Starting phenix.real_space_refine on Fri Jun 28 20:29:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgr_19147/06_2024/8rgr_19147_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgr_19147/06_2024/8rgr_19147.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgr_19147/06_2024/8rgr_19147_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgr_19147/06_2024/8rgr_19147_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgr_19147/06_2024/8rgr_19147_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgr_19147/06_2024/8rgr_19147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgr_19147/06_2024/8rgr_19147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgr_19147/06_2024/8rgr_19147_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgr_19147/06_2024/8rgr_19147_updated.pdb" } resolution = 2.9 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= 0.002 sd= 0.006 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 51 5.49 5 Mg 1 5.21 5 S 494 5.16 5 C 44104 2.51 5 N 11207 2.21 5 O 12254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 68141 Number of models: 1 Model: "" Number of chains: 69 Chain: "6" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1258 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 146} Chain: "C" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1730 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "D" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3464 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 25, '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: {'PCIS': 1, 'PTRANS': 20, '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: {'PCIS': 1, 'PTRANS': 8, '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: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 923 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} 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: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} 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: {'PCIS': 3, 'PTRANS': 17, '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: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 897 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 94} 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: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 562 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 6, 'TRANS': 58} 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: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 117 Unusual residues: {'PC1': 2, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'CDL:plan-3': 1} Unresolved non-hydrogen planarities: 3 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: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 175 Unusual residues: {'3PE': 1, 'CDL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 76 Chain: "M" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 138 Unusual residues: {'3PE': 3} 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 182 Unusual residues: {'3PE': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 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: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 221 Unusual residues: {'3PE': 2, 'CDL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 81 Chain: "Z" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 130 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 72 Chain: "h" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 70 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 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 766 SG CYS 6 129 59.490 133.546 105.294 1.00 75.60 S ATOM 269 SG CYS 6 65 54.214 130.515 102.681 1.00 78.00 S ATOM 263 SG CYS 6 64 56.683 127.880 107.648 1.00 69.21 S ATOM 996 SG CYS 6 159 54.050 133.915 108.287 1.00 73.75 S ATOM 7258 SG CYS 2 103 25.748 172.451 160.170 1.00 64.43 S ATOM 7292 SG CYS 2 108 23.446 171.719 162.820 1.00 65.45 S ATOM 7576 SG CYS 2 144 30.169 172.104 163.452 1.00 81.63 S ATOM 7599 SG CYS 2 148 28.233 171.233 166.203 1.00 81.92 S ATOM 10837 SG CYS 1 365 42.252 163.983 152.888 1.00 64.45 S ATOM 11159 SG CYS 1 405 45.597 166.454 157.912 1.00 63.00 S ATOM 10817 SG CYS 1 362 47.748 163.568 152.290 1.00 74.16 S ATOM 10798 SG CYS 1 359 45.388 169.936 152.582 1.00 55.21 S ATOM 12263 SG CYS 3 114 52.938 157.931 132.889 1.00 71.21 S ATOM 12202 SG CYS 3 105 47.802 155.106 129.946 1.00 65.19 S ATOM 12223 SG CYS 3 108 49.827 161.119 128.257 1.00 52.20 S ATOM 12595 SG CYS 3 156 54.110 166.625 140.470 1.00 62.77 S ATOM 12572 SG CYS 3 153 48.043 168.220 138.210 1.00 51.68 S ATOM 12619 SG CYS 3 159 52.922 172.450 137.887 1.00 69.92 S ATOM 12948 SG CYS 3 203 53.108 167.034 134.256 1.00 57.23 S ATOM 11709 SG CYS 3 41 56.174 164.595 146.601 1.00 60.59 S ATOM 11795 SG CYS 3 52 54.691 161.155 145.703 1.00 75.79 S ATOM 11820 SG CYS 3 55 58.386 159.700 150.145 1.00 82.72 S ATOM 11921 SG CYS 3 69 59.164 163.294 150.003 1.00 73.22 S ATOM 17709 SG CYS 9 121 51.447 139.036 114.564 1.00 80.71 S ATOM 17683 SG CYS 9 118 51.040 140.984 108.238 1.00 88.31 S ATOM 17730 SG CYS 9 124 47.916 144.124 113.072 1.00 69.48 S ATOM 17457 SG CYS 9 89 54.466 144.354 112.471 1.00 83.96 S ATOM 17759 SG CYS 9 128 43.640 149.949 117.219 1.00 68.27 S ATOM 17429 SG CYS 9 85 49.665 150.078 114.741 1.00 58.96 S ATOM 17387 SG CYS 9 79 45.847 155.238 113.984 1.00 64.18 S ATOM 17406 SG CYS 9 82 48.085 153.255 120.059 1.00 62.51 S ATOM 22419 SG CYS 7 59 32.482 159.890 123.378 1.00 70.78 S ATOM 22595 SG CYS 7 84 36.172 160.945 122.957 1.00 69.15 S ATOM 22617 SG CYS 7 87 34.072 160.230 120.229 1.00 69.65 S Time building chain proxies: 25.58, per 1000 atoms: 0.38 Number of scatterers: 68141 At special positions: 0 Unit cell: (233.2, 217.3, 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 494 16.00 P 51 15.00 Mg 1 11.99 O 12254 8.00 N 11207 7.00 C 44104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.03 Simple disulfide: pdb=" SG CYS o 58 " - pdb=" SG CYS o 89 " distance=2.03 Simple disulfide: pdb=" SG CYS o 68 " - pdb=" SG CYS o 79 " distance=2.04 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: 19.40 Conformation dependent library (CDL) restraints added in 8.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 301 " pdb="FE1 FES 2 301 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 301 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 301 " - pdb=" SG CYS 2 108 " 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="FE4 SF4 1 502 " - pdb=" SG CYS 1 359 " pdb="FE3 SF4 1 502 " - pdb=" SG CYS 1 362 " 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="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " 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="FE3 SF4 9 201 " - pdb=" NE2 HIS 9 67 " pdb=" SF4 9 202 " pdb="FE4 SF4 9 202 " - pdb=" SG CYS 9 82 " pdb="FE2 SF4 9 202 " - pdb=" SG CYS 9 85 " pdb="FE3 SF4 9 202 " - pdb=" SG CYS 9 79 " pdb="FE1 SF4 9 202 " - pdb=" SG CYS 9 128 " 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 87 " pdb="ZN ZN 7 201 " - pdb=" SG CYS 7 84 " pdb="ZN ZN 7 201 " - pdb=" SG CYS 7 59 " Number of angles added : 3 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15506 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 336 helices and 29 sheets defined 52.4% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.30 Creating SS restraints... Processing helix chain '6' and resid 35 through 53 Processing helix chain '6' and resid 64 through 73 Processing helix chain '6' and resid 79 through 82 No H-bonds generated for 'chain '6' and resid 79 through 82' 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 188 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.631A pdb=" N VAL C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix 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 14 removed outlier: 4.409A pdb=" N PHE D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 96 through 106 Proline residue: D 101 - end of helix removed outlier: 4.011A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.859A 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 185 Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.972A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 258 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 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 426 through 429 No H-bonds generated for 'chain 'D' and resid 426 through 429' Processing helix chain '2' and resid 25 through 36 Processing helix chain '2' and resid 43 through 58 removed outlier: 4.585A 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: 4.489A 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 237 Proline residue: 1 232 - end of helix Processing helix chain '1' and resid 239 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 386 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 437 Processing helix chain '3' and resid 26 through 33 Processing helix chain '3' and resid 84 through 100 removed outlier: 4.167A pdb=" N ASN 3 100 " --> pdb=" O PHE 3 96 " (cutoff:3.500A) Processing helix chain '3' and resid 105 through 107 No H-bonds generated for 'chain '3' and resid 105 through 107' 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: 4.805A pdb=" N TYR 3 271 " --> pdb=" O THR 3 267 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASP 3 272 " --> pdb=" O ARG 3 268 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLY 3 273 " --> pdb=" O PHE 3 269 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU 3 274 " --> pdb=" O ALA 3 270 " (cutoff:3.500A) removed outlier: 4.440A 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 362 Processing helix chain '3' and resid 367 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 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 481 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 607 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: 4.244A pdb=" N ALA 9 169 " --> pdb=" O ALA 9 165 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 41 removed outlier: 4.112A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) 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: 4.390A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 4.823A 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 221 through 223 No H-bonds generated for 'chain 'P' and resid 221 through 223' 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 310 through 313 No H-bonds generated for 'chain 'P' and resid 310 through 313' 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 20 through 23 No H-bonds generated for 'chain 'Q' and resid 20 through 23' 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 23 through 27 removed outlier: 3.703A pdb=" N ARG 7 27 " --> pdb=" O ARG 7 24 " (cutoff:3.500A) Processing helix chain '7' and resid 40 through 45 Processing helix chain '7' and resid 64 through 66 No H-bonds generated for 'chain '7' and resid 64 through 66' Processing helix chain 'S' and resid 27 through 46 removed outlier: 4.841A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN S 38 " --> pdb=" O PHE S 35 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TYR S 40 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL S 41 " --> pdb=" O GLN S 38 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU S 42 " --> 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 21 Processing helix chain 'T' and resid 44 through 58 Processing helix chain 'T' and resid 64 through 66 No H-bonds generated for 'chain 'T' and resid 64 through 66' Processing helix chain 'T' and resid 73 through 83 Processing helix chain 'V' and resid 19 through 36 removed outlier: 4.012A 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 96 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 108 removed outlier: 4.431A pdb=" N PHE W 108 " --> pdb=" O HIS W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 126 Processing helix chain 'q' and resid 3 through 16 Processing helix chain 'q' and resid 20 through 29 Processing helix chain 'q' and resid 79 through 81 No H-bonds generated for 'chain 'q' and resid 79 through 81' 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: 4.584A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) removed outlier: 4.923A 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 56 through 80 Proline residue: A 74 - end of helix removed outlier: 5.650A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 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 157 Processing helix chain 'H' and resid 163 through 170 Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 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 217 through 241 Processing helix chain 'H' and resid 253 through 276 Processing helix chain 'H' and resid 282 through 291 removed outlier: 3.609A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 311 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 138 through 143 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 85 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 157 Processing helix chain 'L' and resid 162 through 193 Processing helix chain 'L' and resid 198 through 206 removed outlier: 5.043A pdb=" N ASN L 206 " --> pdb=" O MET L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 232 through 238 removed outlier: 4.801A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 249 Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.335A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 4.300A pdb=" N THR L 294 " --> pdb=" O ILE L 290 " (cutoff:3.500A) 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: 5.156A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 Processing helix chain 'L' and resid 448 through 471 Proline residue: L 453 - end of helix removed outlier: 6.150A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.194A 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 548 removed outlier: 3.572A pdb=" N PHE L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 3.712A pdb=" N ILE L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS L 534 " --> pdb=" O SER L 531 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.608A pdb=" N LEU L 542 " --> pdb=" O MET L 539 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN L 543 " --> pdb=" O LYS L 540 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU L 546 " --> pdb=" O ASN L 543 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS L 547 " --> pdb=" O LEU L 544 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR L 548 " --> pdb=" O SER L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 550 through 554 Processing helix chain 'L' and resid 557 through 561 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: 4.175A 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: 4.221A pdb=" N THR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 80 Proline residue: M 74 - end of helix 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: 3.589A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE M 158 " --> pdb=" O ILE M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.636A 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: 4.519A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 4.479A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 249 removed outlier: 5.615A pdb=" N LEU M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LYS M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE M 248 " --> pdb=" O ILE M 244 " (cutoff:3.500A) removed outlier: 5.382A 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: 3.634A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE M 394 " --> pdb=" O PHE M 391 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER M 407 " --> pdb=" O GLY M 404 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET M 408 " --> pdb=" O MET M 405 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 449 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 451 through 454 removed outlier: 3.628A pdb=" N ILE M 454 " --> pdb=" O PRO M 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 451 through 454' 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 115 through 119 Processing helix chain 'N' and resid 124 through 148 removed outlier: 5.528A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.605A pdb=" N ILE N 145 " --> pdb=" O ILE N 141 " (cutoff:3.500A) Proline residue: N 147 - 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: 4.286A pdb=" N ASN N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 236 removed outlier: 4.203A pdb=" N LEU N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N TRP N 234 " --> pdb=" O ILE N 230 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS N 236 " --> pdb=" O LEU N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.685A pdb=" N LEU N 241 " --> pdb=" O PRO N 238 " (cutoff:3.500A) removed outlier: 4.714A 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 324 through 334 removed outlier: 4.195A pdb=" N THR N 328 " --> pdb=" O LEU N 324 " (cutoff:3.500A) 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 14 through 17 No H-bonds generated for 'chain 'O' and resid 14 through 17' 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 92 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: 5.088A 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 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'U' and resid 8 through 21 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 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 78 through 90 Processing helix chain 'X' and resid 101 through 112 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 80 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 98 Proline residue: Z 72 - end of helix removed outlier: 3.784A pdb=" N LYS Z 98 " --> pdb=" O ALA Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 124 Processing helix chain 'Z' and resid 129 through 141 removed outlier: 6.022A pdb=" N PHE Z 139 " --> pdb=" O ALA Z 135 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N THR Z 140 " --> pdb=" O ASN Z 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 4 No H-bonds generated for 'chain 'a' and resid 2 through 4' Processing helix chain 'a' and resid 6 through 30 Proline residue: a 19 - end of helix Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'b' and resid 3 through 14 Processing helix chain 'b' and resid 16 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 4.028A 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 46 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 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 43 Processing helix chain 'e' and resid 48 through 54 Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 through 88 Processing helix chain 'e' and resid 95 through 98 No H-bonds generated for 'chain 'e' and resid 95 through 98' Processing helix chain 'f' and resid 6 through 9 No H-bonds generated for 'chain 'f' and resid 6 through 9' Processing helix chain 'f' and resid 11 through 33 removed outlier: 3.524A pdb=" N ILE f 14 " --> pdb=" O TRP f 11 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU f 15 " --> pdb=" O VAL f 12 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL f 16 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 17 - end of helix Processing helix chain 'g' and resid 35 through 38 No H-bonds generated for 'chain 'g' and resid 35 through 38' Processing helix chain 'g' and resid 49 through 63 Processing helix chain 'g' and resid 70 through 76 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: 6.275A pdb=" N GLU g 85 " --> pdb=" O ARG g 82 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP g 86 " --> pdb=" O MET g 83 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG g 98 " --> pdb=" O VAL g 95 " (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 65 through 72 removed outlier: 3.761A pdb=" N PHE i 69 " --> pdb=" O ARG i 65 " (cutoff:3.500A) 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: 3.592A pdb=" N ARG k 44 " --> pdb=" O LYS k 40 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 58 Processing helix chain 'k' and resid 60 through 62 No H-bonds generated for 'chain 'k' and resid 60 through 62' 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 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: 6.110A pdb=" N LEU l 139 " --> pdb=" O ASN l 135 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU l 140 " --> pdb=" O ASN l 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 22 No H-bonds generated for 'chain 'm' and resid 19 through 22' 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 30 Processing helix chain 'n' and resid 33 through 49 Processing helix chain 'n' and resid 57 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 100 through 103 removed outlier: 3.560A pdb=" N LEU n 103 " --> pdb=" O GLU n 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 100 through 103' Processing helix chain 'n' and resid 108 through 113 Processing helix chain 'n' and resid 115 through 142 removed outlier: 4.149A pdb=" N ASP n 133 " --> pdb=" O MET n 129 " (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 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: 4.929A 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: 6.618A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N TYR p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLN p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.402A 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: 6.637A pdb=" N TYR 6 122 " --> pdb=" O MET 6 96 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL 6 98 " --> pdb=" O TYR 6 122 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL 6 124 " --> pdb=" O VAL 6 98 " (cutoff:3.500A) removed outlier: 6.280A 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: 6.612A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU C 48 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LYS C 108 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE C 50 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N TYR C 110 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 8.752A 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 removed outlier: 6.338A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 361 through 369 Processing sheet with id= F, first strand: chain '2' and resid 137 through 142 removed outlier: 6.331A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '1' and resid 219 through 224 removed outlier: 6.211A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.378A 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 9 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: 8.484A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain '3' and resid 490 through 493 removed outlier: 8.014A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.378A 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 67 through 69 Processing sheet with id= R, first strand: chain '9' and resid 94 through 100 removed outlier: 5.934A pdb=" N GLU 9 99 " --> pdb=" O THR 9 108 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N THR 9 108 " --> pdb=" O GLU 9 99 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.676A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARG P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (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: 6.536A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS S 63 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.569A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= AB, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.869A pdb=" N MET L 78 " --> pdb=" O THR L 65 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 219 through 223 removed outlier: 6.443A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TYR O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) 2994 hydrogen bonds defined for protein. 8487 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: 21.01 Time building geometry restraints manager: 21.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 28469 1.42 - 1.64: 40469 1.64 - 1.86: 807 1.86 - 2.09: 0 2.09 - 2.31: 80 Bond restraints: 69825 Sorted by residual: bond pdb=" C2' DGT O 401 " pdb=" C3' DGT O 401 " ideal model delta sigma weight residual 1.284 1.524 -0.240 2.00e-02 2.50e+03 1.43e+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 7.54e+01 bond pdb=" C4 DGT O 401 " pdb=" N3 DGT O 401 " ideal model delta sigma weight residual 1.502 1.344 0.158 2.00e-02 2.50e+03 6.25e+01 bond pdb=" C13 ZMP W 201 " pdb=" N1 ZMP W 201 " ideal model delta sigma weight residual 1.487 1.335 0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" C13 ZMP n 201 " pdb=" N1 ZMP n 201 " ideal model delta sigma weight residual 1.487 1.338 0.149 2.00e-02 2.50e+03 5.54e+01 ... (remaining 69820 not shown) Histogram of bond angle deviations from ideal: 68.89 - 82.28: 76 82.28 - 95.67: 0 95.67 - 109.05: 5747 109.05 - 122.44: 80314 122.44 - 135.82: 8273 Bond angle restraints: 94410 Sorted by residual: angle pdb=" PA NDP P 501 " pdb=" O3 NDP P 501 " pdb=" PN NDP P 501 " ideal model delta sigma weight residual 107.74 131.45 -23.71 1.95e+00 2.62e-01 1.47e+02 angle pdb=" N ASN 1 96 " pdb=" CA ASN 1 96 " pdb=" C ASN 1 96 " ideal model delta sigma weight residual 108.67 96.89 11.78 1.55e+00 4.16e-01 5.78e+01 angle pdb=" C5B NDP P 501 " pdb=" O5B NDP P 501 " pdb=" PA NDP P 501 " ideal model delta sigma weight residual 103.84 118.16 -14.32 1.91e+00 2.73e-01 5.59e+01 angle pdb=" C5D NDP P 501 " pdb=" O5D NDP P 501 " pdb=" PN NDP P 501 " ideal model delta sigma weight residual 104.93 124.63 -19.70 2.66e+00 1.41e-01 5.49e+01 angle pdb=" O2X NDP P 501 " pdb=" P2B NDP P 501 " pdb=" O3X NDP P 501 " ideal model delta sigma weight residual 117.33 108.26 9.07 1.48e+00 4.57e-01 3.76e+01 ... (remaining 94405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 41291 35.12 - 70.25: 1042 70.25 - 105.37: 51 105.37 - 140.50: 5 140.50 - 175.62: 2 Dihedral angle restraints: 42391 sinusoidal: 18360 harmonic: 24031 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 81.97 175.62 1 2.00e+01 2.50e-03 4.79e+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 93.00 151.37 -58.37 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CA HIS L 230 " pdb=" C HIS L 230 " pdb=" N PRO L 231 " pdb=" CA PRO L 231 " ideal model delta harmonic sigma weight residual 180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 42388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.229: 10204 4.229 - 8.457: 0 8.457 - 12.686: 0 12.686 - 16.914: 0 16.914 - 21.143: 24 Chirality restraints: 10228 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 10.59 -21.14 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="FE2 SF4 1 502 " pdb=" S1 SF4 1 502 " pdb=" S3 SF4 1 502 " pdb=" S4 SF4 1 502 " both_signs ideal model delta sigma weight residual False 10.55 -10.57 21.12 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10225 not shown) Planarity restraints: 11768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ D 501 " 0.006 2.00e-02 2.50e+03 7.58e-02 1.72e+02 pdb=" C2 UQ D 501 " 0.015 2.00e-02 2.50e+03 pdb=" C3 UQ D 501 " -0.020 2.00e-02 2.50e+03 pdb=" C4 UQ D 501 " -0.016 2.00e-02 2.50e+03 pdb=" C5 UQ D 501 " -0.013 2.00e-02 2.50e+03 pdb=" C6 UQ D 501 " -0.041 2.00e-02 2.50e+03 pdb=" C7 UQ D 501 " -0.135 2.00e-02 2.50e+03 pdb=" CM5 UQ D 501 " 0.144 2.00e-02 2.50e+03 pdb=" O1 UQ D 501 " 0.055 2.00e-02 2.50e+03 pdb=" O2 UQ D 501 " 0.100 2.00e-02 2.50e+03 pdb=" O3 UQ D 501 " -0.117 2.00e-02 2.50e+03 pdb=" O4 UQ D 501 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN 1 501 " -0.135 2.00e-02 2.50e+03 5.80e-02 1.60e+02 pdb=" C10 FMN 1 501 " -0.037 2.00e-02 2.50e+03 pdb=" C2 FMN 1 501 " 0.051 2.00e-02 2.50e+03 pdb=" C4 FMN 1 501 " -0.017 2.00e-02 2.50e+03 pdb=" C4A FMN 1 501 " -0.047 2.00e-02 2.50e+03 pdb=" C5A FMN 1 501 " -0.033 2.00e-02 2.50e+03 pdb=" C6 FMN 1 501 " -0.008 2.00e-02 2.50e+03 pdb=" C7 FMN 1 501 " 0.027 2.00e-02 2.50e+03 pdb=" C7M FMN 1 501 " 0.050 2.00e-02 2.50e+03 pdb=" C8 FMN 1 501 " 0.035 2.00e-02 2.50e+03 pdb=" C8M FMN 1 501 " 0.074 2.00e-02 2.50e+03 pdb=" C9 FMN 1 501 " 0.008 2.00e-02 2.50e+03 pdb=" C9A FMN 1 501 " -0.026 2.00e-02 2.50e+03 pdb=" N1 FMN 1 501 " 0.003 2.00e-02 2.50e+03 pdb=" N10 FMN 1 501 " -0.041 2.00e-02 2.50e+03 pdb=" N3 FMN 1 501 " 0.033 2.00e-02 2.50e+03 pdb=" N5 FMN 1 501 " -0.053 2.00e-02 2.50e+03 pdb=" O2 FMN 1 501 " 0.145 2.00e-02 2.50e+03 pdb=" O4 FMN 1 501 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C42 UQ D 501 " -0.109 2.00e-02 2.50e+03 9.17e-02 1.05e+02 pdb=" C43 UQ D 501 " 0.130 2.00e-02 2.50e+03 pdb=" C44 UQ D 501 " 0.066 2.00e-02 2.50e+03 pdb=" C45 UQ D 501 " 0.006 2.00e-02 2.50e+03 pdb=" C46 UQ D 501 " -0.093 2.00e-02 2.50e+03 ... (remaining 11765 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.74: 5088 2.74 - 3.34: 80336 3.34 - 3.94: 143047 3.94 - 4.54: 198965 4.54 - 5.14: 294545 Nonbonded interactions: 721981 Sorted by model distance: nonbonded pdb=" OH TYR H 114 " pdb=" O LEU J 60 " model vdw 2.134 2.440 nonbonded pdb=" O1A DGT O 401 " pdb="MG MG O 402 " model vdw 2.175 2.170 nonbonded pdb=" O2B DGT O 401 " pdb="MG MG O 402 " model vdw 2.176 2.170 nonbonded pdb=" O GLU 6 119 " pdb=" OH TYR P 54 " model vdw 2.178 2.440 nonbonded pdb=" O ALA O 286 " pdb=" OG SER O 290 " model vdw 2.182 2.440 ... (remaining 721976 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 3.450 Check model and map are aligned: 0.370 Set scattering table: 0.580 Process input model: 148.490 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 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 : 0.006 0.240 69825 Z= 0.414 Angle : 0.755 23.708 94410 Z= 0.385 Chirality : 1.022 21.143 10228 Planarity : 0.006 0.092 11768 Dihedral : 14.295 175.624 26861 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.47 % Favored : 96.52 % Rotamer: Outliers : 1.62 % Allowed : 4.90 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: 8129 helix: 0.74 (0.07), residues: 4514 sheet: -0.29 (0.25), residues: 387 loop : -0.54 (0.11), residues: 3228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.010 0.001 HIS 7 68 PHE 0.038 0.002 PHE N 292 TYR 0.033 0.002 TYR M 406 ARG 0.006 0.000 ARG N 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1341 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1224 time to evaluate : 5.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 224 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8795 (mt-10) REVERT: D 429 ASP cc_start: 0.9433 (m-30) cc_final: 0.9111 (m-30) REVERT: 1 431 GLN cc_start: 0.9466 (tm-30) cc_final: 0.9145 (tm-30) REVERT: 3 512 GLU cc_start: 0.9372 (tp30) cc_final: 0.9025 (tp30) REVERT: 3 540 ASP cc_start: 0.8870 (p0) cc_final: 0.8348 (p0) REVERT: 9 39 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8725 (p) REVERT: P 170 ASP cc_start: 0.9382 (m-30) cc_final: 0.9127 (m-30) REVERT: P 196 LEU cc_start: 0.9306 (tp) cc_final: 0.9018 (tm) REVERT: Q 18 ASP cc_start: 0.9227 (t0) cc_final: 0.9000 (t0) REVERT: 7 51 GLU cc_start: 0.9155 (tp30) cc_final: 0.8860 (tp30) REVERT: 7 80 LYS cc_start: 0.9210 (ttpp) cc_final: 0.9000 (ptmm) REVERT: T 47 GLN cc_start: 0.9215 (tm-30) cc_final: 0.8826 (tm-30) REVERT: T 48 VAL cc_start: 0.9305 (p) cc_final: 0.9013 (m) REVERT: V 32 ASP cc_start: 0.9186 (m-30) cc_final: 0.8870 (m-30) REVERT: W 91 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.9000 (mp0) REVERT: r 90 GLU cc_start: 0.8563 (pt0) cc_final: 0.8230 (tm-30) REVERT: r 91 LYS cc_start: 0.9376 (ptmt) cc_final: 0.9169 (ptmm) REVERT: s 51 ASP cc_start: 0.9196 (t0) cc_final: 0.8950 (t0) REVERT: A 32 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8867 (mp0) REVERT: A 38 GLU cc_start: 0.9300 (tp30) cc_final: 0.9086 (tp30) REVERT: A 68 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9142 (mt-10) REVERT: A 112 GLU cc_start: 0.9282 (mm-30) cc_final: 0.9079 (mm-30) REVERT: J 116 ASN cc_start: 0.7138 (t0) cc_final: 0.6895 (t0) REVERT: L 145 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8574 (mp0) REVERT: L 335 PHE cc_start: 0.7532 (m-10) cc_final: 0.7264 (m-10) REVERT: L 517 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8405 (p0) REVERT: L 539 MET cc_start: 0.9293 (tmm) cc_final: 0.8964 (tmm) REVERT: M 46 ASP cc_start: 0.8792 (t70) cc_final: 0.8490 (t0) REVERT: M 87 ASP cc_start: 0.9094 (t0) cc_final: 0.8865 (t0) REVERT: M 281 ASP cc_start: 0.8934 (t70) cc_final: 0.8431 (t70) REVERT: M 314 MET cc_start: 0.9572 (mtp) cc_final: 0.9358 (mtm) REVERT: M 459 MET cc_start: 0.8691 (ptp) cc_final: 0.8423 (ptp) REVERT: N 226 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8848 (p) REVERT: N 325 MET cc_start: 0.9433 (ttp) cc_final: 0.9229 (ttp) REVERT: O 44 GLN cc_start: 0.9437 (tm-30) cc_final: 0.9154 (tm-30) REVERT: U 52 MET cc_start: 0.9310 (mtp) cc_final: 0.8898 (mtm) REVERT: U 65 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7992 (tt) REVERT: X 133 ASP cc_start: 0.9197 (p0) cc_final: 0.8891 (p0) REVERT: Y 38 TYR cc_start: 0.9284 (m-80) cc_final: 0.8983 (m-80) REVERT: Y 42 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9307 (mm) REVERT: Y 50 GLU cc_start: 0.8872 (pm20) cc_final: 0.8665 (pm20) REVERT: Y 81 GLU cc_start: 0.9112 (mp0) cc_final: 0.8798 (mp0) REVERT: Y 85 ASP cc_start: 0.9032 (t0) cc_final: 0.8374 (t0) REVERT: Y 117 MET cc_start: 0.9400 (mtp) cc_final: 0.9185 (mtp) REVERT: a 4 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8851 (mm-30) REVERT: a 51 ASP cc_start: 0.9208 (m-30) cc_final: 0.8877 (m-30) REVERT: b 10 ASN cc_start: 0.9457 (t0) cc_final: 0.9232 (t0) REVERT: b 59 ASP cc_start: 0.8979 (p0) cc_final: 0.8203 (p0) REVERT: c 13 ASN cc_start: 0.9354 (t0) cc_final: 0.8863 (t0) REVERT: c 33 GLN cc_start: 0.9221 (mm110) cc_final: 0.8853 (mm110) REVERT: c 37 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.9006 (mm-30) REVERT: f 8 ARG cc_start: 0.7922 (mpp-170) cc_final: 0.7584 (mpt180) REVERT: f 9 GLU cc_start: 0.8354 (pt0) cc_final: 0.8094 (pt0) REVERT: g 97 TYR cc_start: 0.9457 (t80) cc_final: 0.9142 (t80) REVERT: g 101 ASN cc_start: 0.9408 (m110) cc_final: 0.8940 (m110) REVERT: g 112 ASP cc_start: 0.9107 (t0) cc_final: 0.8865 (t0) REVERT: h 112 ARG cc_start: 0.9121 (ttp80) cc_final: 0.8678 (ttm-80) REVERT: i 7 GLU cc_start: 0.9208 (tp30) cc_final: 0.8960 (mm-30) REVERT: i 68 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8468 (pt) REVERT: i 114 GLU cc_start: 0.8337 (pp20) cc_final: 0.7934 (pp20) REVERT: j 55 ASP cc_start: 0.9376 (t0) cc_final: 0.9147 (t0) REVERT: j 58 GLN cc_start: 0.9167 (mp-120) cc_final: 0.8826 (mm-40) REVERT: l 5 LYS cc_start: 0.9500 (mmtm) cc_final: 0.9182 (tppt) REVERT: l 48 MET cc_start: 0.9225 (mtm) cc_final: 0.9023 (mtp) REVERT: l 150 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8594 (tm-30) REVERT: m 34 GLU cc_start: 0.9448 (mt-10) cc_final: 0.9241 (mt-10) REVERT: m 61 ASP cc_start: 0.9193 (t70) cc_final: 0.8641 (t70) REVERT: m 107 ASP cc_start: 0.9502 (t0) cc_final: 0.9242 (t0) REVERT: m 117 GLU cc_start: 0.9087 (pt0) cc_final: 0.8813 (pt0) REVERT: n 97 LYS cc_start: 0.9229 (mttp) cc_final: 0.9020 (mmmm) REVERT: n 123 GLN cc_start: 0.9330 (mt0) cc_final: 0.9036 (mt0) REVERT: n 131 SER cc_start: 0.8360 (m) cc_final: 0.7802 (p) REVERT: o 5 THR cc_start: 0.9468 (t) cc_final: 0.8945 (t) REVERT: o 17 ASP cc_start: 0.8861 (p0) cc_final: 0.8661 (p0) REVERT: o 43 GLN cc_start: 0.9190 (tp-100) cc_final: 0.8354 (tp-100) REVERT: o 47 ASP cc_start: 0.9301 (m-30) cc_final: 0.8723 (m-30) REVERT: o 75 ASN cc_start: 0.8454 (t0) cc_final: 0.8086 (t0) REVERT: o 100 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8935 (mm-30) outliers start: 117 outliers final: 21 residues processed: 1311 average time/residue: 1.4814 time to fit residues: 2528.5807 Evaluate side-chains 1034 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1004 time to evaluate : 5.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 1 residue 45 THR Chi-restraints excluded: chain 1 residue 273 SER Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 9 residue 39 THR Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 272 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 91 GLU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain L residue 517 ASN Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 275 CYS Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain c residue 37 GLU Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 71 VAL Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain p residue 16 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 678 optimal weight: 7.9990 chunk 608 optimal weight: 9.9990 chunk 337 optimal weight: 40.0000 chunk 207 optimal weight: 0.9990 chunk 410 optimal weight: 10.0000 chunk 325 optimal weight: 0.8980 chunk 629 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 382 optimal weight: 7.9990 chunk 468 optimal weight: 0.9980 chunk 729 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN Q 46 GLN 7 95 HIS q 12 GLN A 10 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 ASN M 366 ASN N 63 GLN ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN X 108 GLN Y 43 ASN Y 78 GLN c 46 ASN e 6 GLN e 44 HIS e 96 HIS g 84 GLN ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 108 GLN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 GLN ** o 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.269 69825 Z= 0.535 Angle : 1.547 51.125 94410 Z= 1.004 Chirality : 0.307 6.438 10228 Planarity : 0.005 0.057 11768 Dihedral : 12.390 177.827 10617 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.22 % Favored : 96.76 % Rotamer: Outliers : 2.16 % Allowed : 11.69 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: 0.91 (0.09), residues: 8129 helix: 1.34 (0.08), residues: 4507 sheet: -0.25 (0.26), residues: 375 loop : -0.24 (0.11), residues: 3247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 85 HIS 0.007 0.001 HIS 9 67 PHE 0.028 0.001 PHE M 151 TYR 0.026 0.001 TYR L 422 ARG 0.007 0.000 ARG m 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1225 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1069 time to evaluate : 5.958 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: D 429 ASP cc_start: 0.9466 (m-30) cc_final: 0.9166 (m-30) REVERT: 1 431 GLN cc_start: 0.9435 (tm-30) cc_final: 0.9143 (tm-30) REVERT: 3 19 MET cc_start: 0.9338 (mmm) cc_final: 0.9129 (mmm) REVERT: 3 512 GLU cc_start: 0.9403 (tp30) cc_final: 0.9030 (tp30) REVERT: 3 540 ASP cc_start: 0.8762 (p0) cc_final: 0.8292 (p0) REVERT: 3 693 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8476 (pt0) REVERT: P 57 MET cc_start: 0.9513 (mmm) cc_final: 0.9164 (mmp) REVERT: P 170 ASP cc_start: 0.9375 (m-30) cc_final: 0.9110 (m-30) REVERT: Q 15 GLU cc_start: 0.8616 (mp0) cc_final: 0.8086 (mp0) REVERT: Q 16 LYS cc_start: 0.8999 (tppt) cc_final: 0.8663 (tmtt) REVERT: 7 31 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8680 (mtt180) REVERT: 7 51 GLU cc_start: 0.9146 (tp30) cc_final: 0.8838 (tp30) REVERT: 7 80 LYS cc_start: 0.9219 (ttpp) cc_final: 0.9016 (ptmm) REVERT: T 23 ASP cc_start: 0.9407 (p0) cc_final: 0.9139 (p0) REVERT: T 47 GLN cc_start: 0.9233 (tm-30) cc_final: 0.8846 (tm-30) REVERT: T 48 VAL cc_start: 0.9224 (p) cc_final: 0.8976 (m) REVERT: T 71 MET cc_start: 0.7493 (ptt) cc_final: 0.7194 (ppp) REVERT: V 32 ASP cc_start: 0.9194 (m-30) cc_final: 0.8863 (m-30) REVERT: r 90 GLU cc_start: 0.8564 (pt0) cc_final: 0.8197 (tm-30) REVERT: s 51 ASP cc_start: 0.9174 (t0) cc_final: 0.8958 (t0) REVERT: A 32 GLU cc_start: 0.9396 (mm-30) cc_final: 0.8866 (mp0) REVERT: A 38 GLU cc_start: 0.9348 (tp30) cc_final: 0.9117 (tp30) REVERT: A 68 GLU cc_start: 0.9473 (mm-30) cc_final: 0.9194 (mt-10) REVERT: A 112 GLU cc_start: 0.9272 (mm-30) cc_final: 0.9071 (mm-30) REVERT: J 85 ASN cc_start: 0.8842 (t0) cc_final: 0.8622 (t0) REVERT: J 116 ASN cc_start: 0.7110 (t0) cc_final: 0.6752 (m110) REVERT: L 517 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8559 (p0) REVERT: L 539 MET cc_start: 0.9421 (tmm) cc_final: 0.9018 (tmm) REVERT: M 46 ASP cc_start: 0.8679 (t70) cc_final: 0.8417 (t0) REVERT: M 87 ASP cc_start: 0.9077 (t0) cc_final: 0.8804 (t70) REVERT: M 114 GLU cc_start: 0.8758 (tp30) cc_final: 0.8181 (tm-30) REVERT: M 281 ASP cc_start: 0.8918 (t70) cc_final: 0.8415 (t70) REVERT: N 226 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8850 (p) REVERT: N 325 MET cc_start: 0.9173 (ttp) cc_final: 0.8931 (ttp) REVERT: O 44 GLN cc_start: 0.9424 (tm-30) cc_final: 0.9172 (tm-30) REVERT: X 133 ASP cc_start: 0.9199 (p0) cc_final: 0.8899 (p0) REVERT: Y 3 ARG cc_start: 0.9044 (pmt-80) cc_final: 0.8697 (mpp-170) REVERT: Y 5 PHE cc_start: 0.8939 (m-80) cc_final: 0.8605 (m-80) REVERT: Y 6 GLU cc_start: 0.9359 (mm-30) cc_final: 0.9136 (mm-30) REVERT: Y 38 TYR cc_start: 0.9241 (m-80) cc_final: 0.8953 (m-80) REVERT: Y 81 GLU cc_start: 0.9104 (mp0) cc_final: 0.8774 (mp0) REVERT: Y 85 ASP cc_start: 0.8907 (t0) cc_final: 0.8568 (t0) REVERT: a 4 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8840 (mm-30) REVERT: a 51 ASP cc_start: 0.9149 (m-30) cc_final: 0.8852 (m-30) REVERT: b 10 ASN cc_start: 0.9445 (t0) cc_final: 0.9234 (t0) REVERT: c 13 ASN cc_start: 0.9327 (t0) cc_final: 0.8794 (t0) REVERT: c 33 GLN cc_start: 0.9169 (mm110) cc_final: 0.8808 (mm110) REVERT: g 101 ASN cc_start: 0.9449 (m110) cc_final: 0.9094 (m110) REVERT: g 112 ASP cc_start: 0.9081 (t0) cc_final: 0.8823 (t0) REVERT: h 6 LYS cc_start: 0.8092 (tppp) cc_final: 0.7878 (tppp) REVERT: h 112 ARG cc_start: 0.9107 (ttp80) cc_final: 0.8653 (ttm-80) REVERT: i 7 GLU cc_start: 0.9208 (tp30) cc_final: 0.8961 (mm-30) REVERT: i 114 GLU cc_start: 0.8352 (pp20) cc_final: 0.7931 (pp20) REVERT: j 55 ASP cc_start: 0.9309 (t0) cc_final: 0.9034 (t0) REVERT: j 58 GLN cc_start: 0.9045 (mp-120) cc_final: 0.8687 (mm-40) REVERT: l 5 LYS cc_start: 0.9415 (mmtm) cc_final: 0.9068 (tppt) REVERT: l 140 GLU cc_start: 0.9500 (OUTLIER) cc_final: 0.9294 (pm20) REVERT: l 150 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8549 (tm-30) REVERT: m 34 GLU cc_start: 0.9442 (mt-10) cc_final: 0.9236 (mt-10) REVERT: m 61 ASP cc_start: 0.9190 (t70) cc_final: 0.8893 (t70) REVERT: m 117 GLU cc_start: 0.9137 (pt0) cc_final: 0.8705 (pt0) REVERT: m 119 LYS cc_start: 0.9273 (mptt) cc_final: 0.8919 (mmtt) REVERT: n 123 GLN cc_start: 0.9301 (mt0) cc_final: 0.9066 (mt0) REVERT: o 17 ASP cc_start: 0.8949 (p0) cc_final: 0.8626 (p0) REVERT: o 43 GLN cc_start: 0.9217 (tp-100) cc_final: 0.8496 (tp-100) REVERT: o 47 ASP cc_start: 0.9311 (m-30) cc_final: 0.8821 (m-30) REVERT: o 75 ASN cc_start: 0.8411 (t0) cc_final: 0.8069 (t0) outliers start: 156 outliers final: 51 residues processed: 1145 average time/residue: 1.4881 time to fit residues: 2226.2535 Evaluate side-chains 1069 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1013 time to evaluate : 5.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 1 residue 164 LYS Chi-restraints excluded: chain 1 residue 273 SER Chi-restraints excluded: chain 1 residue 365 CYS Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 693 GLU Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 272 LEU Chi-restraints excluded: chain 7 residue 31 ARG Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain s residue 35 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain J residue 4 TYR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain L residue 517 ASN Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 177 MET Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 376 MET Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain X residue 73 ILE Chi-restraints excluded: chain X residue 93 MET Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 126 HIS Chi-restraints excluded: chain j residue 7 ILE Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 140 GLU Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain p residue 16 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 405 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 606 optimal weight: 6.9990 chunk 496 optimal weight: 0.8980 chunk 201 optimal weight: 7.9990 chunk 730 optimal weight: 7.9990 chunk 789 optimal weight: 20.0000 chunk 650 optimal weight: 20.0000 chunk 724 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 586 optimal weight: 0.0170 overall best weight: 3.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 71 HIS 3 653 ASN Q 44 ASN q 12 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 ASN X 142 HIS Y 43 ASN Y 78 GLN b 82 ASN d 117 HIS e 6 GLN e 24 GLN h 86 ASN h 108 GLN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 72 GLN o 53 GLN ** o 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.275 69825 Z= 0.539 Angle : 1.543 50.918 94410 Z= 1.002 Chirality : 0.308 6.486 10228 Planarity : 0.004 0.055 11768 Dihedral : 11.652 176.127 10588 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.26 % Favored : 96.73 % Rotamer: Outliers : 2.46 % Allowed : 12.45 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: 1.20 (0.09), residues: 8129 helix: 1.56 (0.08), residues: 4504 sheet: -0.25 (0.26), residues: 378 loop : -0.07 (0.11), residues: 3247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 144 HIS 0.008 0.001 HIS 9 67 PHE 0.036 0.001 PHE P 261 TYR 0.025 0.001 TYR H 142 ARG 0.011 0.000 ARG i 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1056 time to evaluate : 5.856 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: D 164 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8526 (pmm) REVERT: D 429 ASP cc_start: 0.9471 (m-30) cc_final: 0.9185 (m-30) REVERT: 2 183 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8932 (pptt) REVERT: 1 431 GLN cc_start: 0.9444 (tm-30) cc_final: 0.9142 (tm-30) REVERT: 3 540 ASP cc_start: 0.8818 (p0) cc_final: 0.8615 (p0) REVERT: 3 693 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8497 (pt0) REVERT: 9 7 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9156 (tttp) REVERT: P 57 MET cc_start: 0.9568 (mmm) cc_final: 0.9190 (mmp) REVERT: P 170 ASP cc_start: 0.9378 (m-30) cc_final: 0.9077 (m-30) REVERT: Q 16 LYS cc_start: 0.8974 (tppt) cc_final: 0.8749 (tmmt) REVERT: 7 31 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8762 (mtt180) REVERT: 7 51 GLU cc_start: 0.9122 (tp30) cc_final: 0.8819 (tp30) REVERT: S 78 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8884 (pp) REVERT: T 23 ASP cc_start: 0.9425 (p0) cc_final: 0.9141 (p0) REVERT: T 47 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8813 (tm-30) REVERT: T 48 VAL cc_start: 0.9209 (p) cc_final: 0.8954 (m) REVERT: T 55 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8970 (mt-10) REVERT: V 32 ASP cc_start: 0.9215 (m-30) cc_final: 0.8871 (m-30) REVERT: s 51 ASP cc_start: 0.9166 (t0) cc_final: 0.8958 (t0) REVERT: A 32 GLU cc_start: 0.9419 (mm-30) cc_final: 0.8843 (mp0) REVERT: A 68 GLU cc_start: 0.9473 (mm-30) cc_final: 0.9206 (mt-10) REVERT: A 112 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9077 (mm-30) REVERT: J 85 ASN cc_start: 0.8888 (t0) cc_final: 0.8632 (t0) REVERT: J 98 MET cc_start: 0.8969 (tmm) cc_final: 0.8702 (tpt) REVERT: J 116 ASN cc_start: 0.7067 (t0) cc_final: 0.6808 (t0) REVERT: J 152 MET cc_start: 0.9388 (tpp) cc_final: 0.8602 (tpp) REVERT: L 78 MET cc_start: 0.9288 (ttm) cc_final: 0.9010 (ttm) REVERT: L 116 ARG cc_start: 0.9074 (ttm-80) cc_final: 0.8057 (ttm-80) REVERT: L 539 MET cc_start: 0.9433 (tmm) cc_final: 0.9018 (tmm) REVERT: M 46 ASP cc_start: 0.8607 (t70) cc_final: 0.8356 (t0) REVERT: M 87 ASP cc_start: 0.9112 (t0) cc_final: 0.8781 (t70) REVERT: M 114 GLU cc_start: 0.8758 (tp30) cc_final: 0.8267 (tm-30) REVERT: M 281 ASP cc_start: 0.8858 (t70) cc_final: 0.8384 (t70) REVERT: X 133 ASP cc_start: 0.9189 (p0) cc_final: 0.8889 (p0) REVERT: Y 5 PHE cc_start: 0.8953 (m-80) cc_final: 0.8662 (m-80) REVERT: Y 81 GLU cc_start: 0.9105 (mp0) cc_final: 0.8798 (mp0) REVERT: Y 85 ASP cc_start: 0.8967 (t0) cc_final: 0.8718 (t0) REVERT: a 4 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8855 (mm-30) REVERT: a 51 ASP cc_start: 0.9155 (m-30) cc_final: 0.8890 (m-30) REVERT: c 13 ASN cc_start: 0.9352 (t0) cc_final: 0.8747 (t0) REVERT: c 33 GLN cc_start: 0.9081 (mm110) cc_final: 0.8854 (mm110) REVERT: d 25 LYS cc_start: 0.8735 (tttp) cc_final: 0.8235 (tttm) REVERT: g 101 ASN cc_start: 0.9498 (m110) cc_final: 0.9220 (m110) REVERT: g 112 ASP cc_start: 0.9037 (t0) cc_final: 0.8787 (t0) REVERT: h 112 ARG cc_start: 0.9113 (ttp80) cc_final: 0.8654 (ttm-80) REVERT: i 114 GLU cc_start: 0.8321 (pp20) cc_final: 0.7956 (pp20) REVERT: i 125 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7494 (tp-100) REVERT: j 55 ASP cc_start: 0.9312 (t0) cc_final: 0.8976 (t0) REVERT: j 58 GLN cc_start: 0.9026 (mp-120) cc_final: 0.8659 (mm-40) REVERT: j 60 THR cc_start: 0.9081 (p) cc_final: 0.8871 (p) REVERT: l 5 LYS cc_start: 0.9382 (mmtm) cc_final: 0.9037 (tppt) REVERT: l 140 GLU cc_start: 0.9489 (OUTLIER) cc_final: 0.8903 (pm20) REVERT: l 150 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8545 (tm-30) REVERT: m 23 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.6916 (t70) REVERT: m 61 ASP cc_start: 0.9230 (t70) cc_final: 0.8958 (t70) REVERT: m 117 GLU cc_start: 0.9128 (pt0) cc_final: 0.8828 (pt0) REVERT: m 119 LYS cc_start: 0.9281 (mptt) cc_final: 0.9003 (mptt) REVERT: n 123 GLN cc_start: 0.9288 (mt0) cc_final: 0.9056 (mt0) REVERT: o 17 ASP cc_start: 0.8977 (p0) cc_final: 0.8674 (p0) REVERT: o 43 GLN cc_start: 0.9292 (tp-100) cc_final: 0.8623 (tp-100) REVERT: o 47 ASP cc_start: 0.9330 (m-30) cc_final: 0.8848 (m-30) REVERT: o 75 ASN cc_start: 0.8231 (t0) cc_final: 0.7898 (t0) REVERT: o 112 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9154 (ttmm) REVERT: o 116 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9309 (mm) REVERT: o 117 LYS cc_start: 0.9421 (tppp) cc_final: 0.9002 (tptt) outliers start: 178 outliers final: 66 residues processed: 1143 average time/residue: 1.5096 time to fit residues: 2250.9314 Evaluate side-chains 1080 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1004 time to evaluate : 5.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 2 residue 183 LYS Chi-restraints excluded: chain 1 residue 273 SER Chi-restraints excluded: chain 1 residue 337 MET Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 639 THR Chi-restraints excluded: chain 3 residue 693 GLU Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 272 LEU Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain 7 residue 31 ARG Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain J residue 4 TYR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 597 LEU Chi-restraints excluded: chain M residue 243 MET Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 405 MET Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain X residue 73 ILE Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 42 MET Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain h residue 86 ASN Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 126 HIS Chi-restraints excluded: chain j residue 7 ILE Chi-restraints excluded: chain j residue 26 GLU Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 74 GLU Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 140 GLU Chi-restraints excluded: chain m residue 23 ASP Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain o residue 116 LEU Chi-restraints excluded: chain p residue 16 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 721 optimal weight: 8.9990 chunk 549 optimal weight: 7.9990 chunk 379 optimal weight: 20.0000 chunk 80 optimal weight: 0.0570 chunk 348 optimal weight: 5.9990 chunk 490 optimal weight: 5.9990 chunk 733 optimal weight: 4.9990 chunk 776 optimal weight: 2.9990 chunk 383 optimal weight: 7.9990 chunk 694 optimal weight: 6.9990 chunk 209 optimal weight: 7.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 653 ASN Q 44 ASN q 12 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 ASN M 44 GLN ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 57 GLN Y 43 ASN b 82 ASN e 6 GLN g 84 GLN h 86 ASN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.269 69825 Z= 0.538 Angle : 1.543 50.811 94410 Z= 1.002 Chirality : 0.309 6.487 10228 Planarity : 0.004 0.055 11768 Dihedral : 11.326 175.658 10582 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.33 % Favored : 96.65 % Rotamer: Outliers : 2.34 % Allowed : 13.51 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: 1.30 (0.10), residues: 8129 helix: 1.64 (0.08), residues: 4501 sheet: -0.15 (0.26), residues: 390 loop : -0.01 (0.11), residues: 3238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP j 59 HIS 0.007 0.001 HIS 9 67 PHE 0.027 0.001 PHE N 292 TYR 0.027 0.001 TYR N 146 ARG 0.011 0.000 ARG i 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1040 time to evaluate : 5.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 429 ASP cc_start: 0.9478 (m-30) cc_final: 0.9189 (m-30) REVERT: 1 431 GLN cc_start: 0.9442 (tm-30) cc_final: 0.9149 (tm-30) REVERT: 3 19 MET cc_start: 0.9351 (mmm) cc_final: 0.9114 (mmm) REVERT: 3 540 ASP cc_start: 0.8825 (p0) cc_final: 0.8624 (p0) REVERT: 3 693 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8519 (pt0) REVERT: 9 7 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9154 (tttp) REVERT: 9 8 LYS cc_start: 0.8198 (pptt) cc_final: 0.7901 (pptt) REVERT: P 170 ASP cc_start: 0.9363 (m-30) cc_final: 0.9062 (m-30) REVERT: Q 16 LYS cc_start: 0.9073 (tppt) cc_final: 0.8800 (tmtt) REVERT: 7 31 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8762 (mtt180) REVERT: S 78 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8848 (pp) REVERT: T 23 ASP cc_start: 0.9416 (p0) cc_final: 0.9116 (p0) REVERT: T 25 ILE cc_start: 0.9020 (mt) cc_final: 0.8762 (pp) REVERT: T 47 GLN cc_start: 0.9182 (tm-30) cc_final: 0.8793 (tm-30) REVERT: T 48 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8940 (m) REVERT: T 55 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8978 (mt-10) REVERT: T 71 MET cc_start: 0.7185 (ptt) cc_final: 0.6950 (ppp) REVERT: V 32 ASP cc_start: 0.9214 (m-30) cc_final: 0.8872 (m-30) REVERT: A 32 GLU cc_start: 0.9410 (mm-30) cc_final: 0.8831 (mp0) REVERT: A 68 GLU cc_start: 0.9463 (mm-30) cc_final: 0.9201 (mt-10) REVERT: A 112 GLU cc_start: 0.9313 (mm-30) cc_final: 0.9085 (mm-30) REVERT: J 85 ASN cc_start: 0.8955 (t0) cc_final: 0.8643 (t0) REVERT: J 152 MET cc_start: 0.9413 (tpp) cc_final: 0.8584 (tpp) REVERT: L 116 ARG cc_start: 0.9112 (ttm-80) cc_final: 0.8105 (ttm-80) REVERT: L 517 ASN cc_start: 0.9081 (OUTLIER) cc_final: 0.8616 (p0) REVERT: L 539 MET cc_start: 0.9438 (tmm) cc_final: 0.9013 (tmm) REVERT: M 46 ASP cc_start: 0.8892 (t70) cc_final: 0.8429 (t0) REVERT: M 87 ASP cc_start: 0.9099 (t0) cc_final: 0.8827 (t70) REVERT: M 281 ASP cc_start: 0.8889 (t70) cc_final: 0.8288 (t70) REVERT: U 87 TYR cc_start: 0.9290 (p90) cc_final: 0.9011 (p90) REVERT: X 133 ASP cc_start: 0.9190 (p0) cc_final: 0.8896 (p0) REVERT: Y 3 ARG cc_start: 0.9042 (pmt-80) cc_final: 0.8673 (mpp-170) REVERT: Y 4 PHE cc_start: 0.8765 (t80) cc_final: 0.8536 (t80) REVERT: Y 5 PHE cc_start: 0.8993 (m-80) cc_final: 0.8685 (m-80) REVERT: Y 81 GLU cc_start: 0.9120 (mp0) cc_final: 0.8815 (mp0) REVERT: a 51 ASP cc_start: 0.9153 (m-30) cc_final: 0.8887 (m-30) REVERT: c 13 ASN cc_start: 0.9337 (t0) cc_final: 0.8713 (t0) REVERT: c 33 GLN cc_start: 0.9015 (mm110) cc_final: 0.8814 (mm110) REVERT: d 25 LYS cc_start: 0.8766 (tttp) cc_final: 0.8265 (tttm) REVERT: g 101 ASN cc_start: 0.9515 (m110) cc_final: 0.9248 (m-40) REVERT: g 112 ASP cc_start: 0.9055 (t0) cc_final: 0.8806 (t0) REVERT: h 112 ARG cc_start: 0.9099 (ttp80) cc_final: 0.8656 (ttm-80) REVERT: i 114 GLU cc_start: 0.8320 (pp20) cc_final: 0.7951 (pp20) REVERT: i 125 GLN cc_start: 0.7728 (tp-100) cc_final: 0.7433 (tp-100) REVERT: j 26 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: j 55 ASP cc_start: 0.9291 (t0) cc_final: 0.9034 (t0) REVERT: j 58 GLN cc_start: 0.9006 (mp-120) cc_final: 0.8719 (mm-40) REVERT: l 5 LYS cc_start: 0.9376 (mmtm) cc_final: 0.9032 (tppt) REVERT: l 140 GLU cc_start: 0.9482 (OUTLIER) cc_final: 0.9270 (pm20) REVERT: l 150 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8564 (tm-30) REVERT: m 23 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.6860 (t70) REVERT: m 61 ASP cc_start: 0.9214 (t70) cc_final: 0.8978 (t70) REVERT: m 117 GLU cc_start: 0.9107 (pt0) cc_final: 0.8866 (pt0) REVERT: m 119 LYS cc_start: 0.9300 (mptt) cc_final: 0.9069 (mptt) REVERT: n 123 GLN cc_start: 0.9286 (mt0) cc_final: 0.8960 (mt0) REVERT: o 17 ASP cc_start: 0.8988 (p0) cc_final: 0.8591 (p0) REVERT: o 43 GLN cc_start: 0.9301 (tp-100) cc_final: 0.8686 (tp-100) REVERT: o 47 ASP cc_start: 0.9323 (m-30) cc_final: 0.8887 (m-30) REVERT: o 75 ASN cc_start: 0.8268 (t0) cc_final: 0.7933 (t0) REVERT: o 116 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9292 (mm) REVERT: o 117 LYS cc_start: 0.9446 (tppp) cc_final: 0.9020 (tptt) REVERT: p 135 THR cc_start: 0.9552 (OUTLIER) cc_final: 0.9340 (m) outliers start: 169 outliers final: 73 residues processed: 1127 average time/residue: 1.5724 time to fit residues: 2316.8752 Evaluate side-chains 1090 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1006 time to evaluate : 5.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain 1 residue 273 SER Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 253 ARG Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 639 THR Chi-restraints excluded: chain 3 residue 693 GLU Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 272 LEU Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain 7 residue 31 ARG Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain J residue 4 TYR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 517 ASN Chi-restraints excluded: chain L residue 597 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 243 MET Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain X residue 73 ILE Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 62 MET Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 42 MET Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 126 HIS Chi-restraints excluded: chain j residue 26 GLU Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 140 GLU Chi-restraints excluded: chain m residue 23 ASP Chi-restraints excluded: chain o residue 116 LEU Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 135 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 646 optimal weight: 8.9990 chunk 440 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 577 optimal weight: 0.1980 chunk 320 optimal weight: 6.9990 chunk 662 optimal weight: 5.9990 chunk 536 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 396 optimal weight: 0.8980 chunk 696 optimal weight: 10.0000 chunk 195 optimal weight: 0.0670 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 113 HIS ** 1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 653 ASN Q 44 ASN q 12 GLN H 5 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 505 ASN M 81 GLN N 289 ASN Y 9 HIS Y 43 ASN b 10 ASN b 82 ASN g 55 ASN h 86 ASN h 108 GLN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 13 GLN n 72 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.264 69825 Z= 0.521 Angle : 1.538 50.757 94410 Z= 1.000 Chirality : 0.308 6.456 10228 Planarity : 0.004 0.054 11768 Dihedral : 11.001 176.820 10581 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.09 % Favored : 96.90 % Rotamer: Outliers : 1.94 % Allowed : 14.62 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: 1.37 (0.10), residues: 8129 helix: 1.68 (0.08), residues: 4485 sheet: -0.02 (0.26), residues: 386 loop : 0.03 (0.11), residues: 3258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP Z 103 HIS 0.006 0.001 HIS 9 67 PHE 0.027 0.001 PHE P 261 TYR 0.032 0.001 TYR H 142 ARG 0.010 0.000 ARG m 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1197 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1057 time to evaluate : 5.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 112 LYS cc_start: 0.9598 (tppp) cc_final: 0.9371 (tppp) REVERT: D 429 ASP cc_start: 0.9467 (m-30) cc_final: 0.9195 (m-30) REVERT: 1 431 GLN cc_start: 0.9434 (tm-30) cc_final: 0.9126 (tm-30) REVERT: 3 253 ARG cc_start: 0.9256 (OUTLIER) cc_final: 0.8972 (mtp180) REVERT: 3 540 ASP cc_start: 0.8805 (p0) cc_final: 0.8350 (p0) REVERT: 3 693 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8561 (pt0) REVERT: P 57 MET cc_start: 0.9577 (mmm) cc_final: 0.9300 (mmp) REVERT: P 170 ASP cc_start: 0.9356 (m-30) cc_final: 0.9049 (m-30) REVERT: Q 16 LYS cc_start: 0.9032 (tppt) cc_final: 0.8800 (tmmt) REVERT: 7 31 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8765 (mtt180) REVERT: 7 80 LYS cc_start: 0.9422 (ptmm) cc_final: 0.9134 (ptmm) REVERT: S 78 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8763 (pp) REVERT: S 85 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8698 (pm20) REVERT: T 12 LYS cc_start: 0.9320 (ttpp) cc_final: 0.9055 (tmmm) REVERT: T 23 ASP cc_start: 0.9392 (p0) cc_final: 0.9079 (p0) REVERT: T 47 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8762 (tm-30) REVERT: T 48 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8928 (m) REVERT: T 55 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8978 (mt-10) REVERT: T 71 MET cc_start: 0.7180 (ptt) cc_final: 0.6899 (ppp) REVERT: V 32 ASP cc_start: 0.9206 (m-30) cc_final: 0.8862 (m-30) REVERT: A 32 GLU cc_start: 0.9425 (mm-30) cc_final: 0.8827 (mp0) REVERT: A 68 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9214 (mt-10) REVERT: J 22 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.8854 (mtmm) REVERT: J 85 ASN cc_start: 0.8951 (t0) cc_final: 0.8649 (t0) REVERT: J 98 MET cc_start: 0.8948 (tmm) cc_final: 0.8704 (tpt) REVERT: K 36 MET cc_start: 0.9484 (mtm) cc_final: 0.9265 (mtp) REVERT: L 145 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8440 (mp0) REVERT: L 235 SER cc_start: 0.9145 (t) cc_final: 0.8931 (p) REVERT: L 517 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8641 (p0) REVERT: L 539 MET cc_start: 0.9441 (tmm) cc_final: 0.8972 (tmm) REVERT: L 559 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8845 (tp30) REVERT: M 46 ASP cc_start: 0.8797 (t70) cc_final: 0.8389 (t0) REVERT: M 87 ASP cc_start: 0.9136 (t0) cc_final: 0.8868 (t70) REVERT: M 114 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8006 (tm-30) REVERT: M 281 ASP cc_start: 0.8859 (t70) cc_final: 0.8284 (t70) REVERT: M 405 MET cc_start: 0.9454 (mmp) cc_final: 0.9241 (mmm) REVERT: N 215 MET cc_start: 0.9394 (mmm) cc_final: 0.9170 (tpp) REVERT: O 6 LEU cc_start: 0.9601 (tp) cc_final: 0.9399 (tm) REVERT: O 192 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8692 (mmm) REVERT: U 65 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.7819 (tt) REVERT: U 68 GLU cc_start: 0.9329 (pm20) cc_final: 0.8855 (pm20) REVERT: X 133 ASP cc_start: 0.9183 (p0) cc_final: 0.8887 (p0) REVERT: Y 5 PHE cc_start: 0.8962 (m-80) cc_final: 0.8693 (m-80) REVERT: Y 50 GLU cc_start: 0.9003 (pm20) cc_final: 0.8801 (pm20) REVERT: Y 81 GLU cc_start: 0.9120 (mp0) cc_final: 0.8795 (mp0) REVERT: a 49 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8975 (mm-30) REVERT: a 51 ASP cc_start: 0.9134 (m-30) cc_final: 0.8888 (m-30) REVERT: c 13 ASN cc_start: 0.9330 (t0) cc_final: 0.8713 (t0) REVERT: d 25 LYS cc_start: 0.8747 (tttp) cc_final: 0.8546 (tttp) REVERT: d 104 LYS cc_start: 0.8714 (tptp) cc_final: 0.8182 (tptp) REVERT: d 105 GLU cc_start: 0.8745 (tp30) cc_final: 0.8481 (pm20) REVERT: g 97 TYR cc_start: 0.9196 (t80) cc_final: 0.8957 (t80) REVERT: g 101 ASN cc_start: 0.9546 (m110) cc_final: 0.9297 (m110) REVERT: g 112 ASP cc_start: 0.9047 (t0) cc_final: 0.8797 (t0) REVERT: h 6 LYS cc_start: 0.7692 (tppp) cc_final: 0.7417 (tppp) REVERT: h 86 ASN cc_start: 0.9021 (OUTLIER) cc_final: 0.8703 (t0) REVERT: h 112 ARG cc_start: 0.9105 (ttp80) cc_final: 0.8644 (ttm-80) REVERT: i 114 GLU cc_start: 0.8284 (pp20) cc_final: 0.7948 (pp20) REVERT: i 120 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7679 (mtp85) REVERT: i 125 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7487 (tp-100) REVERT: j 55 ASP cc_start: 0.9277 (t0) cc_final: 0.8893 (t0) REVERT: j 58 GLN cc_start: 0.9019 (mp-120) cc_final: 0.8622 (mm-40) REVERT: l 5 LYS cc_start: 0.9384 (mmtm) cc_final: 0.9034 (tppt) REVERT: l 150 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8584 (tm-30) REVERT: m 61 ASP cc_start: 0.9257 (t70) cc_final: 0.9025 (t0) REVERT: m 117 GLU cc_start: 0.9082 (pt0) cc_final: 0.8821 (pt0) REVERT: m 119 LYS cc_start: 0.9281 (mptt) cc_final: 0.9043 (mptt) REVERT: n 123 GLN cc_start: 0.9266 (mt0) cc_final: 0.8938 (mt0) REVERT: o 17 ASP cc_start: 0.8910 (p0) cc_final: 0.8318 (p0) REVERT: o 43 GLN cc_start: 0.9292 (tp-100) cc_final: 0.8692 (tp-100) REVERT: o 47 ASP cc_start: 0.9323 (m-30) cc_final: 0.8902 (m-30) REVERT: o 116 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9293 (mm) REVERT: o 117 LYS cc_start: 0.9437 (tppp) cc_final: 0.9018 (tptt) outliers start: 140 outliers final: 56 residues processed: 1138 average time/residue: 1.4841 time to fit residues: 2204.2919 Evaluate side-chains 1085 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1017 time to evaluate : 5.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain 1 residue 273 SER Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 253 ARG Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 639 THR Chi-restraints excluded: chain 3 residue 693 GLU Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 112 ASP Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 272 LEU Chi-restraints excluded: chain 7 residue 31 ARG Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain q residue 3 LEU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain J residue 4 TYR Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 517 ASN Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 243 MET Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain N residue 90 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain O residue 192 MET Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain X residue 73 ILE Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 27 LEU Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain h residue 86 ASN Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 126 HIS Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain o residue 116 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 261 optimal weight: 20.0000 chunk 698 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 455 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 776 optimal weight: 2.9990 chunk 644 optimal weight: 9.9990 chunk 359 optimal weight: 0.2980 chunk 64 optimal weight: 10.0000 chunk 257 optimal weight: 3.9990 chunk 407 optimal weight: 20.0000 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 653 ASN P 203 GLN Q 44 ASN q 12 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 57 GLN Y 9 HIS Y 43 ASN b 82 ASN c 33 GLN g 55 ASN ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 49 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.264 69825 Z= 0.526 Angle : 1.540 50.777 94410 Z= 1.001 Chirality : 0.308 6.461 10228 Planarity : 0.004 0.064 11768 Dihedral : 10.769 176.689 10579 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.17 % Favored : 96.81 % Rotamer: Outliers : 2.09 % Allowed : 15.04 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: 1.45 (0.10), residues: 8129 helix: 1.74 (0.08), residues: 4477 sheet: -0.01 (0.26), residues: 393 loop : 0.09 (0.11), residues: 3259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP j 59 HIS 0.006 0.001 HIS 9 67 PHE 0.023 0.001 PHE L 335 TYR 0.034 0.001 TYR N 146 ARG 0.015 0.000 ARG i 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1045 time to evaluate : 5.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 112 LYS cc_start: 0.9592 (tppp) cc_final: 0.9356 (tppp) REVERT: D 429 ASP cc_start: 0.9465 (m-30) cc_final: 0.9189 (m-30) REVERT: 1 431 GLN cc_start: 0.9433 (tm-30) cc_final: 0.9130 (tm-30) REVERT: 3 253 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.8964 (mtp180) REVERT: 3 540 ASP cc_start: 0.8868 (p0) cc_final: 0.8666 (p0) REVERT: 3 693 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8567 (pt0) REVERT: P 57 MET cc_start: 0.9581 (mmm) cc_final: 0.9293 (mmp) REVERT: P 170 ASP cc_start: 0.9355 (m-30) cc_final: 0.9053 (m-30) REVERT: Q 16 LYS cc_start: 0.9085 (tppt) cc_final: 0.8855 (tmmt) REVERT: 7 31 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8781 (mtt180) REVERT: 7 80 LYS cc_start: 0.9439 (ptmm) cc_final: 0.9204 (ptmm) REVERT: S 78 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8757 (pp) REVERT: T 21 LEU cc_start: 0.9748 (mt) cc_final: 0.9486 (mp) REVERT: T 23 ASP cc_start: 0.9377 (p0) cc_final: 0.9060 (p0) REVERT: T 47 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8779 (tm-30) REVERT: T 48 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8899 (m) REVERT: T 55 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8953 (mt-10) REVERT: T 71 MET cc_start: 0.7209 (ptt) cc_final: 0.6962 (ppp) REVERT: V 32 ASP cc_start: 0.9208 (m-30) cc_final: 0.8868 (m-30) REVERT: A 32 GLU cc_start: 0.9435 (mm-30) cc_final: 0.8832 (mp0) REVERT: A 68 GLU cc_start: 0.9463 (mm-30) cc_final: 0.9213 (mt-10) REVERT: J 85 ASN cc_start: 0.8944 (t0) cc_final: 0.8592 (t0) REVERT: J 98 MET cc_start: 0.8956 (tmm) cc_final: 0.8696 (tpt) REVERT: J 152 MET cc_start: 0.9347 (tpp) cc_final: 0.8561 (tpp) REVERT: K 36 MET cc_start: 0.9485 (mtm) cc_final: 0.9257 (mtp) REVERT: L 116 ARG cc_start: 0.9124 (ttm-80) cc_final: 0.8104 (ttm-80) REVERT: L 145 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8396 (mp0) REVERT: L 235 SER cc_start: 0.9147 (t) cc_final: 0.8931 (p) REVERT: L 517 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8473 (p0) REVERT: L 539 MET cc_start: 0.9441 (tmm) cc_final: 0.9081 (tmm) REVERT: L 559 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8885 (tp30) REVERT: M 46 ASP cc_start: 0.8785 (t70) cc_final: 0.8346 (t0) REVERT: M 87 ASP cc_start: 0.9134 (t0) cc_final: 0.8844 (t70) REVERT: M 114 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8011 (tm-30) REVERT: M 281 ASP cc_start: 0.8852 (t70) cc_final: 0.8287 (t70) REVERT: M 405 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.9175 (mmm) REVERT: O 6 LEU cc_start: 0.9602 (tp) cc_final: 0.9402 (tm) REVERT: O 192 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.8588 (mpp) REVERT: U 65 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.7653 (tt) REVERT: U 68 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.8984 (pm20) REVERT: X 133 ASP cc_start: 0.9185 (p0) cc_final: 0.8895 (p0) REVERT: Y 1 VAL cc_start: 0.8361 (m) cc_final: 0.7740 (t) REVERT: Y 3 ARG cc_start: 0.9100 (pmt-80) cc_final: 0.8729 (mpp-170) REVERT: Y 5 PHE cc_start: 0.8965 (m-80) cc_final: 0.8631 (m-80) REVERT: Y 81 GLU cc_start: 0.9122 (mp0) cc_final: 0.8786 (mp0) REVERT: Y 82 LYS cc_start: 0.9546 (mtpp) cc_final: 0.9067 (ptpp) REVERT: Y 85 ASP cc_start: 0.8939 (t0) cc_final: 0.8645 (t0) REVERT: Z 129 LYS cc_start: 0.9482 (mmpt) cc_final: 0.8983 (tptt) REVERT: a 49 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8961 (mm-30) REVERT: a 51 ASP cc_start: 0.9140 (m-30) cc_final: 0.8891 (m-30) REVERT: c 13 ASN cc_start: 0.9329 (t0) cc_final: 0.8703 (t0) REVERT: d 104 LYS cc_start: 0.8559 (tptp) cc_final: 0.8295 (tptp) REVERT: g 97 TYR cc_start: 0.9214 (t80) cc_final: 0.8936 (t80) REVERT: g 101 ASN cc_start: 0.9547 (m110) cc_final: 0.9306 (m-40) REVERT: g 112 ASP cc_start: 0.9042 (t0) cc_final: 0.8790 (t0) REVERT: h 108 GLN cc_start: 0.9252 (tp-100) cc_final: 0.9019 (tp40) REVERT: h 112 ARG cc_start: 0.9110 (ttp80) cc_final: 0.8643 (ttm-80) REVERT: i 114 GLU cc_start: 0.8436 (pp20) cc_final: 0.8083 (pp20) REVERT: i 125 GLN cc_start: 0.7798 (tp-100) cc_final: 0.7523 (tp-100) REVERT: j 55 ASP cc_start: 0.9298 (t0) cc_final: 0.8913 (t0) REVERT: j 58 GLN cc_start: 0.9007 (mp-120) cc_final: 0.8649 (mm-40) REVERT: l 5 LYS cc_start: 0.9378 (mmtm) cc_final: 0.9028 (tppt) REVERT: l 140 GLU cc_start: 0.9510 (OUTLIER) cc_final: 0.9309 (pm20) REVERT: l 150 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8578 (tm-30) REVERT: m 61 ASP cc_start: 0.9246 (t70) cc_final: 0.9012 (t0) REVERT: m 117 GLU cc_start: 0.9052 (pt0) cc_final: 0.8794 (pt0) REVERT: m 119 LYS cc_start: 0.9272 (mptt) cc_final: 0.9016 (mptt) REVERT: o 17 ASP cc_start: 0.8761 (p0) cc_final: 0.8148 (p0) REVERT: o 19 GLU cc_start: 0.9137 (mp0) cc_final: 0.8882 (mp0) REVERT: o 43 GLN cc_start: 0.9302 (tp-100) cc_final: 0.8752 (tp-100) REVERT: o 47 ASP cc_start: 0.9323 (m-30) cc_final: 0.8932 (m-30) REVERT: o 112 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9185 (ttmm) REVERT: o 117 LYS cc_start: 0.9456 (tppp) cc_final: 0.9080 (tptt) outliers start: 151 outliers final: 68 residues processed: 1126 average time/residue: 1.4902 time to fit residues: 2191.1448 Evaluate side-chains 1098 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1018 time to evaluate : 5.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain 1 residue 273 SER Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 253 ARG Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 639 THR Chi-restraints excluded: chain 3 residue 693 GLU Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 272 LEU Chi-restraints excluded: chain 7 residue 31 ARG Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 95 THR Chi-restraints excluded: chain q residue 3 LEU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain J residue 4 TYR Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 517 ASN Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 243 MET Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 351 VAL Chi-restraints excluded: chain M residue 405 MET Chi-restraints excluded: chain N residue 90 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 225 MET Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain O residue 192 MET Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 68 GLU Chi-restraints excluded: chain X residue 73 ILE Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain h residue 18 ASP Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 126 HIS Chi-restraints excluded: chain j residue 7 ILE Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 93 LEU 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 140 GLU Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain o residue 112 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 749 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 442 optimal weight: 5.9990 chunk 567 optimal weight: 7.9990 chunk 439 optimal weight: 10.0000 chunk 654 optimal weight: 5.9990 chunk 433 optimal weight: 6.9990 chunk 773 optimal weight: 3.9990 chunk 484 optimal weight: 9.9990 chunk 471 optimal weight: 5.9990 chunk 357 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 436 GLN 1 437 HIS 3 653 ASN Q 44 ASN q 12 GLN A 108 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 HIS ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 57 GLN Y 9 HIS b 10 ASN b 82 ASN c 33 GLN d 46 ASN g 55 ASN h 86 ASN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 49 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 13 GLN n 72 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.268 69825 Z= 0.550 Angle : 1.550 50.838 94410 Z= 1.004 Chirality : 0.309 6.488 10228 Planarity : 0.004 0.054 11768 Dihedral : 10.712 175.382 10579 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.33 % Favored : 96.65 % Rotamer: Outliers : 2.16 % Allowed : 15.22 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: 1.48 (0.10), residues: 8129 helix: 1.77 (0.08), residues: 4466 sheet: 0.01 (0.26), residues: 391 loop : 0.09 (0.11), residues: 3272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP j 59 HIS 0.007 0.001 HIS 9 67 PHE 0.033 0.001 PHE P 261 TYR 0.036 0.001 TYR N 146 ARG 0.014 0.000 ARG m 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1025 time to evaluate : 6.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 HIS cc_start: 0.9269 (OUTLIER) cc_final: 0.8404 (t-90) REVERT: D 429 ASP cc_start: 0.9483 (m-30) cc_final: 0.9193 (m-30) REVERT: 1 431 GLN cc_start: 0.9441 (tm-30) cc_final: 0.9107 (tm-30) REVERT: 3 653 ASN cc_start: 0.9092 (t0) cc_final: 0.8865 (m110) REVERT: 3 693 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: 9 8 LYS cc_start: 0.8193 (pptt) cc_final: 0.7992 (pptt) REVERT: P 57 MET cc_start: 0.9608 (mmm) cc_final: 0.9323 (mmp) REVERT: P 170 ASP cc_start: 0.9376 (m-30) cc_final: 0.9057 (m-30) REVERT: Q 16 LYS cc_start: 0.9095 (tppt) cc_final: 0.8869 (tmmt) REVERT: 7 31 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8801 (mtt180) REVERT: S 78 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8797 (pp) REVERT: T 21 LEU cc_start: 0.9755 (mt) cc_final: 0.9488 (mp) REVERT: T 23 ASP cc_start: 0.9380 (p0) cc_final: 0.9070 (p0) REVERT: T 38 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8906 (pmtt) REVERT: T 47 GLN cc_start: 0.9217 (tm-30) cc_final: 0.8871 (tm-30) REVERT: T 48 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8846 (m) REVERT: T 71 MET cc_start: 0.7246 (ptt) cc_final: 0.7029 (ppp) REVERT: V 32 ASP cc_start: 0.9226 (m-30) cc_final: 0.8877 (m-30) REVERT: W 36 GLU cc_start: 0.9321 (mm-30) cc_final: 0.8971 (mm-30) REVERT: A 32 GLU cc_start: 0.9462 (mm-30) cc_final: 0.8828 (mp0) REVERT: A 68 GLU cc_start: 0.9458 (mm-30) cc_final: 0.9220 (mt-10) REVERT: A 108 GLN cc_start: 0.9556 (OUTLIER) cc_final: 0.9159 (mp-120) REVERT: J 85 ASN cc_start: 0.8938 (t0) cc_final: 0.8591 (t0) REVERT: J 98 MET cc_start: 0.8977 (tmm) cc_final: 0.8693 (tpt) REVERT: K 36 MET cc_start: 0.9495 (mtm) cc_final: 0.9288 (mtp) REVERT: L 116 ARG cc_start: 0.9167 (ttm-80) cc_final: 0.8135 (ttm-80) REVERT: L 235 SER cc_start: 0.9194 (t) cc_final: 0.8964 (p) REVERT: L 539 MET cc_start: 0.9439 (tmm) cc_final: 0.9059 (tmm) REVERT: L 559 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8914 (tp30) REVERT: M 46 ASP cc_start: 0.8774 (t70) cc_final: 0.8324 (t0) REVERT: M 87 ASP cc_start: 0.9141 (t0) cc_final: 0.8842 (t70) REVERT: M 114 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8103 (tm-30) REVERT: M 281 ASP cc_start: 0.8893 (t70) cc_final: 0.8286 (t70) REVERT: M 310 MET cc_start: 0.9399 (OUTLIER) cc_final: 0.9058 (ttm) REVERT: M 342 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8834 (tmm) REVERT: M 405 MET cc_start: 0.9461 (OUTLIER) cc_final: 0.9232 (mmm) REVERT: O 6 LEU cc_start: 0.9607 (tp) cc_final: 0.9405 (tm) REVERT: O 192 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.8648 (mmm) REVERT: O 268 GLU cc_start: 0.9533 (mt-10) cc_final: 0.9264 (mm-30) REVERT: U 65 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.7572 (tt) REVERT: U 68 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.9026 (pm20) REVERT: X 133 ASP cc_start: 0.9194 (p0) cc_final: 0.8913 (p0) REVERT: Y 1 VAL cc_start: 0.8100 (m) cc_final: 0.7837 (t) REVERT: Y 3 ARG cc_start: 0.8990 (pmt-80) cc_final: 0.8728 (mpp-170) REVERT: Y 4 PHE cc_start: 0.8845 (t80) cc_final: 0.8640 (t80) REVERT: Y 5 PHE cc_start: 0.9032 (m-80) cc_final: 0.8712 (m-80) REVERT: Y 81 GLU cc_start: 0.9143 (mp0) cc_final: 0.8821 (mp0) REVERT: Z 129 LYS cc_start: 0.9497 (mmpt) cc_final: 0.9038 (tptt) REVERT: a 51 ASP cc_start: 0.9153 (m-30) cc_final: 0.8909 (m-30) REVERT: b 14 LYS cc_start: 0.9506 (mmtm) cc_final: 0.9270 (mttp) REVERT: c 13 ASN cc_start: 0.9335 (t0) cc_final: 0.8680 (t0) REVERT: d 104 LYS cc_start: 0.8596 (tptp) cc_final: 0.7958 (tptp) REVERT: d 105 GLU cc_start: 0.8787 (tp30) cc_final: 0.8352 (pm20) REVERT: g 97 TYR cc_start: 0.9230 (t80) cc_final: 0.8887 (t80) REVERT: g 101 ASN cc_start: 0.9550 (m110) cc_final: 0.9231 (m-40) REVERT: g 112 ASP cc_start: 0.9050 (t0) cc_final: 0.8799 (t0) REVERT: h 86 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8739 (t0) REVERT: h 112 ARG cc_start: 0.9181 (ttp80) cc_final: 0.8662 (ttm-80) REVERT: i 65 ARG cc_start: 0.8803 (mmm160) cc_final: 0.8580 (mmm160) REVERT: i 114 GLU cc_start: 0.8265 (pp20) cc_final: 0.7928 (pp20) REVERT: i 125 GLN cc_start: 0.7832 (tp-100) cc_final: 0.7461 (tp-100) REVERT: j 55 ASP cc_start: 0.9278 (t0) cc_final: 0.8921 (t0) REVERT: j 58 GLN cc_start: 0.9012 (mp-120) cc_final: 0.8666 (mm-40) REVERT: l 5 LYS cc_start: 0.9339 (mmtm) cc_final: 0.8998 (tppt) REVERT: l 150 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8545 (tm-30) REVERT: m 61 ASP cc_start: 0.9255 (t70) cc_final: 0.9019 (t0) REVERT: m 117 GLU cc_start: 0.9057 (pt0) cc_final: 0.8786 (pt0) REVERT: m 119 LYS cc_start: 0.9266 (mptt) cc_final: 0.9001 (mptt) REVERT: n 123 GLN cc_start: 0.9171 (mt0) cc_final: 0.8751 (mt0) REVERT: o 17 ASP cc_start: 0.8786 (p0) cc_final: 0.8345 (p0) REVERT: o 38 MET cc_start: 0.9041 (tpt) cc_final: 0.8755 (tpt) REVERT: o 43 GLN cc_start: 0.9305 (tp-100) cc_final: 0.8718 (tp-100) REVERT: o 47 ASP cc_start: 0.9274 (m-30) cc_final: 0.8795 (m-30) REVERT: o 112 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9192 (ttmm) REVERT: o 117 LYS cc_start: 0.9463 (tppp) cc_final: 0.9082 (tptt) outliers start: 156 outliers final: 79 residues processed: 1110 average time/residue: 1.5183 time to fit residues: 2206.0598 Evaluate side-chains 1103 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1009 time to evaluate : 5.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 HIS Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 1 residue 273 SER Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 3 residue 253 ARG Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 639 THR Chi-restraints excluded: chain 3 residue 693 GLU Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 272 LEU Chi-restraints excluded: chain 7 residue 31 ARG Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 38 LYS Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain q residue 3 LEU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain J residue 4 TYR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain L residue 341 MET Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 517 ASN Chi-restraints excluded: chain L residue 597 LEU Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 310 MET Chi-restraints excluded: chain M residue 342 MET Chi-restraints excluded: chain M residue 351 VAL Chi-restraints excluded: chain M residue 405 MET Chi-restraints excluded: chain N residue 90 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 225 MET Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain O residue 192 MET Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 68 GLU Chi-restraints excluded: chain X residue 73 ILE Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 84 ASP Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain h residue 86 ASN Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 126 HIS Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 93 LEU 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 m residue 24 VAL Chi-restraints excluded: chain o residue 20 LYS Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain p residue 16 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 478 optimal weight: 7.9990 chunk 309 optimal weight: 4.9990 chunk 462 optimal weight: 9.9990 chunk 233 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 492 optimal weight: 6.9990 chunk 527 optimal weight: 7.9990 chunk 382 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 608 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN q 12 GLN A 10 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 ASN Y 9 HIS b 82 ASN c 33 GLN e 28 ASN h 86 ASN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 49 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 13 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.268 69825 Z= 0.555 Angle : 1.556 50.828 94410 Z= 1.007 Chirality : 0.309 6.490 10228 Planarity : 0.004 0.061 11768 Dihedral : 10.664 175.442 10579 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.36 % Favored : 96.63 % Rotamer: Outliers : 1.98 % Allowed : 15.66 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: 1.47 (0.10), residues: 8129 helix: 1.76 (0.08), residues: 4455 sheet: 0.02 (0.26), residues: 391 loop : 0.10 (0.11), residues: 3283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP j 59 HIS 0.007 0.001 HIS 9 67 PHE 0.026 0.001 PHE N 292 TYR 0.021 0.001 TYR L 422 ARG 0.014 0.000 ARG m 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1020 time to evaluate : 6.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 HIS cc_start: 0.9281 (OUTLIER) cc_final: 0.8403 (t-90) REVERT: D 429 ASP cc_start: 0.9484 (m-30) cc_final: 0.9176 (m-30) REVERT: 1 431 GLN cc_start: 0.9444 (tm-30) cc_final: 0.9142 (tm-30) REVERT: 3 693 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8537 (pt0) REVERT: 9 7 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.9164 (tttp) REVERT: 9 8 LYS cc_start: 0.8199 (pptt) cc_final: 0.7903 (pptt) REVERT: P 57 MET cc_start: 0.9615 (mmm) cc_final: 0.9341 (mmp) REVERT: P 170 ASP cc_start: 0.9372 (m-30) cc_final: 0.9055 (m-30) REVERT: Q 16 LYS cc_start: 0.9107 (tppt) cc_final: 0.8891 (tmmt) REVERT: 7 31 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8804 (mtt180) REVERT: S 78 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8852 (pp) REVERT: T 21 LEU cc_start: 0.9753 (mt) cc_final: 0.9488 (mp) REVERT: T 23 ASP cc_start: 0.9383 (p0) cc_final: 0.9075 (p0) REVERT: T 38 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8870 (pmtt) REVERT: T 47 GLN cc_start: 0.9233 (tm-30) cc_final: 0.8893 (tm-30) REVERT: T 48 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8924 (m) REVERT: V 32 ASP cc_start: 0.9226 (m-30) cc_final: 0.8878 (m-30) REVERT: A 32 GLU cc_start: 0.9466 (mm-30) cc_final: 0.8815 (mp0) REVERT: A 68 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9222 (mt-10) REVERT: J 85 ASN cc_start: 0.8946 (t0) cc_final: 0.8581 (t0) REVERT: K 36 MET cc_start: 0.9506 (mtm) cc_final: 0.9280 (mtp) REVERT: L 116 ARG cc_start: 0.9168 (ttm-80) cc_final: 0.8125 (ttm-80) REVERT: L 145 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8453 (mp0) REVERT: L 235 SER cc_start: 0.9216 (t) cc_final: 0.8990 (p) REVERT: L 539 MET cc_start: 0.9443 (tmm) cc_final: 0.9058 (tmm) REVERT: L 559 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8933 (tp30) REVERT: M 46 ASP cc_start: 0.8745 (t70) cc_final: 0.8286 (t0) REVERT: M 87 ASP cc_start: 0.9155 (t0) cc_final: 0.8805 (t70) REVERT: M 114 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8165 (tm-30) REVERT: M 123 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8645 (mp0) REVERT: M 281 ASP cc_start: 0.8919 (t70) cc_final: 0.8294 (t70) REVERT: M 342 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8796 (tmm) REVERT: M 405 MET cc_start: 0.9511 (OUTLIER) cc_final: 0.9292 (mmm) REVERT: O 192 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.8659 (mmm) REVERT: O 268 GLU cc_start: 0.9537 (OUTLIER) cc_final: 0.9267 (mm-30) REVERT: U 65 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.7596 (tt) REVERT: U 68 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.8923 (pm20) REVERT: X 133 ASP cc_start: 0.9199 (p0) cc_final: 0.8926 (p0) REVERT: Y 2 LYS cc_start: 0.8469 (tppp) cc_final: 0.8154 (pmmt) REVERT: Y 5 PHE cc_start: 0.9083 (m-80) cc_final: 0.8752 (m-80) REVERT: Y 81 GLU cc_start: 0.9154 (mp0) cc_final: 0.8821 (mp0) REVERT: Y 82 LYS cc_start: 0.9546 (mtpp) cc_final: 0.9099 (ptpp) REVERT: Y 85 ASP cc_start: 0.9040 (t0) cc_final: 0.8765 (t0) REVERT: Z 129 LYS cc_start: 0.9497 (mmpt) cc_final: 0.9040 (tptt) REVERT: a 49 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8978 (mm-30) REVERT: a 51 ASP cc_start: 0.9153 (m-30) cc_final: 0.8920 (m-30) REVERT: c 13 ASN cc_start: 0.9323 (t0) cc_final: 0.8711 (t0) REVERT: d 25 LYS cc_start: 0.8743 (tttp) cc_final: 0.8203 (tttm) REVERT: d 104 LYS cc_start: 0.8610 (tptp) cc_final: 0.8334 (tptp) REVERT: g 97 TYR cc_start: 0.9253 (t80) cc_final: 0.8926 (t80) REVERT: g 101 ASN cc_start: 0.9558 (m110) cc_final: 0.9248 (m-40) REVERT: g 112 ASP cc_start: 0.9054 (t0) cc_final: 0.8807 (t0) REVERT: h 86 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8709 (t0) REVERT: h 112 ARG cc_start: 0.9182 (ttp80) cc_final: 0.8672 (ttm-80) REVERT: i 114 GLU cc_start: 0.8254 (pp20) cc_final: 0.7919 (pp20) REVERT: i 125 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7451 (tp-100) REVERT: j 55 ASP cc_start: 0.9278 (t0) cc_final: 0.9025 (t0) REVERT: j 58 GLN cc_start: 0.9010 (mp-120) cc_final: 0.8758 (mm-40) REVERT: l 5 LYS cc_start: 0.9338 (mmtm) cc_final: 0.8994 (tppt) REVERT: l 150 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8604 (tm-30) REVERT: m 23 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7045 (t70) REVERT: m 61 ASP cc_start: 0.9270 (t70) cc_final: 0.9043 (t0) REVERT: m 117 GLU cc_start: 0.9047 (pt0) cc_final: 0.8773 (pt0) REVERT: m 119 LYS cc_start: 0.9260 (mptt) cc_final: 0.8992 (mptt) REVERT: n 123 GLN cc_start: 0.9193 (mt0) cc_final: 0.8908 (mt0) REVERT: n 131 SER cc_start: 0.7898 (m) cc_final: 0.7348 (p) REVERT: o 17 ASP cc_start: 0.8803 (p0) cc_final: 0.8328 (p0) REVERT: o 43 GLN cc_start: 0.9288 (tp-100) cc_final: 0.8685 (tp-100) REVERT: o 47 ASP cc_start: 0.9260 (m-30) cc_final: 0.8775 (m-30) REVERT: o 112 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9229 (ttmm) REVERT: o 117 LYS cc_start: 0.9483 (tppp) cc_final: 0.9094 (tptt) outliers start: 143 outliers final: 88 residues processed: 1099 average time/residue: 1.5248 time to fit residues: 2178.3298 Evaluate side-chains 1104 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1000 time to evaluate : 5.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 HIS Chi-restraints excluded: chain 6 residue 135 TYR Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 2 residue 74 GLN Chi-restraints excluded: chain 1 residue 273 SER Chi-restraints excluded: chain 1 residue 324 GLN Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 639 THR Chi-restraints excluded: chain 3 residue 693 GLU Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 272 LEU Chi-restraints excluded: chain 7 residue 31 ARG Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 38 LYS Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain q residue 3 LEU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain s residue 51 ASP Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain J residue 4 TYR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 341 MET Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 342 MET Chi-restraints excluded: chain M residue 351 VAL Chi-restraints excluded: chain M residue 405 MET Chi-restraints excluded: chain N residue 90 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 225 MET Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain O residue 192 MET Chi-restraints excluded: chain O residue 268 GLU Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 68 GLU Chi-restraints excluded: chain X residue 73 ILE Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain h residue 86 ASN Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 126 HIS Chi-restraints excluded: chain j residue 7 ILE Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain m residue 23 ASP Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain o residue 20 LYS Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain p residue 16 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 704 optimal weight: 5.9990 chunk 741 optimal weight: 8.9990 chunk 676 optimal weight: 20.0000 chunk 721 optimal weight: 8.9990 chunk 434 optimal weight: 6.9990 chunk 314 optimal weight: 1.9990 chunk 566 optimal weight: 20.0000 chunk 221 optimal weight: 10.0000 chunk 651 optimal weight: 9.9990 chunk 682 optimal weight: 8.9990 chunk 718 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 653 ASN Q 44 ASN q 12 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 9 HIS b 10 ASN b 82 ASN c 33 GLN e 28 ASN h 86 ASN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 49 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 13 GLN n 72 GLN ** o 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 109 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.270 69825 Z= 0.581 Angle : 1.568 50.854 94410 Z= 1.011 Chirality : 0.309 6.503 10228 Planarity : 0.004 0.078 11768 Dihedral : 10.711 177.813 10579 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.38 % Favored : 96.60 % Rotamer: Outliers : 1.90 % Allowed : 16.02 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: 1.44 (0.10), residues: 8129 helix: 1.73 (0.08), residues: 4453 sheet: 0.03 (0.27), residues: 381 loop : 0.09 (0.11), residues: 3295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP j 59 HIS 0.007 0.001 HIS 9 67 PHE 0.034 0.001 PHE P 261 TYR 0.025 0.001 TYR g 81 ARG 0.017 0.001 ARG i 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1015 time to evaluate : 6.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 HIS cc_start: 0.9296 (OUTLIER) cc_final: 0.8388 (t-90) REVERT: D 429 ASP cc_start: 0.9485 (m-30) cc_final: 0.9166 (m-30) REVERT: 1 431 GLN cc_start: 0.9447 (tm-30) cc_final: 0.9218 (tm-30) REVERT: 3 693 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8545 (pt0) REVERT: 9 7 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9171 (tttp) REVERT: 9 8 LYS cc_start: 0.8213 (pptt) cc_final: 0.7915 (pptt) REVERT: P 57 MET cc_start: 0.9633 (mmm) cc_final: 0.9368 (mmp) REVERT: P 170 ASP cc_start: 0.9391 (m-30) cc_final: 0.9063 (m-30) REVERT: 7 31 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8814 (mtt180) REVERT: S 78 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8894 (pp) REVERT: S 85 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8762 (pm20) REVERT: T 23 ASP cc_start: 0.9405 (p0) cc_final: 0.9109 (p0) REVERT: T 47 GLN cc_start: 0.9226 (tm-30) cc_final: 0.8851 (tm-30) REVERT: V 32 ASP cc_start: 0.9228 (m-30) cc_final: 0.8890 (m-30) REVERT: A 32 GLU cc_start: 0.9420 (mm-30) cc_final: 0.8741 (mp0) REVERT: A 108 GLN cc_start: 0.9585 (tp40) cc_final: 0.9371 (mp10) REVERT: A 109 LYS cc_start: 0.9481 (OUTLIER) cc_final: 0.9240 (mttp) REVERT: J 85 ASN cc_start: 0.8965 (t0) cc_final: 0.8610 (t0) REVERT: K 36 MET cc_start: 0.9515 (mtm) cc_final: 0.9295 (mtp) REVERT: L 145 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8508 (mp0) REVERT: L 539 MET cc_start: 0.9428 (tmm) cc_final: 0.9020 (tmm) REVERT: L 559 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8970 (tp30) REVERT: M 46 ASP cc_start: 0.8753 (t70) cc_final: 0.8276 (t0) REVERT: M 85 LYS cc_start: 0.9375 (pttt) cc_final: 0.9170 (pttm) REVERT: M 87 ASP cc_start: 0.9144 (t0) cc_final: 0.8836 (t70) REVERT: M 114 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8335 (tm-30) REVERT: M 281 ASP cc_start: 0.8957 (t70) cc_final: 0.8363 (t70) REVERT: N 321 LYS cc_start: 0.8906 (tptt) cc_final: 0.8385 (tppt) REVERT: O 192 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.8663 (mmm) REVERT: O 268 GLU cc_start: 0.9540 (OUTLIER) cc_final: 0.9276 (mm-30) REVERT: U 65 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8036 (tt) REVERT: U 68 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.9034 (pm20) REVERT: X 133 ASP cc_start: 0.9189 (p0) cc_final: 0.8926 (p0) REVERT: Y 3 ARG cc_start: 0.8984 (pmt-80) cc_final: 0.8709 (mpp-170) REVERT: Y 81 GLU cc_start: 0.9155 (mp0) cc_final: 0.8826 (mp0) REVERT: Y 82 LYS cc_start: 0.9539 (mtpp) cc_final: 0.9168 (ptpp) REVERT: Y 85 ASP cc_start: 0.9063 (t0) cc_final: 0.8393 (t70) REVERT: Z 129 LYS cc_start: 0.9501 (mmpt) cc_final: 0.9043 (tptt) REVERT: a 49 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8990 (mm-30) REVERT: a 51 ASP cc_start: 0.9161 (m-30) cc_final: 0.8935 (m-30) REVERT: c 13 ASN cc_start: 0.9339 (t0) cc_final: 0.8683 (t0) REVERT: d 104 LYS cc_start: 0.8643 (tptp) cc_final: 0.8219 (tptp) REVERT: d 105 GLU cc_start: 0.8831 (tp30) cc_final: 0.8311 (pp20) REVERT: g 97 TYR cc_start: 0.9243 (t80) cc_final: 0.8892 (t80) REVERT: g 101 ASN cc_start: 0.9539 (m110) cc_final: 0.9172 (m-40) REVERT: g 112 ASP cc_start: 0.9049 (t0) cc_final: 0.8801 (t0) REVERT: g 120 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8413 (tp30) REVERT: h 112 ARG cc_start: 0.9159 (ttp80) cc_final: 0.8645 (ttm-80) REVERT: i 114 GLU cc_start: 0.8278 (pp20) cc_final: 0.7940 (pp20) REVERT: i 125 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7525 (tp-100) REVERT: j 55 ASP cc_start: 0.9189 (t0) cc_final: 0.8742 (t0) REVERT: j 58 GLN cc_start: 0.9033 (mp-120) cc_final: 0.8701 (mm-40) REVERT: l 5 LYS cc_start: 0.9336 (mmtm) cc_final: 0.8843 (tptp) REVERT: l 150 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8617 (tm-30) REVERT: m 61 ASP cc_start: 0.9297 (t70) cc_final: 0.9071 (t0) REVERT: m 117 GLU cc_start: 0.9051 (pt0) cc_final: 0.8766 (pt0) REVERT: m 119 LYS cc_start: 0.9261 (mptt) cc_final: 0.8988 (mptt) REVERT: n 123 GLN cc_start: 0.9214 (mt0) cc_final: 0.8959 (mt0) REVERT: n 131 SER cc_start: 0.7949 (m) cc_final: 0.7404 (p) REVERT: o 17 ASP cc_start: 0.8789 (p0) cc_final: 0.8264 (p0) REVERT: o 38 MET cc_start: 0.9023 (tpt) cc_final: 0.8724 (tpt) REVERT: o 43 GLN cc_start: 0.9274 (tp-100) cc_final: 0.8636 (tp-100) REVERT: o 47 ASP cc_start: 0.9255 (m-30) cc_final: 0.8741 (m-30) REVERT: o 117 LYS cc_start: 0.9491 (tppp) cc_final: 0.9089 (tptt) outliers start: 137 outliers final: 79 residues processed: 1085 average time/residue: 1.5509 time to fit residues: 2185.0875 Evaluate side-chains 1088 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 997 time to evaluate : 5.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 HIS Chi-restraints excluded: chain 6 residue 177 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 1 residue 273 SER Chi-restraints excluded: chain 1 residue 324 GLN Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 639 THR Chi-restraints excluded: chain 3 residue 693 GLU Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 272 LEU Chi-restraints excluded: chain 7 residue 31 ARG Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain q residue 3 LEU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain J residue 4 TYR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain N residue 90 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 225 MET Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain O residue 192 MET Chi-restraints excluded: chain O residue 268 GLU Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 68 GLU Chi-restraints excluded: chain X residue 73 ILE Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain e residue 75 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 120 GLU Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 126 HIS Chi-restraints excluded: chain j residue 7 ILE Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain p residue 16 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 473 optimal weight: 5.9990 chunk 762 optimal weight: 0.0570 chunk 465 optimal weight: 5.9990 chunk 361 optimal weight: 0.7980 chunk 530 optimal weight: 10.0000 chunk 799 optimal weight: 8.9990 chunk 736 optimal weight: 5.9990 chunk 637 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 492 optimal weight: 6.9990 chunk 390 optimal weight: 7.9990 overall best weight: 2.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN q 12 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN M 220 HIS Y 9 HIS c 33 GLN h 86 ASN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 49 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 13 GLN ** o 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 109 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.264 69825 Z= 0.530 Angle : 1.557 50.765 94410 Z= 1.007 Chirality : 0.308 6.463 10228 Planarity : 0.004 0.068 11768 Dihedral : 10.493 179.397 10579 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.26 % Favored : 96.73 % Rotamer: Outliers : 1.44 % Allowed : 16.84 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: 1.45 (0.10), residues: 8129 helix: 1.74 (0.08), residues: 4448 sheet: -0.04 (0.26), residues: 390 loop : 0.10 (0.11), residues: 3291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP j 59 HIS 0.006 0.001 HIS T 35 PHE 0.023 0.001 PHE N 292 TYR 0.026 0.001 TYR L 422 ARG 0.016 0.000 ARG m 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16258 Ramachandran restraints generated. 8129 Oldfield, 0 Emsley, 8129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1033 time to evaluate : 5.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 HIS cc_start: 0.9258 (OUTLIER) cc_final: 0.8371 (t-90) REVERT: 6 112 LYS cc_start: 0.9617 (tppp) cc_final: 0.9377 (tppp) REVERT: D 429 ASP cc_start: 0.9463 (m-30) cc_final: 0.9151 (m-30) REVERT: 1 431 GLN cc_start: 0.9453 (tm-30) cc_final: 0.9140 (tm-30) REVERT: 3 693 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8498 (pt0) REVERT: 9 7 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.9167 (tttp) REVERT: 9 8 LYS cc_start: 0.8159 (pptt) cc_final: 0.7870 (pptt) REVERT: P 170 ASP cc_start: 0.9355 (m-30) cc_final: 0.9031 (m-30) REVERT: 7 31 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8810 (mtt180) REVERT: S 78 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8805 (pp) REVERT: S 85 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8699 (pm20) REVERT: T 12 LYS cc_start: 0.9319 (ttpp) cc_final: 0.9083 (tmmm) REVERT: T 21 LEU cc_start: 0.9754 (mt) cc_final: 0.9480 (mp) REVERT: T 23 ASP cc_start: 0.9391 (p0) cc_final: 0.9087 (p0) REVERT: T 47 GLN cc_start: 0.9164 (tm-30) cc_final: 0.8698 (tm-30) REVERT: T 55 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8523 (mm-30) REVERT: V 32 ASP cc_start: 0.9208 (m-30) cc_final: 0.8866 (m-30) REVERT: s 28 ASP cc_start: 0.8084 (t0) cc_final: 0.7869 (t0) REVERT: A 68 GLU cc_start: 0.9427 (mt-10) cc_final: 0.9195 (mt-10) REVERT: J 85 ASN cc_start: 0.8955 (t0) cc_final: 0.8563 (t0) REVERT: K 36 MET cc_start: 0.9493 (mtm) cc_final: 0.9255 (mtp) REVERT: L 145 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8415 (mp0) REVERT: L 539 MET cc_start: 0.9439 (tmm) cc_final: 0.9051 (tmm) REVERT: L 559 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8943 (tp30) REVERT: M 46 ASP cc_start: 0.8731 (t70) cc_final: 0.8362 (t0) REVERT: M 85 LYS cc_start: 0.9349 (pttt) cc_final: 0.9142 (pttm) REVERT: M 87 ASP cc_start: 0.9135 (t0) cc_final: 0.8817 (t70) REVERT: M 114 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8203 (tm-30) REVERT: M 123 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8765 (mp0) REVERT: M 281 ASP cc_start: 0.8942 (t70) cc_final: 0.8287 (t70) REVERT: M 310 MET cc_start: 0.9454 (ttp) cc_final: 0.9025 (ttm) REVERT: N 321 LYS cc_start: 0.8840 (tptt) cc_final: 0.8366 (tppt) REVERT: O 192 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8472 (mpp) REVERT: O 268 GLU cc_start: 0.9534 (mt-10) cc_final: 0.9262 (mm-30) REVERT: U 65 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.7885 (tt) REVERT: U 68 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.8938 (pm20) REVERT: X 133 ASP cc_start: 0.9195 (p0) cc_final: 0.8932 (p0) REVERT: Y 81 GLU cc_start: 0.9147 (mp0) cc_final: 0.8857 (mp0) REVERT: Y 82 LYS cc_start: 0.9529 (mtpp) cc_final: 0.9179 (ptpp) REVERT: Y 85 ASP cc_start: 0.9073 (t0) cc_final: 0.8597 (t70) REVERT: Z 129 LYS cc_start: 0.9497 (mmpt) cc_final: 0.9040 (tptt) REVERT: a 49 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8946 (mm-30) REVERT: a 51 ASP cc_start: 0.9143 (m-30) cc_final: 0.8919 (m-30) REVERT: c 13 ASN cc_start: 0.9304 (t0) cc_final: 0.8676 (t0) REVERT: d 25 LYS cc_start: 0.8650 (tttp) cc_final: 0.8168 (tttm) REVERT: d 104 LYS cc_start: 0.8668 (tptp) cc_final: 0.8324 (tptp) REVERT: d 105 GLU cc_start: 0.8831 (tp30) cc_final: 0.8322 (pp20) REVERT: d 106 LYS cc_start: 0.9225 (mtpp) cc_final: 0.8661 (tptm) REVERT: g 97 TYR cc_start: 0.9259 (t80) cc_final: 0.8952 (t80) REVERT: g 101 ASN cc_start: 0.9553 (m110) cc_final: 0.9230 (m-40) REVERT: g 112 ASP cc_start: 0.9055 (t0) cc_final: 0.8802 (t0) REVERT: g 120 GLU cc_start: 0.8779 (tp30) cc_final: 0.8397 (tp30) REVERT: h 68 LYS cc_start: 0.8790 (tmtt) cc_final: 0.8571 (tptp) REVERT: h 86 ASN cc_start: 0.9027 (OUTLIER) cc_final: 0.8633 (t0) REVERT: h 112 ARG cc_start: 0.9135 (ttp80) cc_final: 0.8594 (ttm-80) REVERT: i 114 GLU cc_start: 0.8211 (pp20) cc_final: 0.7917 (pp20) REVERT: i 125 GLN cc_start: 0.7860 (tp-100) cc_final: 0.7445 (tp-100) REVERT: j 55 ASP cc_start: 0.9255 (t0) cc_final: 0.8895 (t0) REVERT: j 58 GLN cc_start: 0.9064 (mp-120) cc_final: 0.8747 (mm-40) REVERT: l 5 LYS cc_start: 0.9321 (mmtm) cc_final: 0.8978 (tppt) REVERT: l 136 ASN cc_start: 0.9378 (t0) cc_final: 0.9161 (t0) REVERT: l 150 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8608 (tm-30) REVERT: m 61 ASP cc_start: 0.9286 (t70) cc_final: 0.9061 (t0) REVERT: m 117 GLU cc_start: 0.9027 (pt0) cc_final: 0.8732 (pt0) REVERT: m 119 LYS cc_start: 0.9258 (mptt) cc_final: 0.8981 (mptt) REVERT: n 123 GLN cc_start: 0.9203 (mt0) cc_final: 0.8921 (mt0) REVERT: o 17 ASP cc_start: 0.8765 (p0) cc_final: 0.8299 (p0) REVERT: o 43 GLN cc_start: 0.9249 (tp-100) cc_final: 0.8650 (tp-100) REVERT: o 47 ASP cc_start: 0.9251 (m-30) cc_final: 0.8766 (m-30) REVERT: o 117 LYS cc_start: 0.9483 (tppp) cc_final: 0.9077 (tptt) outliers start: 104 outliers final: 70 residues processed: 1100 average time/residue: 1.5110 time to fit residues: 2172.5019 Evaluate side-chains 1087 residues out of total 7222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1007 time to evaluate : 5.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 HIS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 1 residue 273 SER Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 544 VAL Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 639 THR Chi-restraints excluded: chain 3 residue 693 GLU Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 112 ASP Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 272 LEU Chi-restraints excluded: chain 7 residue 31 ARG Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain q residue 3 LEU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain J residue 4 TYR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 351 VAL Chi-restraints excluded: chain N residue 90 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 225 MET Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain O residue 192 MET Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 68 GLU Chi-restraints excluded: chain X residue 73 ILE Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain h residue 86 ASN Chi-restraints excluded: chain h residue 127 THR Chi-restraints excluded: chain i residue 126 HIS Chi-restraints excluded: chain j residue 7 ILE Chi-restraints excluded: chain k residue 67 THR Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain p residue 16 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 506 optimal weight: 20.0000 chunk 678 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 587 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 177 optimal weight: 6.9990 chunk 638 optimal weight: 20.0000 chunk 267 optimal weight: 9.9990 chunk 655 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN q 12 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 9 HIS b 10 ASN b 82 ASN c 33 GLN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 49 GLN ** m 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 72 GLN ** o 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 109 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.055623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.045253 restraints weight = 182503.290| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 2.14 r_work: 0.2561 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.262 69825 Z= 0.541 Angle : 1.578 59.199 94410 Z= 1.020 Chirality : 0.308 6.467 10228 Planarity : 0.004 0.064 11768 Dihedral : 10.492 179.418 10579 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.25 % Favored : 96.74 % Rotamer: Outliers : 1.37 % Allowed : 16.95 % Favored : 81.68 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.26 % 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: 1.44 (0.10), residues: 8129 helix: 1.74 (0.08), residues: 4448 sheet: -0.04 (0.26), residues: 390 loop : 0.10 (0.11), residues: 3291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP j 59 HIS 0.005 0.001 HIS 9 67 PHE 0.023 0.001 PHE N 292 TYR 0.025 0.001 TYR L 422 ARG 0.013 0.000 ARG m 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28775.63 seconds wall clock time: 497 minutes 43.12 seconds (29863.12 seconds total)