.9337 (m-30) cc_final: 0.9036 (m-30) REVERT: r 59 ARG cc_start: 0.9344 (OUTLIER) cc_final: 0.8996 (ttp-110) REVERT: s 43 TYR cc_start: 0.9351 (m-80) cc_final: 0.9127 (m-80) REVERT: A 23 TRP cc_start: 0.8600 (m100) cc_final: 0.8376 (m100) REVERT: H 181 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8999 (mpp) REVERT: J 152 MET cc_start: 0.9495 (tpp) cc_final: 0.8946 (tpp) REVERT: L 60 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8386 (mm-30) REVERT: L 179 ASP cc_start: 0.8787 (m-30) cc_final: 0.8518 (m-30) REVERT: L 539 MET cc_start: 0.9331 (tmm) cc_final: 0.8637 (tmm) REVERT: L 589 MET cc_start: 0.9316 (tpt) cc_final: 0.9063 (tpt) REVERT: M 245 ARG cc_start: 0.9305 (OUTLIER) cc_final: 0.8612 (mpt90) REVERT: M 250 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8555 (mt) REVERT: M 271 MET cc_start: 0.9449 (mmm) cc_final: 0.9127 (mmm) REVERT: N 117 GLU cc_start: 0.9303 (mm-30) cc_final: 0.9084 (mm-30) REVERT: N 220 MET cc_start: 0.9284 (mtp) cc_final: 0.8985 (mtm) REVERT: O 140 ASN cc_start: 0.9211 (t0) cc_final: 0.8963 (t0) REVERT: O 268 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8700 (mm-30) REVERT: U 28 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7157 (mm-30) REVERT: X 6 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8789 (pp) REVERT: Y 6 GLU cc_start: 0.9303 (mm-30) cc_final: 0.9028 (mm-30) REVERT: Y 42 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8977 (mm) REVERT: Y 82 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8918 (ptmm) REVERT: Y 85 ASP cc_start: 0.9229 (t70) cc_final: 0.8726 (t0) REVERT: Y 130 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8959 (mt-10) REVERT: Z 26 ARG cc_start: 0.8921 (mmm160) cc_final: 0.8621 (tmm-80) REVERT: Z 49 MET cc_start: 0.9402 (tpp) cc_final: 0.9041 (tpp) REVERT: Z 79 ASP cc_start: 0.8834 (m-30) cc_final: 0.8476 (m-30) REVERT: a 18 ILE cc_start: 0.9268 (mt) cc_final: 0.9059 (mp) REVERT: d 16 ASP cc_start: 0.8653 (m-30) cc_final: 0.8174 (t70) REVERT: d 25 LYS cc_start: 0.8288 (ptmt) cc_final: 0.7839 (ptpt) REVERT: d 105 GLU cc_start: 0.8957 (pp20) cc_final: 0.8655 (pp20) REVERT: d 111 GLU cc_start: 0.8892 (mp0) cc_final: 0.8578 (mp0) REVERT: e 83 GLU cc_start: 0.8770 (tt0) cc_final: 0.8132 (tm-30) REVERT: e 87 LYS cc_start: 0.9216 (mmtp) cc_final: 0.8968 (tppp) REVERT: f 45 GLN cc_start: 0.8474 (tt0) cc_final: 0.8108 (tm-30) REVERT: g 33 GLU cc_start: 0.8319 (pm20) cc_final: 0.8054 (pt0) REVERT: g 80 ASP cc_start: 0.8650 (t70) cc_final: 0.7940 (t0) REVERT: g 112 ASP cc_start: 0.8989 (t70) cc_final: 0.8765 (t0) REVERT: h 102 GLU cc_start: 0.9082 (tp30) cc_final: 0.8790 (tp30) REVERT: h 117 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7858 (pmt100) REVERT: j 43 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8691 (p0) REVERT: j 55 ASP cc_start: 0.8853 (t0) cc_final: 0.8464 (t0) REVERT: j 58 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8665 (mm-40) REVERT: k 52 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8753 (mtm-85) REVERT: l 28 MET cc_start: 0.9107 (mtp) cc_final: 0.8794 (mtm) REVERT: m 61 ASP cc_start: 0.9058 (t0) cc_final: 0.8785 (t70) REVERT: m 109 ASP cc_start: 0.9479 (m-30) cc_final: 0.9268 (m-30) REVERT: m 119 LYS cc_start: 0.8993 (mttp) cc_final: 0.8594 (mtmm) REVERT: n 131 SER cc_start: 0.9088 (t) cc_final: 0.8758 (t) REVERT: o 104 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8293 (tm-30) REVERT: p 37 ASP cc_start: 0.8525 (m-30) cc_final: 0.8081 (m-30) outliers start: 271 outliers final: 160 residues processed: 1166 average time/residue: 1.4793 time to fit residues: 2275.9523 Evaluate side-chains 1142 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 962 time to evaluate : 5.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 154 VAL Chi-restraints excluded: chain 2 residue 164 LEU Chi-restraints excluded: chain 2 residue 201 SER Chi-restraints excluded: chain 1 residue 45 THR Chi-restraints excluded: chain 1 residue 273 SER Chi-restraints excluded: chain 1 residue 323 VAL Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 363 THR Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 436 GLN Chi-restraints excluded: chain 1 residue 437 HIS Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 52 CYS Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 366 THR Chi-restraints excluded: chain 3 residue 368 ILE Chi-restraints excluded: chain 3 residue 437 HIS Chi-restraints excluded: chain 3 residue 441 GLU Chi-restraints excluded: chain 3 residue 451 VAL Chi-restraints excluded: chain 3 residue 540 ASP Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 559 VAL Chi-restraints excluded: chain 3 residue 583 THR Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 3 residue 656 VAL Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 254 ILE Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 81 ASN Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 105 VAL Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain 7 residue 17 VAL Chi-restraints excluded: chain S residue 17 GLU Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 75 VAL Chi-restraints excluded: chain W residue 118 LYS Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 59 ARG Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 577 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 205 ILE Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 274 SER Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain O residue 19 HIS Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 87 TYR Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 34 GLN Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 68 ASN Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain Y residue 41 SER Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 80 ARG Chi-restraints excluded: chain Y residue 82 LYS Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Z residue 50 MET Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain c residue 9 ASN Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain d residue 3 ASN Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 49 THR Chi-restraints excluded: chain e residue 54 GLU Chi-restraints excluded: chain g residue 105 ILE Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 117 ARG Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 112 THR Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 18 THR Chi-restraints excluded: chain j residue 43 ASP Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 52 ARG Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 14 ARG Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 144 ASP Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 49 GLN Chi-restraints excluded: chain m residue 110 ARG Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 116 ASP Chi-restraints excluded: chain n residue 149 MET Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 20 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 150 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 260 optimal weight: 2.9990 chunk 698 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 455 optimal weight: 0.9990 chunk 191 optimal weight: 20.0000 chunk 775 optimal weight: 40.0000 chunk 644 optimal weight: 9.9990 chunk 359 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 256 optimal weight: 9.9990 chunk 407 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 324 GLN 1 437 HIS P 8 HIS ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 91 GLN H 258 ASN L 170 GLN L 295 GLN Z 102 ASN e 28 ASN i 12 GLN ** m 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.239 69554 Z= 0.600 Angle : 1.571 50.651 94074 Z= 1.014 Chirality : 0.309 6.390 10205 Planarity : 0.004 0.054 11741 Dihedral : 11.043 167.140 10449 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.66 % Allowed : 15.37 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.65 (0.10), residues: 8115 helix: 1.56 (0.08), residues: 4424 sheet: -0.64 (0.27), residues: 389 loop : -1.01 (0.11), residues: 3302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 85 HIS 0.021 0.001 HIS 1 437 PHE 0.030 0.001 PHE N 292 TYR 0.021 0.001 TYR M 406 ARG 0.012 0.000 ARG O 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 968 time to evaluate : 5.945 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: 6 78 ASP cc_start: 0.8912 (t0) cc_final: 0.8503 (t0) REVERT: 6 164 GLU cc_start: 0.9294 (tp30) cc_final: 0.8968 (tm-30) REVERT: D 259 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7943 (mmm) REVERT: D 410 MET cc_start: 0.9003 (mtm) cc_final: 0.8757 (mtm) REVERT: 1 312 CYS cc_start: 0.9471 (m) cc_final: 0.9179 (m) REVERT: 1 436 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8770 (pp30) REVERT: 3 21 GLU cc_start: 0.9039 (mp0) cc_final: 0.8801 (mp0) REVERT: 3 52 CYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8644 (p) REVERT: 3 272 ASP cc_start: 0.9145 (t70) cc_final: 0.8941 (t0) REVERT: 3 436 ARG cc_start: 0.8593 (mtt90) cc_final: 0.8383 (mtt90) REVERT: 3 437 HIS cc_start: 0.8129 (OUTLIER) cc_final: 0.7564 (m-70) REVERT: 3 583 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8728 (t) REVERT: Q 14 ASP cc_start: 0.8761 (p0) cc_final: 0.8235 (p0) REVERT: S 92 ASN cc_start: 0.8751 (t0) cc_final: 0.8476 (t0) REVERT: T 64 ASP cc_start: 0.7798 (t0) cc_final: 0.7239 (t70) REVERT: T 83 LYS cc_start: 0.8861 (tptm) cc_final: 0.8602 (mmmm) REVERT: W 44 GLU cc_start: 0.9192 (tp30) cc_final: 0.8767 (tp30) REVERT: W 53 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.7904 (mm-40) REVERT: W 113 GLU cc_start: 0.8968 (pt0) cc_final: 0.8690 (pp20) REVERT: W 114 THR cc_start: 0.9236 (m) cc_final: 0.8892 (m) REVERT: q 5 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8347 (tm-30) REVERT: q 76 ASP cc_start: 0.9353 (m-30) cc_final: 0.9049 (m-30) REVERT: r 59 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.8965 (ttp-110) REVERT: r 108 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8713 (p0) REVERT: s 43 TYR cc_start: 0.9356 (m-80) cc_final: 0.9137 (m-80) REVERT: H 181 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8979 (mpp) REVERT: J 152 MET cc_start: 0.9507 (tpp) cc_final: 0.8971 (tpp) REVERT: L 179 ASP cc_start: 0.8813 (m-30) cc_final: 0.8532 (m-30) REVERT: L 321 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: L 539 MET cc_start: 0.9354 (tmm) cc_final: 0.8630 (tmm) REVERT: L 589 MET cc_start: 0.9318 (tpt) cc_final: 0.9022 (tpt) REVERT: M 187 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8354 (p0) REVERT: M 245 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8529 (mpt90) REVERT: M 250 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8565 (mt) REVERT: N 117 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8949 (mm-30) REVERT: N 220 MET cc_start: 0.9290 (mtp) cc_final: 0.8967 (mtm) REVERT: O 48 MET cc_start: 0.9382 (mmm) cc_final: 0.9077 (mtp) REVERT: O 140 ASN cc_start: 0.9214 (t0) cc_final: 0.8948 (t0) REVERT: O 195 THR cc_start: 0.9577 (OUTLIER) cc_final: 0.9233 (p) REVERT: O 268 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8679 (mm-30) REVERT: X 6 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8775 (pp) REVERT: Y 6 GLU cc_start: 0.9312 (mm-30) cc_final: 0.9070 (mm-30) REVERT: Y 81 GLU cc_start: 0.8406 (mp0) cc_final: 0.8087 (tp30) REVERT: Y 82 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8831 (ptmm) REVERT: Y 85 ASP cc_start: 0.9163 (t70) cc_final: 0.8510 (t0) REVERT: Y 130 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8939 (mt-10) REVERT: Z 26 ARG cc_start: 0.8930 (mmm160) cc_final: 0.8646 (tmm-80) REVERT: Z 49 MET cc_start: 0.9408 (tpp) cc_final: 0.9081 (tpp) REVERT: Z 79 ASP cc_start: 0.8850 (m-30) cc_final: 0.8496 (m-30) REVERT: a 18 ILE cc_start: 0.9282 (mt) cc_final: 0.9073 (mp) REVERT: d 16 ASP cc_start: 0.8725 (m-30) cc_final: 0.8243 (t70) REVERT: d 25 LYS cc_start: 0.8317 (ptmt) cc_final: 0.7871 (ptpt) REVERT: d 105 GLU cc_start: 0.8956 (pp20) cc_final: 0.8618 (pp20) REVERT: d 111 GLU cc_start: 0.8978 (mp0) cc_final: 0.8773 (mp0) REVERT: e 83 GLU cc_start: 0.8776 (tt0) cc_final: 0.8143 (tm-30) REVERT: e 87 LYS cc_start: 0.9232 (mmtp) cc_final: 0.9026 (tppp) REVERT: f 45 GLN cc_start: 0.8530 (tt0) cc_final: 0.8149 (tm-30) REVERT: g 80 ASP cc_start: 0.8674 (t70) cc_final: 0.7997 (t0) REVERT: g 112 ASP cc_start: 0.8995 (t70) cc_final: 0.8773 (t0) REVERT: h 102 GLU cc_start: 0.9097 (tp30) cc_final: 0.8810 (tp30) REVERT: h 117 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7903 (pmt100) REVERT: j 11 TYR cc_start: 0.8607 (t80) cc_final: 0.8376 (t80) REVERT: j 43 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8690 (p0) REVERT: j 55 ASP cc_start: 0.8862 (t0) cc_final: 0.8397 (t0) REVERT: j 58 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8637 (mm-40) REVERT: k 52 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8647 (mtm-85) REVERT: k 92 PHE cc_start: 0.8427 (t80) cc_final: 0.8070 (t80) REVERT: l 28 MET cc_start: 0.9123 (mtp) cc_final: 0.8851 (mtm) REVERT: m 61 ASP cc_start: 0.9091 (t0) cc_final: 0.8812 (t70) REVERT: m 109 ASP cc_start: 0.9471 (m-30) cc_final: 0.9223 (m-30) REVERT: m 117 GLU cc_start: 0.8188 (pt0) cc_final: 0.7782 (pt0) REVERT: m 119 LYS cc_start: 0.9040 (mttp) cc_final: 0.8675 (mtmm) REVERT: n 131 SER cc_start: 0.9098 (t) cc_final: 0.8769 (t) REVERT: o 104 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8507 (tm-30) REVERT: p 37 ASP cc_start: 0.8512 (m-30) cc_final: 0.8072 (m-30) outliers start: 264 outliers final: 163 residues processed: 1139 average time/residue: 1.4761 time to fit residues: 2202.3251 Evaluate side-chains 1132 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 948 time to evaluate : 5.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain 6 residue 113 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 154 VAL Chi-restraints excluded: chain 2 residue 164 LEU Chi-restraints excluded: chain 2 residue 201 SER Chi-restraints excluded: chain 1 residue 45 THR Chi-restraints excluded: chain 1 residue 323 VAL Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 363 THR Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 436 GLN Chi-restraints excluded: chain 1 residue 437 HIS Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 52 CYS Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 366 THR Chi-restraints excluded: chain 3 residue 368 ILE Chi-restraints excluded: chain 3 residue 437 HIS Chi-restraints excluded: chain 3 residue 441 GLU Chi-restraints excluded: chain 3 residue 451 VAL Chi-restraints excluded: chain 3 residue 540 ASP Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 559 VAL Chi-restraints excluded: chain 3 residue 583 THR Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 3 residue 656 VAL Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 254 ILE Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 81 ASN Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 105 VAL Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain 7 residue 17 VAL Chi-restraints excluded: chain 7 residue 87 CYS Chi-restraints excluded: chain S residue 17 GLU Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 75 VAL Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 59 ARG Chi-restraints excluded: chain r residue 108 ASP Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 321 GLN Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 577 THR Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 205 ILE Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 274 SER Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain O residue 19 HIS Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 195 THR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 87 TYR Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 34 GLN Chi-restraints excluded: chain X residue 68 ASN Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain Y residue 41 SER Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 80 ARG Chi-restraints excluded: chain Y residue 82 LYS Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Z residue 50 MET Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain c residue 9 ASN Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain d residue 3 ASN Chi-restraints excluded: chain d residue 47 MET Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 49 THR Chi-restraints excluded: chain e residue 54 GLU Chi-restraints excluded: chain g residue 105 ILE Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 117 ARG Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 112 THR Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 18 THR Chi-restraints excluded: chain j residue 43 ASP Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 52 ARG Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 14 ARG Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 144 ASP Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 49 GLN Chi-restraints excluded: chain m residue 110 ARG Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 116 ASP Chi-restraints excluded: chain n residue 149 MET Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 20 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 150 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 748 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 442 optimal weight: 8.9990 chunk 566 optimal weight: 10.0000 chunk 439 optimal weight: 3.9990 chunk 653 optimal weight: 7.9990 chunk 433 optimal weight: 4.9990 chunk 772 optimal weight: 2.9990 chunk 483 optimal weight: 10.0000 chunk 471 optimal weight: 7.9990 chunk 356 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 324 GLN 1 437 HIS P 8 HIS ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 95 HIS H 258 ASN L 175 ASN L 295 GLN ** O 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 102 ASN i 12 GLN ** m 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 69554 Z= 0.590 Angle : 1.570 50.642 94074 Z= 1.013 Chirality : 0.309 6.385 10205 Planarity : 0.004 0.055 11741 Dihedral : 10.943 167.179 10449 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.51 % Allowed : 15.90 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.68 (0.10), residues: 8115 helix: 1.59 (0.08), residues: 4415 sheet: -0.64 (0.27), residues: 388 loop : -0.99 (0.11), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 85 HIS 0.004 0.001 HIS 3 101 PHE 0.035 0.001 PHE L 335 TYR 0.021 0.001 TYR M 406 ARG 0.011 0.000 ARG O 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 973 time to evaluate : 5.841 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: 6 78 ASP cc_start: 0.8919 (t0) cc_final: 0.8548 (t0) REVERT: D 259 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7936 (mmm) REVERT: D 410 MET cc_start: 0.8993 (mtm) cc_final: 0.8769 (mtm) REVERT: 1 312 CYS cc_start: 0.9464 (m) cc_final: 0.9175 (m) REVERT: 1 436 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8806 (tm-30) REVERT: 1 437 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.8129 (m-70) REVERT: 3 21 GLU cc_start: 0.9037 (mp0) cc_final: 0.8798 (mp0) REVERT: 3 52 CYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8640 (p) REVERT: 3 436 ARG cc_start: 0.8604 (mtt90) cc_final: 0.8395 (mtt90) REVERT: 3 437 HIS cc_start: 0.8156 (OUTLIER) cc_final: 0.7528 (m-70) REVERT: 3 583 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8707 (t) REVERT: P 8 HIS cc_start: 0.8744 (p90) cc_final: 0.8538 (p-80) REVERT: Q 14 ASP cc_start: 0.8751 (p0) cc_final: 0.8228 (p0) REVERT: 7 3 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8663 (mm110) REVERT: S 92 ASN cc_start: 0.8729 (t0) cc_final: 0.8461 (t0) REVERT: T 30 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8397 (mp) REVERT: T 64 ASP cc_start: 0.7803 (t0) cc_final: 0.7229 (t70) REVERT: T 72 CYS cc_start: 0.8492 (m) cc_final: 0.8124 (t) REVERT: T 83 LYS cc_start: 0.8868 (tptm) cc_final: 0.8608 (mmmm) REVERT: W 44 GLU cc_start: 0.9190 (tp30) cc_final: 0.8765 (tp30) REVERT: W 53 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7879 (mm-40) REVERT: W 113 GLU cc_start: 0.8974 (pt0) cc_final: 0.8700 (pp20) REVERT: W 114 THR cc_start: 0.9253 (m) cc_final: 0.8919 (m) REVERT: q 5 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8341 (tm-30) REVERT: q 76 ASP cc_start: 0.9351 (m-30) cc_final: 0.9047 (m-30) REVERT: r 59 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.8939 (ttp-110) REVERT: r 108 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8706 (p0) REVERT: s 43 TYR cc_start: 0.9349 (m-80) cc_final: 0.9117 (m-80) REVERT: H 181 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8990 (mpp) REVERT: J 152 MET cc_start: 0.9487 (tpp) cc_final: 0.8920 (tpp) REVERT: L 179 ASP cc_start: 0.8797 (m-30) cc_final: 0.8523 (m-30) REVERT: L 321 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: L 539 MET cc_start: 0.9350 (tmm) cc_final: 0.8627 (tmm) REVERT: L 589 MET cc_start: 0.9328 (tpt) cc_final: 0.9079 (tpt) REVERT: M 123 GLU cc_start: 0.9312 (mp0) cc_final: 0.8861 (mp0) REVERT: M 187 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8374 (p0) REVERT: M 210 TYR cc_start: 0.8826 (t80) cc_final: 0.8513 (t80) REVERT: M 245 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.8504 (mpt90) REVERT: M 250 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8566 (mt) REVERT: M 271 MET cc_start: 0.9469 (mmm) cc_final: 0.9176 (mmm) REVERT: N 40 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9140 (tt) REVERT: N 117 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8943 (mm-30) REVERT: O 140 ASN cc_start: 0.9209 (t0) cc_final: 0.8947 (t0) REVERT: O 268 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8685 (mm-30) REVERT: X 6 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8773 (pp) REVERT: Y 6 GLU cc_start: 0.9278 (mm-30) cc_final: 0.9003 (mm-30) REVERT: Y 80 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7344 (ptt90) REVERT: Y 130 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8929 (mt-10) REVERT: Z 26 ARG cc_start: 0.8955 (mmm160) cc_final: 0.8689 (tmm-80) REVERT: Z 49 MET cc_start: 0.9401 (tpp) cc_final: 0.9095 (tpp) REVERT: Z 79 ASP cc_start: 0.8841 (m-30) cc_final: 0.8489 (m-30) REVERT: a 18 ILE cc_start: 0.9278 (mt) cc_final: 0.9069 (mp) REVERT: d 16 ASP cc_start: 0.8718 (m-30) cc_final: 0.8240 (t70) REVERT: d 25 LYS cc_start: 0.8322 (ptmt) cc_final: 0.7876 (ptpt) REVERT: d 44 MET cc_start: 0.9397 (tpp) cc_final: 0.9177 (tpp) REVERT: d 105 GLU cc_start: 0.8902 (pp20) cc_final: 0.8587 (pp20) REVERT: d 111 GLU cc_start: 0.8983 (mp0) cc_final: 0.8656 (mp0) REVERT: e 63 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8557 (tt0) REVERT: e 83 GLU cc_start: 0.8771 (tt0) cc_final: 0.8216 (tm-30) REVERT: e 87 LYS cc_start: 0.9221 (mmtp) cc_final: 0.9010 (tppp) REVERT: f 45 GLN cc_start: 0.8529 (tt0) cc_final: 0.8098 (tm-30) REVERT: g 80 ASP cc_start: 0.8641 (t70) cc_final: 0.7953 (t0) REVERT: g 112 ASP cc_start: 0.8987 (t70) cc_final: 0.8768 (t0) REVERT: h 102 GLU cc_start: 0.9095 (tp30) cc_final: 0.8813 (tp30) REVERT: h 117 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7894 (pmt100) REVERT: j 13 GLU cc_start: 0.9313 (mp0) cc_final: 0.8852 (mp0) REVERT: j 43 ASP cc_start: 0.9025 (OUTLIER) cc_final: 0.8683 (p0) REVERT: j 55 ASP cc_start: 0.8871 (t0) cc_final: 0.8360 (t0) REVERT: j 58 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8573 (mm-40) REVERT: k 52 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.8651 (mtm-85) REVERT: k 92 PHE cc_start: 0.8427 (t80) cc_final: 0.8074 (t80) REVERT: l 7 MET cc_start: 0.9060 (ptt) cc_final: 0.8739 (pmt) REVERT: m 61 ASP cc_start: 0.9107 (t0) cc_final: 0.8823 (t70) REVERT: m 109 ASP cc_start: 0.9481 (m-30) cc_final: 0.9275 (m-30) REVERT: m 117 GLU cc_start: 0.8196 (pt0) cc_final: 0.7776 (pt0) REVERT: m 119 LYS cc_start: 0.9041 (mttp) cc_final: 0.8668 (mtmm) REVERT: n 131 SER cc_start: 0.9092 (t) cc_final: 0.8762 (t) REVERT: o 104 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8499 (tm-30) REVERT: p 72 ASP cc_start: 0.8362 (t0) cc_final: 0.8036 (t0) outliers start: 253 outliers final: 164 residues processed: 1140 average time/residue: 1.4560 time to fit residues: 2174.6223 Evaluate side-chains 1136 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 948 time to evaluate : 5.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 136 LEU Chi-restraints excluded: chain 2 residue 154 VAL Chi-restraints excluded: chain 2 residue 164 LEU Chi-restraints excluded: chain 2 residue 201 SER Chi-restraints excluded: chain 1 residue 45 THR Chi-restraints excluded: chain 1 residue 323 VAL Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 363 THR Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 436 GLN Chi-restraints excluded: chain 1 residue 437 HIS Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 52 CYS Chi-restraints excluded: chain 3 residue 103 LEU Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 366 THR Chi-restraints excluded: chain 3 residue 368 ILE Chi-restraints excluded: chain 3 residue 437 HIS Chi-restraints excluded: chain 3 residue 441 GLU Chi-restraints excluded: chain 3 residue 451 VAL Chi-restraints excluded: chain 3 residue 540 ASP Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 559 VAL Chi-restraints excluded: chain 3 residue 583 THR Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 3 residue 656 VAL Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 254 ILE Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 81 ASN Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 105 VAL Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain 7 residue 17 VAL Chi-restraints excluded: chain 7 residue 87 CYS Chi-restraints excluded: chain S residue 17 GLU Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 75 VAL Chi-restraints excluded: chain W residue 128 HIS Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 59 ARG Chi-restraints excluded: chain r residue 108 ASP Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 321 GLN Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 577 THR Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 184 HIS Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 205 ILE Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 274 SER Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 257 LEU Chi-restraints excluded: chain O residue 19 HIS Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 87 TYR Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 34 GLN Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 68 ASN Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain Y residue 41 SER Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 80 ARG Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Z residue 50 MET Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain c residue 9 ASN Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain d residue 3 ASN Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 49 THR Chi-restraints excluded: chain e residue 54 GLU Chi-restraints excluded: chain e residue 63 GLU Chi-restraints excluded: chain g residue 105 ILE Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 117 ARG Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain i residue 112 THR Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 18 THR Chi-restraints excluded: chain j residue 43 ASP Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 52 ARG Chi-restraints excluded: chain k residue 73 LEU Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 14 ARG Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 82 MET Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 144 ASP Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 49 GLN Chi-restraints excluded: chain m residue 110 ARG Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 149 MET Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 20 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 150 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 478 optimal weight: 9.9990 chunk 308 optimal weight: 5.9990 chunk 461 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 491 optimal weight: 7.9990 chunk 526 optimal weight: 0.9990 chunk 382 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 607 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 GLN 1 324 GLN ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 95 HIS H 258 ASN L 295 GLN Z 102 ASN i 12 GLN ** m 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.240 69554 Z= 0.588 Angle : 1.573 50.627 94074 Z= 1.014 Chirality : 0.309 6.386 10205 Planarity : 0.004 0.055 11741 Dihedral : 10.849 167.128 10447 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.48 % Allowed : 16.08 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.68 (0.10), residues: 8115 helix: 1.60 (0.08), residues: 4411 sheet: -0.63 (0.26), residues: 398 loop : -0.99 (0.11), residues: 3306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 85 HIS 0.007 0.001 HIS 1 437 PHE 0.029 0.001 PHE N 292 TYR 0.023 0.001 TYR L 422 ARG 0.013 0.000 ARG Y 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1219 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 968 time to evaluate : 5.915 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: 6 78 ASP cc_start: 0.8916 (t0) cc_final: 0.8573 (t0) REVERT: C 20 LYS cc_start: 0.9092 (mmmt) cc_final: 0.8734 (tppt) REVERT: D 227 GLU cc_start: 0.9446 (OUTLIER) cc_final: 0.9174 (tp30) REVERT: D 259 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7913 (mmm) REVERT: D 410 MET cc_start: 0.8986 (mtm) cc_final: 0.8771 (mtm) REVERT: 1 312 CYS cc_start: 0.9459 (m) cc_final: 0.9173 (m) REVERT: 3 21 GLU cc_start: 0.9032 (mp0) cc_final: 0.8792 (mp0) REVERT: 3 52 CYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8638 (p) REVERT: 3 436 ARG cc_start: 0.8632 (mtt90) cc_final: 0.8414 (mtt90) REVERT: 3 437 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7505 (m-70) REVERT: 3 583 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8686 (t) REVERT: Q 14 ASP cc_start: 0.8742 (p0) cc_final: 0.8221 (p0) REVERT: S 92 ASN cc_start: 0.8700 (t0) cc_final: 0.8438 (t0) REVERT: T 30 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8454 (mp) REVERT: T 64 ASP cc_start: 0.7804 (t0) cc_final: 0.7250 (t70) REVERT: T 72 CYS cc_start: 0.8479 (m) cc_final: 0.8104 (t) REVERT: T 83 LYS cc_start: 0.8876 (tptm) cc_final: 0.8627 (mmmm) REVERT: W 44 GLU cc_start: 0.9179 (tp30) cc_final: 0.8763 (tp30) REVERT: W 53 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7854 (mm-40) REVERT: W 113 GLU cc_start: 0.8973 (pt0) cc_final: 0.8702 (pp20) REVERT: W 114 THR cc_start: 0.9255 (m) cc_final: 0.8906 (m) REVERT: q 5 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8309 (tm-30) REVERT: q 76 ASP cc_start: 0.9351 (m-30) cc_final: 0.9046 (m-30) REVERT: r 59 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.8973 (ttp-110) REVERT: r 108 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8705 (p0) REVERT: s 43 TYR cc_start: 0.9348 (m-80) cc_final: 0.9116 (m-80) REVERT: A 68 GLU cc_start: 0.9235 (tt0) cc_final: 0.9006 (tt0) REVERT: H 181 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8990 (mpp) REVERT: J 152 MET cc_start: 0.9477 (tpp) cc_final: 0.8929 (tpp) REVERT: L 179 ASP cc_start: 0.8794 (m-30) cc_final: 0.8515 (m-30) REVERT: L 321 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.7935 (mt0) REVERT: L 539 MET cc_start: 0.9348 (tmm) cc_final: 0.8623 (tmm) REVERT: M 123 GLU cc_start: 0.9297 (mp0) cc_final: 0.8821 (mp0) REVERT: M 187 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8328 (p0) REVERT: M 245 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.8452 (mpt90) REVERT: M 250 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8555 (mt) REVERT: N 40 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9128 (tt) REVERT: N 117 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8895 (mm-30) REVERT: O 48 MET cc_start: 0.9361 (mmm) cc_final: 0.9123 (mtp) REVERT: O 140 ASN cc_start: 0.9201 (t0) cc_final: 0.8936 (t0) REVERT: O 195 THR cc_start: 0.9571 (OUTLIER) cc_final: 0.9307 (p) REVERT: O 268 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8722 (mm-30) REVERT: X 6 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8782 (pp) REVERT: Y 2 LYS cc_start: 0.8439 (tppt) cc_final: 0.7556 (tppt) REVERT: Y 6 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8961 (mm-30) REVERT: Y 82 LYS cc_start: 0.9175 (pptt) cc_final: 0.8969 (pptt) REVERT: Y 85 ASP cc_start: 0.9119 (t70) cc_final: 0.8738 (t0) REVERT: Y 130 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8919 (mt-10) REVERT: Z 26 ARG cc_start: 0.8984 (mmm160) cc_final: 0.8720 (tmm-80) REVERT: Z 49 MET cc_start: 0.9397 (tpp) cc_final: 0.9104 (tpp) REVERT: Z 79 ASP cc_start: 0.8842 (m-30) cc_final: 0.8488 (m-30) REVERT: a 18 ILE cc_start: 0.9271 (mt) cc_final: 0.9060 (mp) REVERT: d 16 ASP cc_start: 0.8748 (m-30) cc_final: 0.8275 (t70) REVERT: d 25 LYS cc_start: 0.8317 (ptmt) cc_final: 0.7869 (ptpt) REVERT: d 105 GLU cc_start: 0.8900 (pp20) cc_final: 0.8587 (pp20) REVERT: d 111 GLU cc_start: 0.8998 (mp0) cc_final: 0.8583 (mp0) REVERT: e 63 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: e 83 GLU cc_start: 0.8772 (tt0) cc_final: 0.8207 (tm-30) REVERT: e 87 LYS cc_start: 0.9223 (mmtp) cc_final: 0.8957 (tppp) REVERT: e 98 SER cc_start: 0.8948 (t) cc_final: 0.8695 (p) REVERT: f 45 GLN cc_start: 0.8511 (tt0) cc_final: 0.8090 (tm-30) REVERT: g 56 MET cc_start: 0.9521 (tmm) cc_final: 0.9309 (ttp) REVERT: g 80 ASP cc_start: 0.8625 (t70) cc_final: 0.7937 (t0) REVERT: g 112 ASP cc_start: 0.8983 (t70) cc_final: 0.8766 (t0) REVERT: h 102 GLU cc_start: 0.9092 (tp30) cc_final: 0.8816 (tp30) REVERT: h 117 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7928 (pmt100) REVERT: j 43 ASP cc_start: 0.9034 (OUTLIER) cc_final: 0.8687 (p0) REVERT: j 55 ASP cc_start: 0.8872 (t0) cc_final: 0.8361 (t0) REVERT: j 58 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8576 (mm-40) REVERT: k 52 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.8646 (mtm-85) REVERT: k 92 PHE cc_start: 0.8437 (t80) cc_final: 0.8081 (t80) REVERT: l 7 MET cc_start: 0.9053 (ptt) cc_final: 0.8737 (pmt) REVERT: m 61 ASP cc_start: 0.9129 (t0) cc_final: 0.8820 (t70) REVERT: m 109 ASP cc_start: 0.9475 (m-30) cc_final: 0.9269 (m-30) REVERT: m 117 GLU cc_start: 0.8248 (pt0) cc_final: 0.7837 (pt0) REVERT: m 119 LYS cc_start: 0.9041 (mttp) cc_final: 0.8662 (mtmm) REVERT: n 131 SER cc_start: 0.9085 (t) cc_final: 0.8757 (t) REVERT: o 104 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8431 (tm-30) REVERT: p 72 ASP cc_start: 0.8396 (t0) cc_final: 0.8062 (t0) outliers start: 251 outliers final: 176 residues processed: 1137 average time/residue: 1.4671 time to fit residues: 2192.1969 Evaluate side-chains 1153 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 954 time to evaluate : 5.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain 6 residue 113 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain 2 residue 55 GLN Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 136 LEU Chi-restraints excluded: chain 2 residue 154 VAL Chi-restraints excluded: chain 2 residue 187 ARG Chi-restraints excluded: chain 2 residue 201 SER Chi-restraints excluded: chain 1 residue 45 THR Chi-restraints excluded: chain 1 residue 297 VAL Chi-restraints excluded: chain 1 residue 323 VAL Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 363 THR Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 52 CYS Chi-restraints excluded: chain 3 residue 103 LEU Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 366 THR Chi-restraints excluded: chain 3 residue 368 ILE Chi-restraints excluded: chain 3 residue 437 HIS Chi-restraints excluded: chain 3 residue 441 GLU Chi-restraints excluded: chain 3 residue 451 VAL Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 559 VAL Chi-restraints excluded: chain 3 residue 583 THR Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 3 residue 656 VAL Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 254 ILE Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 81 ASN Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 105 VAL Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain 7 residue 17 VAL Chi-restraints excluded: chain 7 residue 87 CYS Chi-restraints excluded: chain S residue 17 GLU Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 75 VAL Chi-restraints excluded: chain W residue 128 HIS Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 59 ARG Chi-restraints excluded: chain r residue 108 ASP Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 237 MET Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 321 GLN Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 577 THR Chi-restraints excluded: chain L residue 604 ILE Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 184 HIS Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 205 ILE Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 274 SER Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain O residue 19 HIS Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 195 THR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 87 TYR Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 34 GLN Chi-restraints excluded: chain X residue 68 ASN Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain Y residue 1 VAL Chi-restraints excluded: chain Y residue 41 SER Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 80 ARG Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Z residue 50 MET Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain c residue 9 ASN Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain d residue 3 ASN Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 4 ASP Chi-restraints excluded: chain e residue 49 THR Chi-restraints excluded: chain e residue 54 GLU Chi-restraints excluded: chain e residue 63 GLU Chi-restraints excluded: chain g residue 105 ILE Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 117 ARG Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain i residue 112 THR Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 18 THR Chi-restraints excluded: chain j residue 43 ASP Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 52 ARG Chi-restraints excluded: chain k residue 73 LEU Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 14 ARG Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 82 MET Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 144 ASP Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 49 GLN Chi-restraints excluded: chain m residue 110 ARG Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 116 ASP Chi-restraints excluded: chain n residue 149 MET Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 20 LYS Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 150 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 703 optimal weight: 9.9990 chunk 740 optimal weight: 7.9990 chunk 675 optimal weight: 10.0000 chunk 720 optimal weight: 6.9990 chunk 433 optimal weight: 1.9990 chunk 313 optimal weight: 6.9990 chunk 565 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 650 optimal weight: 10.0000 chunk 681 optimal weight: 10.0000 chunk 717 optimal weight: 0.5980 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 437 HIS P 86 GLN ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 95 HIS S 91 GLN H 258 ASN L 295 GLN Z 102 ASN i 12 GLN m 78 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 69554 Z= 0.584 Angle : 1.574 50.619 94074 Z= 1.014 Chirality : 0.309 6.383 10205 Planarity : 0.004 0.058 11741 Dihedral : 10.745 167.120 10445 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.27 % Allowed : 16.55 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.71 (0.10), residues: 8115 helix: 1.61 (0.08), residues: 4408 sheet: -0.62 (0.26), residues: 398 loop : -0.96 (0.11), residues: 3309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP j 59 HIS 0.004 0.001 HIS T 35 PHE 0.044 0.001 PHE L 335 TYR 0.022 0.001 TYR L 422 ARG 0.013 0.000 ARG O 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 969 time to evaluate : 5.980 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: 6 78 ASP cc_start: 0.8919 (t0) cc_final: 0.8591 (t0) REVERT: D 259 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7897 (mmm) REVERT: 1 312 CYS cc_start: 0.9452 (m) cc_final: 0.9169 (m) REVERT: 1 436 GLN cc_start: 0.9148 (tt0) cc_final: 0.8757 (tm-30) REVERT: 1 437 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.8286 (m-70) REVERT: 3 21 GLU cc_start: 0.9028 (mp0) cc_final: 0.8795 (mp0) REVERT: 3 52 CYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8639 (p) REVERT: 3 436 ARG cc_start: 0.8654 (mtt90) cc_final: 0.8440 (mtt90) REVERT: 3 437 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7554 (m-70) REVERT: 3 583 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8684 (t) REVERT: Q 14 ASP cc_start: 0.8734 (p0) cc_final: 0.8215 (p0) REVERT: S 92 ASN cc_start: 0.8676 (t0) cc_final: 0.8425 (t0) REVERT: T 14 ARG cc_start: 0.8777 (ttp-170) cc_final: 0.8542 (ttp-170) REVERT: T 30 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8478 (mp) REVERT: T 64 ASP cc_start: 0.7871 (t0) cc_final: 0.7259 (t70) REVERT: T 66 ASP cc_start: 0.8612 (p0) cc_final: 0.8042 (p0) REVERT: T 72 CYS cc_start: 0.8428 (m) cc_final: 0.7592 (t) REVERT: T 83 LYS cc_start: 0.8863 (tptm) cc_final: 0.8611 (mmmm) REVERT: W 44 GLU cc_start: 0.9178 (tp30) cc_final: 0.8760 (tp30) REVERT: W 53 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.7837 (mm-40) REVERT: W 113 GLU cc_start: 0.8965 (pt0) cc_final: 0.8706 (pp20) REVERT: W 114 THR cc_start: 0.9239 (m) cc_final: 0.8882 (m) REVERT: q 5 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8305 (tm-30) REVERT: q 76 ASP cc_start: 0.9350 (m-30) cc_final: 0.9044 (m-30) REVERT: r 59 ARG cc_start: 0.9337 (OUTLIER) cc_final: 0.8997 (ttp-110) REVERT: r 108 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8699 (p0) REVERT: s 43 TYR cc_start: 0.9342 (m-80) cc_final: 0.9114 (m-80) REVERT: A 68 GLU cc_start: 0.9193 (tt0) cc_final: 0.8937 (tt0) REVERT: H 181 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8998 (mpp) REVERT: J 99 GLU cc_start: 0.6018 (OUTLIER) cc_final: 0.5384 (mm-30) REVERT: J 152 MET cc_start: 0.9463 (tpp) cc_final: 0.8925 (tpp) REVERT: J 171 ARG cc_start: 0.8399 (ttp80) cc_final: 0.8180 (ttp80) REVERT: L 179 ASP cc_start: 0.8791 (m-30) cc_final: 0.8524 (m-30) REVERT: L 321 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: L 539 MET cc_start: 0.9345 (tmm) cc_final: 0.8635 (tmm) REVERT: L 589 MET cc_start: 0.9350 (tpt) cc_final: 0.9072 (tpt) REVERT: M 187 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8340 (p0) REVERT: M 245 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.8398 (mpt90) REVERT: M 250 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8492 (mt) REVERT: M 271 MET cc_start: 0.9421 (mmm) cc_final: 0.9203 (mmm) REVERT: N 40 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9125 (tt) REVERT: N 117 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8890 (mm-30) REVERT: O 140 ASN cc_start: 0.9196 (t0) cc_final: 0.8943 (t0) REVERT: O 195 THR cc_start: 0.9572 (OUTLIER) cc_final: 0.9327 (p) REVERT: O 268 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8718 (mm-30) REVERT: X 6 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8761 (pp) REVERT: Y 2 LYS cc_start: 0.8366 (tppt) cc_final: 0.7519 (tppt) REVERT: Y 6 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8972 (mm-30) REVERT: Y 82 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8882 (pptt) REVERT: Y 85 ASP cc_start: 0.9112 (t70) cc_final: 0.8676 (t0) REVERT: Y 130 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8914 (mt-10) REVERT: Z 26 ARG cc_start: 0.8992 (mmm160) cc_final: 0.8736 (tmm-80) REVERT: Z 49 MET cc_start: 0.9386 (tpp) cc_final: 0.9083 (tpp) REVERT: Z 79 ASP cc_start: 0.8847 (m-30) cc_final: 0.8493 (m-30) REVERT: a 18 ILE cc_start: 0.9264 (mt) cc_final: 0.9053 (mp) REVERT: d 16 ASP cc_start: 0.8705 (m-30) cc_final: 0.8233 (t70) REVERT: d 25 LYS cc_start: 0.8306 (ptmt) cc_final: 0.7857 (ptpt) REVERT: d 105 GLU cc_start: 0.8892 (pp20) cc_final: 0.8577 (pp20) REVERT: d 111 GLU cc_start: 0.8992 (mp0) cc_final: 0.8580 (mp0) REVERT: e 63 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: e 83 GLU cc_start: 0.8771 (tt0) cc_final: 0.8206 (tm-30) REVERT: e 87 LYS cc_start: 0.9222 (mmtp) cc_final: 0.8945 (tppp) REVERT: e 98 SER cc_start: 0.8949 (t) cc_final: 0.8675 (p) REVERT: f 45 GLN cc_start: 0.8495 (tt0) cc_final: 0.8079 (tm-30) REVERT: g 80 ASP cc_start: 0.8609 (t70) cc_final: 0.7940 (t0) REVERT: g 112 ASP cc_start: 0.8977 (t70) cc_final: 0.8764 (t0) REVERT: h 102 GLU cc_start: 0.9090 (tp30) cc_final: 0.8814 (tp30) REVERT: j 43 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8660 (p0) REVERT: j 55 ASP cc_start: 0.8870 (t0) cc_final: 0.8364 (t0) REVERT: j 58 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8566 (mm-40) REVERT: k 35 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8503 (tp30) REVERT: k 52 ARG cc_start: 0.9302 (OUTLIER) cc_final: 0.8669 (mtm-85) REVERT: k 92 PHE cc_start: 0.8464 (t80) cc_final: 0.8118 (t80) REVERT: l 7 MET cc_start: 0.9073 (ptt) cc_final: 0.8747 (pmt) REVERT: m 61 ASP cc_start: 0.9129 (t0) cc_final: 0.8815 (t70) REVERT: m 117 GLU cc_start: 0.8222 (pt0) cc_final: 0.7802 (pt0) REVERT: m 119 LYS cc_start: 0.9005 (mttp) cc_final: 0.8577 (mtmm) REVERT: n 131 SER cc_start: 0.9080 (t) cc_final: 0.8749 (t) REVERT: o 104 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8551 (tm-30) REVERT: p 72 ASP cc_start: 0.8401 (t0) cc_final: 0.8042 (t0) outliers start: 236 outliers final: 172 residues processed: 1129 average time/residue: 1.4754 time to fit residues: 2183.6433 Evaluate side-chains 1151 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 954 time to evaluate : 5.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain 6 residue 113 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain 2 residue 55 GLN Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 136 LEU Chi-restraints excluded: chain 2 residue 154 VAL Chi-restraints excluded: chain 2 residue 187 ARG Chi-restraints excluded: chain 2 residue 201 SER Chi-restraints excluded: chain 1 residue 45 THR Chi-restraints excluded: chain 1 residue 162 ILE Chi-restraints excluded: chain 1 residue 297 VAL Chi-restraints excluded: chain 1 residue 323 VAL Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 363 THR Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 437 HIS Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 52 CYS Chi-restraints excluded: chain 3 residue 103 LEU Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 366 THR Chi-restraints excluded: chain 3 residue 368 ILE Chi-restraints excluded: chain 3 residue 437 HIS Chi-restraints excluded: chain 3 residue 451 VAL Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 559 VAL Chi-restraints excluded: chain 3 residue 583 THR Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 3 residue 656 VAL Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 254 ILE Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 81 ASN Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 105 VAL Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain 7 residue 17 VAL Chi-restraints excluded: chain 7 residue 87 CYS Chi-restraints excluded: chain S residue 17 GLU Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 35 HIS Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 75 VAL Chi-restraints excluded: chain W residue 128 HIS Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 59 ARG Chi-restraints excluded: chain r residue 108 ASP Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 321 GLN Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 577 THR Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 184 HIS Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 205 ILE Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain O residue 19 HIS Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 195 THR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 87 TYR Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 11 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 34 GLN Chi-restraints excluded: chain X residue 68 ASN Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain Y residue 41 SER Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 80 ARG Chi-restraints excluded: chain Y residue 82 LYS Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Z residue 50 MET Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain c residue 9 ASN Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain d residue 3 ASN Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 4 ASP Chi-restraints excluded: chain e residue 49 THR Chi-restraints excluded: chain e residue 54 GLU Chi-restraints excluded: chain e residue 63 GLU Chi-restraints excluded: chain g residue 38 LYS Chi-restraints excluded: chain g residue 105 ILE Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 112 THR Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 18 THR Chi-restraints excluded: chain j residue 43 ASP Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 35 GLU Chi-restraints excluded: chain k residue 52 ARG Chi-restraints excluded: chain k residue 73 LEU Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 14 ARG Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 82 MET Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 144 ASP Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 49 GLN Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 116 ASP Chi-restraints excluded: chain n residue 149 MET Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 20 LYS Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 150 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 473 optimal weight: 0.9990 chunk 761 optimal weight: 9.9990 chunk 464 optimal weight: 8.9990 chunk 361 optimal weight: 0.8980 chunk 529 optimal weight: 10.0000 chunk 798 optimal weight: 5.9990 chunk 735 optimal weight: 0.9990 chunk 636 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 491 optimal weight: 8.9990 chunk 390 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 324 GLN 1 437 HIS P 86 GLN ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 GLN S 91 GLN L 170 GLN L 295 GLN ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 228 ASN Z 102 ASN i 12 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 99 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 69554 Z= 0.556 Angle : 1.566 50.627 94074 Z= 1.010 Chirality : 0.308 6.374 10205 Planarity : 0.004 0.059 11741 Dihedral : 10.484 169.109 10445 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.16 % Allowed : 17.84 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.75 (0.10), residues: 8115 helix: 1.66 (0.08), residues: 4392 sheet: -0.63 (0.27), residues: 385 loop : -0.95 (0.11), residues: 3338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP j 59 HIS 0.012 0.001 HIS 1 437 PHE 0.039 0.001 PHE L 335 TYR 0.030 0.001 TYR L 422 ARG 0.014 0.000 ARG O 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16230 Ramachandran restraints generated. 8115 Oldfield, 0 Emsley, 8115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1191 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1035 time to evaluate : 5.946 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: 6 78 ASP cc_start: 0.8878 (t0) cc_final: 0.8547 (t0) REVERT: C 20 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8764 (tppt) REVERT: D 259 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7713 (mmm) REVERT: 1 436 GLN cc_start: 0.9138 (tt0) cc_final: 0.8799 (tm-30) REVERT: 1 437 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.8084 (m-70) REVERT: 3 21 GLU cc_start: 0.9002 (mp0) cc_final: 0.8780 (mp0) REVERT: 3 52 CYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8613 (p) REVERT: 3 437 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.7415 (m-70) REVERT: P 57 MET cc_start: 0.9501 (mmp) cc_final: 0.9202 (mmm) REVERT: Q 14 ASP cc_start: 0.8724 (p0) cc_final: 0.8200 (p0) REVERT: S 56 GLU cc_start: 0.8774 (pm20) cc_final: 0.7920 (pt0) REVERT: S 92 ASN cc_start: 0.8496 (t0) cc_final: 0.8263 (t0) REVERT: T 14 ARG cc_start: 0.8784 (ttp-170) cc_final: 0.8513 (ttp-170) REVERT: T 30 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8547 (mp) REVERT: T 83 LYS cc_start: 0.8837 (tptm) cc_final: 0.8586 (mmmm) REVERT: W 44 GLU cc_start: 0.9112 (tp30) cc_final: 0.8764 (tp30) REVERT: W 53 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7666 (mm-40) REVERT: W 113 GLU cc_start: 0.8938 (pt0) cc_final: 0.8683 (pp20) REVERT: W 114 THR cc_start: 0.9229 (m) cc_final: 0.8860 (m) REVERT: q 5 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8290 (tm-30) REVERT: q 76 ASP cc_start: 0.9337 (m-30) cc_final: 0.9033 (m-30) REVERT: J 99 GLU cc_start: 0.5943 (OUTLIER) cc_final: 0.5366 (mm-30) REVERT: J 152 MET cc_start: 0.9380 (tpp) cc_final: 0.8874 (tpp) REVERT: L 179 ASP cc_start: 0.8737 (m-30) cc_final: 0.8457 (m-30) REVERT: L 194 ASN cc_start: 0.7173 (t0) cc_final: 0.6865 (t0) REVERT: L 202 MET cc_start: 0.8844 (mmp) cc_final: 0.8564 (mmt) REVERT: L 539 MET cc_start: 0.9343 (tmm) cc_final: 0.8634 (tmm) REVERT: L 589 MET cc_start: 0.9292 (tpt) cc_final: 0.9091 (tpt) REVERT: M 245 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8377 (mpt90) REVERT: M 271 MET cc_start: 0.9422 (mmm) cc_final: 0.9152 (mmm) REVERT: N 40 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9052 (tt) REVERT: N 59 TYR cc_start: 0.9225 (t80) cc_final: 0.9012 (t80) REVERT: N 117 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8899 (mm-30) REVERT: O 140 ASN cc_start: 0.9121 (t0) cc_final: 0.8915 (t0) REVERT: O 192 MET cc_start: 0.9427 (mtm) cc_final: 0.9225 (mtp) REVERT: O 268 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8682 (mm-30) REVERT: U 28 GLU cc_start: 0.7273 (mm-30) cc_final: 0.7067 (mm-30) REVERT: X 72 GLN cc_start: 0.9212 (tt0) cc_final: 0.9009 (tt0) REVERT: Y 2 LYS cc_start: 0.8413 (tppt) cc_final: 0.7488 (tppt) REVERT: Y 5 PHE cc_start: 0.8196 (m-80) cc_final: 0.7950 (m-80) REVERT: Y 6 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8941 (mm-30) REVERT: Y 41 SER cc_start: 0.9214 (OUTLIER) cc_final: 0.8942 (p) REVERT: Y 82 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8650 (pptt) REVERT: Z 26 ARG cc_start: 0.8950 (mmm160) cc_final: 0.8719 (tmm-80) REVERT: Z 49 MET cc_start: 0.9357 (tpp) cc_final: 0.9051 (tpp) REVERT: Z 79 ASP cc_start: 0.8842 (m-30) cc_final: 0.8492 (m-30) REVERT: Z 89 ASN cc_start: 0.9056 (m-40) cc_final: 0.8839 (m110) REVERT: a 59 ARG cc_start: 0.9023 (mmt90) cc_final: 0.8716 (mmt-90) REVERT: d 16 ASP cc_start: 0.8677 (m-30) cc_final: 0.8270 (t70) REVERT: d 25 LYS cc_start: 0.8164 (ptmt) cc_final: 0.7721 (ptpt) REVERT: d 105 GLU cc_start: 0.8915 (pp20) cc_final: 0.8608 (pp20) REVERT: d 111 GLU cc_start: 0.8940 (mp0) cc_final: 0.8591 (mp0) REVERT: e 83 GLU cc_start: 0.8789 (tt0) cc_final: 0.8143 (tm-30) REVERT: e 87 LYS cc_start: 0.9168 (mmtp) cc_final: 0.8900 (tppp) REVERT: e 98 SER cc_start: 0.8956 (t) cc_final: 0.8678 (p) REVERT: f 45 GLN cc_start: 0.8299 (tt0) cc_final: 0.8090 (tm-30) REVERT: g 33 GLU cc_start: 0.8229 (pm20) cc_final: 0.7822 (pt0) REVERT: g 80 ASP cc_start: 0.8467 (t70) cc_final: 0.7705 (t0) REVERT: g 112 ASP cc_start: 0.8968 (t70) cc_final: 0.8752 (t0) REVERT: h 102 GLU cc_start: 0.9051 (tp30) cc_final: 0.8789 (tp30) REVERT: i 119 MET cc_start: 0.8627 (mtm) cc_final: 0.8427 (mtm) REVERT: j 13 GLU cc_start: 0.9254 (mp0) cc_final: 0.8816 (mp0) REVERT: j 43 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8583 (p0) REVERT: j 55 ASP cc_start: 0.8864 (t0) cc_final: 0.8353 (t0) REVERT: j 58 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8543 (mm110) REVERT: k 35 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8505 (tp30) REVERT: k 52 ARG cc_start: 0.9303 (OUTLIER) cc_final: 0.8706 (mtm-85) REVERT: k 92 PHE cc_start: 0.8432 (t80) cc_final: 0.8077 (t80) REVERT: l 7 MET cc_start: 0.9018 (ptt) cc_final: 0.8785 (pmt) REVERT: l 28 MET cc_start: 0.9124 (mtp) cc_final: 0.8846 (mtm) REVERT: l 144 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8767 (t0) REVERT: m 61 ASP cc_start: 0.9056 (t0) cc_final: 0.8715 (t70) REVERT: n 131 SER cc_start: 0.9023 (t) cc_final: 0.8686 (t) REVERT: o 45 MET cc_start: 0.9308 (mtm) cc_final: 0.8858 (mtm) REVERT: p 72 ASP cc_start: 0.8360 (t0) cc_final: 0.8066 (t0) outliers start: 156 outliers final: 106 residues processed: 1136 average time/residue: 1.4961 time to fit residues: 2247.3757 Evaluate side-chains 1094 residues out of total 7209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 974 time to evaluate : 5.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain 6 residue 113 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 201 SER Chi-restraints excluded: chain 1 residue 45 THR Chi-restraints excluded: chain 1 residue 297 VAL Chi-restraints excluded: chain 1 residue 323 VAL Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 363 THR Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 437 HIS Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 52 CYS Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 262 TRP Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 366 THR Chi-restraints excluded: chain 3 residue 368 ILE Chi-restraints excluded: chain 3 residue 437 HIS Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 559 VAL Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 3 residue 656 VAL Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain 9 residue 128 CYS Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 254 ILE Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 81 ASN Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain 7 residue 17 VAL Chi-restraints excluded: chain 7 residue 87 CYS Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 128 HIS Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 184 HIS Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain Y residue 41 SER Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 82 LYS Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Z residue 50 MET Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain c residue 9 ASN Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain g residue 105 ILE Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 18 THR Chi-restraints excluded: chain j residue 43 ASP Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 52 ARG Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 144 ASP Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 49 GLN Chi-restraints excluded: chain m residue 51 ASN Chi-restraints excluded: chain n residue 149 MET Chi-restraints excluded: chain n residue 161 ASP Chi-restraints excluded: chain o residue 20 LYS Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain p residue 16 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 505 optimal weight: 5.9990 chunk 677 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 586 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 637 optimal weight: 20.0000 chunk 266 optimal weight: 4.9990 chunk 654 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 437 HIS ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 95 HIS S 91 GLN H 258 ASN Z 102 ASN i 12 GLN p 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.060128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.050764 restraints weight = 163818.636| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.05 r_work: 0.2679 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 69554 Z= 0.577 Angle : 1.576 50.596 94074 Z= 1.015 Chirality : 0.309 6.365 10205 Planarity : 0.004 0.076 11741 Dihedral : 10.473 168.043 10440 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.18 % Allowed : 18.32 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.78 (0.10), residues: 8115 helix: 1.67 (0.08), residues: 4404 sheet: -0.54 (0.27), residues: 397 loop : -0.94 (0.11), residues: 3314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP j 59 HIS 0.008 0.001 HIS T 35 PHE 0.040 0.001 PHE L 335 TYR 0.031 0.001 TYR L 422 ARG 0.016 0.000 ARG Y 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29212.19 seconds wall clock time: 505 minutes 36.23 seconds (30336.23 seconds total)