Starting phenix.real_space_refine on Thu Feb 15 06:12:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca5_16518/02_2024/8ca5_16518_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca5_16518/02_2024/8ca5_16518.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca5_16518/02_2024/8ca5_16518_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca5_16518/02_2024/8ca5_16518_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca5_16518/02_2024/8ca5_16518_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca5_16518/02_2024/8ca5_16518.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca5_16518/02_2024/8ca5_16518.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca5_16518/02_2024/8ca5_16518_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca5_16518/02_2024/8ca5_16518_updated.pdb" } resolution = 3.9 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= 0.005 sd= 0.341 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: 6 Type Number sf(0) Gaussians Fe 28 7.16 5 P 30 5.49 5 S 481 5.16 5 C 41541 2.51 5 N 10598 2.21 5 O 11520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 68": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "F PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ASP 251": "OD1" <-> "OD2" Residue "N TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 55": "OE1" <-> "OE2" Residue "V ASP 17": "OD1" <-> "OD2" Residue "X ASP 36": "OD1" <-> "OD2" Residue "Z ASP 63": "OD1" <-> "OD2" Residue "Z GLU 65": "OE1" <-> "OE2" Residue "a GLU 35": "OE1" <-> "OE2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "g GLU 92": "OE1" <-> "OE2" Residue "j PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 62": "OE1" <-> "OE2" Residue "k PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 140": "OE1" <-> "OE2" Residue "m ASP 23": "OD1" <-> "OD2" Residue "n GLU 94": "OE1" <-> "OE2" Residue "p ASP 140": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 64198 Number of models: 1 Model: "" Number of chains: 62 Chain: "t" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 909 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain breaks: 1 Chain: "A" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 933 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} 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: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "C" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 15, 'TRANS': 191} Chain: "D" Number of atoms: 3463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3463 Classifications: {'peptide': 430} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 403} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1639 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 188} Chain: "F" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3300 Classifications: {'peptide': 428} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 406} Chain: "G" Number of atoms: 5248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5248 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 31, 'TRANS': 656} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 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: "I" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1431 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} Chain: "J" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1300 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 3, 'TRANS': 167} 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: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2696 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 323} 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: "P" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2626 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain: "S" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 594 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 77} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "T" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 611 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "U" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "W" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 935 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} 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: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 556 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "b" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 628 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} 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: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1162 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain: "i" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 778 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 12, 'TRANS': 80} Chain breaks: 1 Chain: "j" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 537 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 6, 'TRANS': 55} Chain: "k" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 609 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain: "l" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1294 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 18, 'TRANS': 135} 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: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1534 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "o" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 979 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 105} Chain: "p" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1424 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 10, 'TRANS': 157} Chain: "r" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 487 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 10, 'TRANS': 50} Chain breaks: 1 Chain: "s" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 269 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'3PE': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'UQ9:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "L" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 235 Unusual residues: {'3PE': 2, 'CDL': 1, 'LMT': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "M" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "O" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" 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: "d" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 130 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 70 Chain: "i" 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2597 SG CYS B 129 67.481 106.544 92.718 1.00 63.41 S ATOM 2100 SG CYS B 65 66.943 100.595 90.603 1.00 65.94 S ATOM 2094 SG CYS B 64 61.773 103.823 92.651 1.00 66.38 S ATOM 2827 SG CYS B 159 65.673 105.904 87.214 1.00 64.76 S ATOM 9075 SG CYS E 103 40.722 140.729 30.032 1.00102.67 S ATOM 9109 SG CYS E 108 37.842 141.156 27.956 1.00109.43 S ATOM 9393 SG CYS E 144 39.097 145.307 33.169 1.00107.28 S ATOM 9416 SG CYS E 148 36.609 145.741 31.510 1.00111.16 S ATOM 12617 SG CYS F 362 46.726 144.708 54.584 1.00 68.65 S ATOM 12637 SG CYS F 365 45.460 141.879 49.702 1.00 67.96 S ATOM 12959 SG CYS F 405 43.531 147.839 49.870 1.00 75.07 S ATOM 12598 SG CYS F 359 49.933 146.649 49.246 1.00 73.19 S ATOM 14037 SG CYS G 114 59.313 133.097 66.496 1.00 48.98 S ATOM 13976 SG CYS G 105 59.203 126.996 64.474 1.00 46.57 S ATOM 13997 SG CYS G 108 64.334 130.805 63.482 1.00 49.47 S ATOM 14369 SG CYS G 156 58.920 143.196 60.359 1.00 51.15 S ATOM 14346 SG CYS G 153 60.080 139.354 55.183 1.00 49.18 S ATOM 14393 SG CYS G 159 63.967 144.204 56.700 1.00 56.82 S ATOM 14722 SG CYS G 203 63.855 139.279 60.809 1.00 55.04 S ATOM 13483 SG CYS G 41 53.186 146.976 62.192 1.00 55.29 S ATOM 13569 SG CYS G 52 51.359 143.461 63.126 1.00 55.52 S ATOM 13594 SG CYS G 55 48.165 147.316 65.969 1.00 63.50 S ATOM 13695 SG CYS G 69 50.241 149.571 64.504 1.00 67.65 S ATOM 22021 SG CYS I 128 65.554 113.873 67.568 1.00 53.49 S ATOM 21691 SG CYS I 85 68.647 116.153 72.816 1.00 52.79 S ATOM 21649 SG CYS I 79 71.589 116.271 67.098 1.00 55.10 S ATOM 21668 SG CYS I 82 66.055 119.851 68.673 1.00 54.18 S ATOM 21971 SG CYS I 121 62.858 111.114 80.571 1.00 51.16 S ATOM 21945 SG CYS I 118 68.627 107.958 81.003 1.00 50.87 S ATOM 21992 SG CYS I 124 66.031 110.608 75.358 1.00 51.47 S ATOM 21719 SG CYS I 89 67.661 114.344 80.584 1.00 51.09 S Time building chain proxies: 24.67, per 1000 atoms: 0.38 Number of scatterers: 64198 At special positions: 0 Unit cell: (143.312, 197.392, 296.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 28 26.01 S 481 16.00 P 30 15.00 O 11520 8.00 N 10598 7.00 C 41541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS X 77 " - pdb=" SG CYS X 109 " distance=2.03 Simple disulfide: pdb=" SG CYS X 87 " - pdb=" SG CYS X 99 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 96 " - pdb=" SG CYS Y 116 " 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=2.04 Simple disulfide: pdb=" SG CYS o 58 " - pdb=" SG CYS o 89 " distance=2.03 Simple disulfide: pdb=" SG CYS p 76 " - pdb=" SG CYS p 83 " distance=2.03 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.04 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.87 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb=" SF4 B 201 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 159 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 64 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 65 " pdb="FE3 SF4 B 201 " - pdb=" NE2 HIS D 190 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 365 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 405 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 359 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 362 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb=" SF4 I 201 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 82 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 128 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 79 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 85 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 118 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 121 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 124 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 89 " pdb="FE3 SF4 I 202 " - pdb=" NE2 HIS I 67 " Number of angles added : 81 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14802 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 325 helices and 23 sheets defined 54.8% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.16 Creating SS restraints... Processing helix chain 't' and resid 59 through 61 No H-bonds generated for 'chain 't' and resid 59 through 61' Processing helix chain 't' and resid 69 through 75 removed outlier: 3.547A pdb=" N ALA t 73 " --> pdb=" O THR t 69 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP t 74 " --> pdb=" O GLU t 70 " (cutoff:3.500A) Processing helix chain 't' and resid 85 through 104 removed outlier: 4.254A pdb=" N LYS t 99 " --> pdb=" O ARG t 95 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE t 100 " --> pdb=" O GLU t 96 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS t 101 " --> pdb=" O GLU t 97 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER t 102 " --> pdb=" O ILE t 98 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN t 103 " --> pdb=" O LYS t 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 24 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: 5.543A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.446A 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 'B' and resid 36 through 53 Processing helix chain 'B' and resid 64 through 73 Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 104 through 116 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 128 through 131 No H-bonds generated for 'chain 'B' and resid 128 through 131' Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 163 through 178 Processing helix chain 'B' and resid 182 through 188 Processing helix chain 'C' and resid 17 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.517A pdb=" N VAL C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 4.583A 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 15 removed outlier: 3.684A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.632A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 Proline residue: D 101 - end of helix removed outlier: 3.848A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (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 removed outlier: 4.002A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.762A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.709A 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 257 through 263 removed outlier: 3.820A pdb=" N GLY D 262 " --> pdb=" O MET D 259 " (cutoff:3.500A) 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 276 through 280 removed outlier: 4.291A pdb=" N ASP D 279 " --> pdb=" O ASP D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 317 Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.541A pdb=" N HIS D 398 " --> pdb=" O PRO D 394 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA D 400 " --> pdb=" O PHE D 396 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 3.910A pdb=" N GLY D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 25 through 37 Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.634A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix Processing helix chain 'E' and resid 63 through 72 Processing helix chain 'E' and resid 77 through 86 Processing helix chain 'E' and resid 106 through 109 No H-bonds generated for 'chain 'E' and resid 106 through 109' Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 166 through 177 Processing helix chain 'F' and resid 33 through 39 Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 53 through 63 Processing helix chain 'F' and resid 75 through 82 removed outlier: 4.409A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 115 through 129 Processing helix chain 'F' and resid 143 through 159 Processing helix chain 'F' and resid 185 through 187 No H-bonds generated for 'chain 'F' and resid 185 through 187' Processing helix chain 'F' and resid 189 through 197 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 225 through 229 Processing helix chain 'F' and resid 231 through 237 Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 276 through 282 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 309 through 314 removed outlier: 4.201A pdb=" N THR F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.519A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 402 removed outlier: 4.379A pdb=" N GLY F 401 " --> pdb=" O GLN F 398 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS F 402 " --> pdb=" O ILE F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 435 Proline residue: F 414 - end of helix Proline residue: F 424 - end of helix Processing helix chain 'G' and resid 26 through 33 Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 123 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 196 through 202 Processing helix chain 'G' and resid 265 through 269 Processing helix chain 'G' and resid 271 through 274 Processing helix chain 'G' and resid 296 through 309 Processing helix chain 'G' and resid 312 through 314 No H-bonds generated for 'chain 'G' and resid 312 through 314' Processing helix chain 'G' and resid 325 through 337 Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 367 through 373 removed outlier: 3.816A pdb=" N GLU G 372 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU G 373 " --> pdb=" O ALA G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 400 Processing helix chain 'G' and resid 427 through 434 Processing helix chain 'G' and resid 438 through 445 Processing helix chain 'G' and resid 455 through 458 No H-bonds generated for 'chain 'G' and resid 455 through 458' Processing helix chain 'G' and resid 463 through 480 Processing helix chain 'G' and resid 499 through 505 Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 596 through 606 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 642 through 651 Processing helix chain 'G' and resid 668 through 671 No H-bonds generated for 'chain 'G' and resid 668 through 671' Processing helix chain 'G' and resid 676 through 680 Processing helix chain 'G' and resid 682 through 692 Processing helix chain 'H' and resid 3 through 31 Proline residue: H 12 - end of helix removed outlier: 3.778A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 4.137A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.769A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 4.587A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 170 removed outlier: 4.077A pdb=" N THR H 167 " --> pdb=" O GLN H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 192 Proline residue: H 180 - end of helix removed outlier: 3.653A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 213 No H-bonds generated for 'chain 'H' and resid 211 through 213' Processing helix chain 'H' and resid 218 through 241 removed outlier: 3.800A pdb=" N ILE H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 276 removed outlier: 3.522A pdb=" N LEU H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 311 removed outlier: 4.137A pdb=" N LEU H 294 " --> pdb=" O TRP H 290 " (cutoff:3.500A) Proline residue: H 295 - end of helix Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 16 through 28 Processing helix chain 'I' and resid 30 through 44 removed outlier: 3.573A pdb=" N PHE I 44 " --> pdb=" O LEU I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 54 No H-bonds generated for 'chain 'I' and resid 52 through 54' Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'I' and resid 123 through 127 Processing helix chain 'I' and resid 146 through 148 No H-bonds generated for 'chain 'I' and resid 146 through 148' Processing helix chain 'I' and resid 153 through 162 Processing helix chain 'I' and resid 164 through 174 Processing helix chain 'J' and resid 4 through 20 Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 50 through 73 Processing helix chain 'J' and resid 86 through 109 Processing helix chain 'J' and resid 137 through 145 removed outlier: 4.506A pdb=" N MET J 144 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TYR J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 170 removed outlier: 3.644A pdb=" N PHE J 164 " --> pdb=" O PHE J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 20 Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 54 through 85 Proline residue: K 58 - end of helix removed outlier: 3.641A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 3 through 23 removed outlier: 3.794A pdb=" N PHE L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.906A pdb=" N LEU L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 107 removed outlier: 3.553A pdb=" N SER L 91 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP L 106 " --> pdb=" O GLN L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 154 Processing helix chain 'L' and resid 162 through 193 removed outlier: 4.246A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 removed outlier: 4.391A pdb=" N PHE L 203 " --> pdb=" O GLN L 199 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 227 through 229 No H-bonds generated for 'chain 'L' and resid 227 through 229' Processing helix chain 'L' and resid 231 through 238 removed outlier: 4.387A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 4.923A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 262 removed outlier: 4.134A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 268 Processing helix chain 'L' and resid 271 through 292 Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.075A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) 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 380 Processing helix chain 'L' and resid 387 through 401 removed outlier: 4.224A pdb=" N SER L 391 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.609A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 Proline residue: L 453 - end of helix removed outlier: 5.575A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N PHE L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 509 removed outlier: 5.064A pdb=" N ALA L 490 " --> pdb=" O LEU L 486 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU L 491 " --> pdb=" O LYS L 487 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET L 509 " --> pdb=" O ASN L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 removed outlier: 3.932A pdb=" N PHE L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 4.807A pdb=" N HIS L 534 " --> pdb=" O SER L 531 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.574A pdb=" N LYS L 547 " --> pdb=" O LEU L 544 " (cutoff:3.500A) 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: 4.087A 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: 3.672A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix removed outlier: 3.649A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) 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 removed outlier: 4.606A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ILE M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix removed outlier: 3.500A pdb=" N TRP M 136 " --> pdb=" O ILE M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 171 removed outlier: 3.882A pdb=" N THR M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY M 156 " --> pdb=" O TYR M 152 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 190 through 206 removed outlier: 5.074A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.908A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 250 removed outlier: 4.643A pdb=" N LEU M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE M 248 " --> pdb=" O ILE M 244 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU M 250 " --> pdb=" O ILE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 255 No H-bonds generated for 'chain 'M' and resid 253 through 255' Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.817A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.911A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.675A pdb=" N ASN M 333 " --> pdb=" O LEU M 329 " (cutoff:3.500A) Processing helix chain 'M' and resid 342 through 344 No H-bonds generated for 'chain 'M' and resid 342 through 344' Processing helix chain 'M' and resid 348 through 350 No H-bonds generated for 'chain 'M' and resid 348 through 350' Processing helix chain 'M' and resid 353 through 367 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.678A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (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 Processing helix chain 'N' and resid 3 through 22 Proline residue: N 17 - end of helix Processing helix chain 'N' and resid 26 through 46 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 113 through 120 removed outlier: 4.247A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 148 removed outlier: 3.890A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.582A pdb=" N ILE N 141 " --> pdb=" O ALA N 137 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU N 142 " --> pdb=" O PRO N 138 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.733A pdb=" N LEU N 170 " --> pdb=" O ALA N 166 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 194 removed outlier: 3.778A pdb=" N ILE N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 Proline residue: N 214 - end of helix removed outlier: 4.088A pdb=" N ASN N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 236 removed outlier: 3.546A pdb=" N LEU N 232 " --> pdb=" O ASN N 228 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N TRP N 234 " --> pdb=" O ILE N 230 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 252 removed outlier: 3.836A pdb=" N THR N 242 " --> pdb=" O ALA N 239 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET N 247 " --> pdb=" O ILE N 244 " (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 removed outlier: 4.302A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN N 289 " --> pdb=" O MET N 285 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU N 290 " --> pdb=" O ALA N 286 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 Processing helix chain 'N' and resid 324 through 334 Processing helix chain 'N' and resid 337 through 343 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 10 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 removed outlier: 3.527A pdb=" N GLU O 41 " --> pdb=" O LYS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 62 Processing helix chain 'O' and resid 71 through 74 No H-bonds generated for 'chain 'O' and resid 71 through 74' Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 131 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 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 196 through 208 Processing helix chain 'O' and resid 210 through 217 removed outlier: 3.807A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET O 217 " --> pdb=" O LYS O 213 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 228 No H-bonds generated for 'chain 'O' and resid 225 through 228' Processing helix chain 'O' and resid 231 through 240 Processing helix chain 'O' and resid 247 through 250 Processing helix chain 'O' and resid 253 through 264 removed outlier: 4.382A pdb=" N TYR O 258 " --> pdb=" O TRP O 254 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 274 removed outlier: 5.222A pdb=" N TYR O 272 " --> pdb=" O GLU O 268 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N THR O 273 " --> pdb=" O VAL O 269 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR O 274 " --> pdb=" O LEU O 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 298 Processing helix chain 'O' and resid 306 through 308 No H-bonds generated for 'chain 'O' and resid 306 through 308' Processing helix chain 'O' and resid 317 through 319 No H-bonds generated for 'chain 'O' and resid 317 through 319' Processing helix chain 'P' and resid 29 through 41 removed outlier: 3.885A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 61 removed outlier: 4.509A pdb=" N HIS P 58 " --> pdb=" O TYR P 54 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU P 59 " --> pdb=" O ASP P 55 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG P 60 " --> pdb=" O ILE P 56 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU P 61 " --> pdb=" O MET P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 84 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: 4.413A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 4.762A 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 removed outlier: 3.773A pdb=" N LYS P 219 " --> pdb=" O VAL P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 248 Processing helix chain 'P' and resid 260 through 272 removed outlier: 3.795A pdb=" N TRP P 265 " --> pdb=" O PHE P 261 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 288 Processing helix chain 'P' and resid 300 through 303 No H-bonds generated for 'chain 'P' and resid 300 through 303' Processing helix chain 'P' and resid 310 through 321 removed outlier: 4.726A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL P 317 " --> pdb=" O LYS P 313 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 331 through 333 No H-bonds generated for 'chain 'P' and resid 331 through 333' Processing helix chain 'S' and resid 28 through 46 removed outlier: 3.589A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N TYR S 40 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL S 41 " --> pdb=" O GLN S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 94 Processing helix chain 'T' and resid 8 through 21 Processing helix chain 'T' and resid 36 through 39 No H-bonds generated for 'chain 'T' and resid 36 through 39' Processing helix chain 'T' and resid 44 through 58 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.683A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 81 Processing helix chain 'U' and resid 8 through 21 removed outlier: 3.857A pdb=" N LYS U 12 " --> pdb=" O LEU U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 58 Processing helix chain 'U' and resid 64 through 68 Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'V' and resid 19 through 36 removed outlier: 3.559A pdb=" N LYS V 35 " --> pdb=" O LEU V 31 " (cutoff:3.500A) removed outlier: 4.206A 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 52 Proline residue: W 46 - end of helix Processing helix chain 'W' and resid 58 through 72 removed outlier: 3.994A pdb=" N ASN W 72 " --> pdb=" O MET W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 97 Processing helix chain 'W' and resid 102 through 108 removed outlier: 3.965A pdb=" N PHE W 108 " --> pdb=" O HIS W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 125 Processing helix chain 'X' and resid 21 through 26 Processing helix chain 'X' and resid 28 through 33 Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 52 through 76 removed outlier: 4.078A pdb=" N LEU X 56 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS X 57 " --> pdb=" O ARG X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 90 removed outlier: 3.685A pdb=" N TYR X 90 " --> pdb=" O THR X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 112 Processing helix chain 'Y' and resid 4 through 11 Processing helix chain 'Y' and resid 19 through 43 Processing helix chain 'Y' and resid 50 through 81 Processing helix chain 'Y' and resid 88 through 106 Processing helix chain 'Y' and resid 109 through 132 Processing helix chain 'Z' and resid 32 through 96 Proline residue: Z 72 - end of helix Processing helix chain 'Z' and resid 120 through 123 No H-bonds generated for 'chain 'Z' and resid 120 through 123' Processing helix chain 'Z' and resid 129 through 137 Processing helix chain 'a' and resid 2 through 30 Proline residue: a 7 - end of helix removed outlier: 4.070A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'b' and resid 5 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: 4.446A pdb=" N SER b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET b 43 " --> pdb=" O LYS b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 81 No H-bonds generated for 'chain 'b' and resid 78 through 81' Processing helix chain 'c' and resid 14 through 45 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 96 Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 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 67 removed outlier: 3.818A pdb=" N LYS e 53 " --> pdb=" O THR e 49 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE e 57 " --> pdb=" O LYS e 53 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLU e 58 " --> pdb=" O GLU e 54 " (cutoff:3.500A) Processing helix chain 'e' and resid 70 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 32 removed outlier: 4.247A pdb=" N VAL f 15 " --> pdb=" O HIS f 12 " (cutoff:3.500A) Proline residue: f 16 - end of helix Processing helix chain 'g' and resid 49 through 63 Processing helix chain 'g' and resid 67 through 77 removed outlier: 3.685A pdb=" N THR g 72 " --> pdb=" O LEU g 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 101 removed outlier: 3.614A pdb=" N GLN g 84 " --> pdb=" O TYR g 81 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLU g 85 " --> pdb=" O ARG g 82 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TRP g 86 " --> pdb=" O MET g 83 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN g 101 " --> pdb=" O ARG g 98 " (cutoff:3.500A) Processing helix chain 'h' and resid 16 through 46 removed outlier: 3.881A pdb=" N THR h 32 " --> pdb=" O TYR h 28 " (cutoff:3.500A) Proline residue: h 35 - end of helix Processing helix chain 'h' and resid 70 through 79 Processing helix chain 'h' and resid 83 through 117 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 25 Processing helix chain 'i' and resid 67 through 74 Processing helix chain 'i' and resid 76 through 87 Processing helix chain 'j' and resid 19 through 48 removed outlier: 6.697A pdb=" N ASP j 45 " --> pdb=" O TRP j 41 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA j 46 " --> pdb=" O HIS j 42 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL j 47 " --> pdb=" O ASP j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' 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: 3.617A pdb=" N ARG k 44 " --> pdb=" O LYS k 40 " (cutoff:3.500A) Processing helix chain 'k' and resid 51 through 58 removed outlier: 4.518A pdb=" N TRP k 56 " --> pdb=" O ARG k 52 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ARG k 57 " --> pdb=" O ASN k 53 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR k 58 " --> pdb=" O GLU k 54 " (cutoff:3.500A) 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 73 Processing helix chain 'k' and resid 76 through 92 Processing helix chain 'l' and resid 5 through 7 No H-bonds generated for 'chain 'l' and resid 5 through 7' Processing helix chain 'l' and resid 16 through 26 Processing helix chain 'l' and resid 54 through 56 No H-bonds generated for 'chain 'l' and resid 54 through 56' Processing helix chain 'l' and resid 80 through 83 No H-bonds generated for 'chain 'l' and resid 80 through 83' Processing helix chain 'l' and resid 97 through 120 Processing helix chain 'l' and resid 133 through 137 Processing helix chain 'm' and resid 26 through 51 Processing helix chain 'm' and resid 62 through 72 Processing helix chain 'm' and resid 74 through 77 No H-bonds generated for 'chain 'm' and resid 74 through 77' Processing helix chain 'm' and resid 83 through 94 Processing helix chain 'm' and resid 96 through 117 Processing helix chain 'n' and resid 11 through 29 Processing helix chain 'n' and resid 33 through 49 Processing helix chain 'n' and resid 56 through 72 Processing helix chain 'n' and resid 92 through 96 removed outlier: 4.111A pdb=" N CYS n 95 " --> pdb=" O ARG n 92 " (cutoff:3.500A) Processing helix chain 'n' and resid 100 through 105 Processing helix chain 'n' and resid 108 through 142 removed outlier: 3.592A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR n 114 " --> pdb=" O GLU n 110 " (cutoff:3.500A) Proline residue: n 115 - end of helix removed outlier: 3.697A pdb=" N PHE n 118 " --> pdb=" O TYR n 114 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER n 119 " --> pdb=" O PRO n 115 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP n 133 " --> pdb=" O MET n 129 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 8 Processing helix chain 'o' and resid 42 through 47 Processing helix chain 'o' and resid 59 through 72 Processing helix chain 'o' and resid 80 through 111 Processing helix chain 'p' and resid 28 through 56 removed outlier: 4.746A 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 81 through 123 removed outlier: 3.532A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLN p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 141 Processing helix chain 'p' and resid 151 through 170 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 36 through 39 removed outlier: 3.617A pdb=" N ASP s 39 " --> pdb=" O GLN s 36 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 36 through 39' Processing helix chain 's' and resid 44 through 55 removed outlier: 4.120A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE s 55 " --> pdb=" O ASP s 51 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 't' and resid 49 through 53 removed outlier: 4.037A pdb=" N GLY t 24 " --> pdb=" O TYR t 32 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TYR t 34 " --> pdb=" O HIS t 22 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N HIS t 22 " --> pdb=" O TYR t 34 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 't' and resid 147 through 149 Processing sheet with id= C, first strand: chain 'B' and resid 95 through 99 removed outlier: 7.053A pdb=" N TYR B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL B 98 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 154 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 74 through 82 removed outlier: 6.655A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE C 90 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU C 48 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LYS C 108 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 50 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N TYR C 110 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N ILE C 52 " --> pdb=" O TYR C 110 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.642A pdb=" N ARG C 182 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 47 through 49 removed outlier: 6.603A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 361 through 369 Processing sheet with id= H, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.929A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N MET E 153 " --> pdb=" O CYS E 103 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 220 through 224 removed outlier: 7.046A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU F 93 " --> pdb=" O ARG F 132 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA F 134 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL F 95 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE F 136 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA F 97 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE F 138 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 266 through 271 removed outlier: 3.692A pdb=" N SER F 259 " --> pdb=" O VAL F 334 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 9 through 13 Processing sheet with id= L, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= M, first strand: chain 'G' and resid 223 through 228 removed outlier: 6.709A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL G 247 " --> pdb=" O ARG G 243 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 315 through 319 removed outlier: 6.346A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 405 through 409 Processing sheet with id= P, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= Q, first strand: chain 'I' and resid 67 through 69 Processing sheet with id= R, first strand: chain 'I' and resid 94 through 100 removed outlier: 6.518A pdb=" N GLU I 99 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N THR I 108 " --> pdb=" O GLU I 99 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.786A pdb=" N MET L 78 " --> pdb=" O THR L 65 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 219 through 224 removed outlier: 6.089A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 164 through 166 removed outlier: 6.646A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 191 through 193 Processing sheet with id= W, first strand: chain 'S' and resid 51 through 56 removed outlier: 3.787A pdb=" N GLN S 72 " --> pdb=" O TYR S 68 " (cutoff:3.500A) 2903 hydrogen bonds defined for protein. 7935 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: 20.45 Time building geometry restraints manager: 22.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 26618 1.41 - 1.63: 38293 1.63 - 1.86: 839 1.86 - 2.09: 0 2.09 - 2.32: 80 Bond restraints: 65830 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.390 1.659 -0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C5A FMN F 502 " pdb=" C9A FMN F 502 " ideal model delta sigma weight residual 1.390 1.580 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C5A FMN F 502 " pdb=" C6 FMN F 502 " ideal model delta sigma weight residual 1.390 1.574 -0.184 2.00e-02 2.50e+03 8.46e+01 bond pdb=" C2 FMN F 502 " pdb=" O2 FMN F 502 " ideal model delta sigma weight residual 1.230 1.401 -0.171 2.00e-02 2.50e+03 7.27e+01 bond pdb=" C6 GTP O 401 " pdb=" O6 GTP O 401 " ideal model delta sigma weight residual 1.230 1.398 -0.168 2.00e-02 2.50e+03 7.02e+01 ... (remaining 65825 not shown) Histogram of bond angle deviations from ideal: 73.14 - 87.53: 76 87.53 - 101.92: 276 101.92 - 116.31: 44013 116.31 - 130.70: 44480 130.70 - 145.09: 344 Bond angle restraints: 89189 Sorted by residual: angle pdb=" CA PRO o 31 " pdb=" N PRO o 31 " pdb=" CD PRO o 31 " ideal model delta sigma weight residual 112.00 94.61 17.39 1.40e+00 5.10e-01 1.54e+02 angle pdb=" N PRO o 31 " pdb=" CD PRO o 31 " pdb=" CG PRO o 31 " ideal model delta sigma weight residual 103.20 90.61 12.59 1.50e+00 4.44e-01 7.04e+01 angle pdb=" C11 CDL d 201 " pdb=" CA5 CDL d 201 " pdb=" OA6 CDL d 201 " ideal model delta sigma weight residual 111.33 122.42 -11.09 1.32e+00 5.72e-01 7.04e+01 angle pdb=" C6 FMN F 502 " pdb=" C5A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 120.00 145.09 -25.09 3.00e+00 1.11e-01 7.00e+01 angle pdb=" C51 CDL M 502 " pdb=" CB5 CDL M 502 " pdb=" OB6 CDL M 502 " ideal model delta sigma weight residual 111.33 121.32 -9.99 1.32e+00 5.72e-01 5.70e+01 ... (remaining 89184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 38417 35.72 - 71.43: 1300 71.43 - 107.15: 100 107.15 - 142.86: 15 142.86 - 178.58: 5 Dihedral angle restraints: 39837 sinusoidal: 16902 harmonic: 22935 Sorted by residual: dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 79.02 178.58 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP O 401 " pdb=" C1' GTP O 401 " pdb=" N9 GTP O 401 " pdb=" O4' GTP O 401 " ideal model delta sinusoidal sigma weight residual 104.59 -28.80 133.40 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" O2G GTP O 401 " pdb=" O3B GTP O 401 " pdb=" PG GTP O 401 " pdb=" PB GTP O 401 " ideal model delta sinusoidal sigma weight residual 177.30 -61.42 -121.28 1 2.00e+01 2.50e-03 3.65e+01 ... (remaining 39834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.279: 9746 4.279 - 8.557: 0 8.557 - 12.836: 0 12.836 - 17.114: 0 17.114 - 21.393: 24 Chirality restraints: 9770 Sorted by residual: chirality pdb="FE3 SF4 B 201 " pdb=" S1 SF4 B 201 " pdb=" S2 SF4 B 201 " pdb=" S4 SF4 B 201 " both_signs ideal model delta sigma weight residual False -10.55 10.84 -21.39 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE3 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.80 -21.35 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE4 SF4 G 802 " pdb=" S1 SF4 G 802 " pdb=" S2 SF4 G 802 " pdb=" S3 SF4 G 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.75 21.31 2.00e-01 2.50e+01 1.13e+04 ... (remaining 9767 not shown) Planarity restraints: 11156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE o 30 " -0.088 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO o 31 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO o 31 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO o 31 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C17 UQ9 H 401 " -0.046 2.00e-02 2.50e+03 3.74e-02 1.75e+01 pdb=" C18 UQ9 H 401 " 0.059 2.00e-02 2.50e+03 pdb=" C19 UQ9 H 401 " 0.009 2.00e-02 2.50e+03 pdb=" C20 UQ9 H 401 " 0.012 2.00e-02 2.50e+03 pdb=" C21 UQ9 H 401 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 41 " 0.022 2.00e-02 2.50e+03 2.62e-02 1.20e+01 pdb=" CG PHE K 41 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE K 41 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE K 41 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE K 41 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE K 41 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE K 41 " 0.004 2.00e-02 2.50e+03 ... (remaining 11153 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 569 2.55 - 3.14: 55992 3.14 - 3.73: 104727 3.73 - 4.31: 147009 4.31 - 4.90: 243637 Nonbonded interactions: 551934 Sorted by model distance: nonbonded pdb=" O GLY F 168 " pdb=" OG SER F 169 " model vdw 1.966 2.440 nonbonded pdb=" OE1 GLN B 172 " pdb=" OG SER I 142 " model vdw 1.976 2.440 nonbonded pdb=" OH TYR m 128 " pdb=" O LEU p 145 " model vdw 1.981 2.440 nonbonded pdb=" OG1 THR o 41 " pdb=" OE2 GLU o 44 " model vdw 1.986 2.440 nonbonded pdb=" OG1 THR t 69 " pdb=" OE2 GLU I 166 " model vdw 1.988 2.440 ... (remaining 551929 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 7 through 82 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 21.250 Check model and map are aligned: 0.700 Set scattering table: 0.450 Process input model: 138.380 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 0.269 65830 Z= 0.422 Angle : 0.818 25.094 89189 Z= 0.397 Chirality : 1.051 21.393 9770 Planarity : 0.005 0.120 11156 Dihedral : 17.461 178.576 25011 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.34 % Favored : 94.54 % Rotamer: Outliers : 0.29 % Allowed : 16.50 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.84 (0.10), residues: 7749 helix: 1.51 (0.08), residues: 4273 sheet: -0.62 (0.27), residues: 344 loop : -0.59 (0.11), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP L 484 HIS 0.012 0.001 HIS I 67 PHE 0.057 0.002 PHE K 41 TYR 0.045 0.002 TYR m 22 ARG 0.012 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1021 time to evaluate : 5.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 51 ILE cc_start: 0.8819 (mp) cc_final: 0.8520 (pt) REVERT: A 32 GLU cc_start: 0.7946 (mp0) cc_final: 0.7454 (mp0) REVERT: A 68 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7900 (tt0) REVERT: A 109 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8302 (mmtt) REVERT: E 111 ARG cc_start: 0.7248 (mmm160) cc_final: 0.6829 (mmm160) REVERT: E 153 MET cc_start: 0.7336 (ttp) cc_final: 0.6821 (tmm) REVERT: E 157 ASN cc_start: 0.7721 (m-40) cc_final: 0.7203 (t0) REVERT: F 42 TRP cc_start: 0.6374 (m100) cc_final: 0.5920 (m100) REVERT: F 60 MET cc_start: 0.7709 (mmp) cc_final: 0.7248 (mmt) REVERT: F 184 TYR cc_start: 0.8024 (t80) cc_final: 0.7518 (t80) REVERT: F 242 PHE cc_start: 0.7094 (t80) cc_final: 0.6795 (t80) REVERT: F 354 TYR cc_start: 0.9020 (m-80) cc_final: 0.8666 (m-10) REVERT: G 150 MET cc_start: 0.8899 (mmt) cc_final: 0.8651 (mmt) REVERT: G 237 ASN cc_start: 0.8583 (m-40) cc_final: 0.8132 (m110) REVERT: G 473 MET cc_start: 0.7240 (tmm) cc_final: 0.6902 (tmm) REVERT: H 51 ASP cc_start: 0.6923 (m-30) cc_final: 0.6699 (m-30) REVERT: I 112 ASP cc_start: 0.8135 (m-30) cc_final: 0.7415 (t0) REVERT: M 316 MET cc_start: 0.8005 (mtp) cc_final: 0.7776 (mtp) REVERT: M 396 MET cc_start: 0.8448 (mmm) cc_final: 0.8177 (mmm) REVERT: N 27 MET cc_start: 0.7973 (tpp) cc_final: 0.7733 (tpp) REVERT: O 295 SER cc_start: 0.8961 (m) cc_final: 0.8729 (p) REVERT: P 278 TRP cc_start: 0.7940 (m-10) cc_final: 0.6607 (m100) REVERT: T 55 GLU cc_start: 0.7598 (mt-10) cc_final: 0.6981 (mt-10) REVERT: W 22 ILE cc_start: 0.8496 (mt) cc_final: 0.8206 (mm) REVERT: W 103 THR cc_start: 0.8612 (p) cc_final: 0.8351 (t) REVERT: Y 91 TYR cc_start: 0.7820 (m-80) cc_final: 0.7519 (m-80) REVERT: Y 102 LEU cc_start: 0.9056 (tp) cc_final: 0.8855 (tt) REVERT: Z 132 MET cc_start: 0.8103 (tpp) cc_final: 0.7893 (tpp) REVERT: a 30 THR cc_start: 0.9368 (p) cc_final: 0.9059 (t) REVERT: d 49 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7792 (mmm-85) REVERT: d 86 LYS cc_start: 0.9200 (ttmm) cc_final: 0.8873 (ttpp) REVERT: f 30 ASP cc_start: 0.8065 (p0) cc_final: 0.7494 (p0) REVERT: h 108 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7288 (mm-40) REVERT: i 11 LEU cc_start: 0.9096 (mp) cc_final: 0.8825 (mm) REVERT: k 93 LEU cc_start: 0.8075 (mt) cc_final: 0.7017 (mt) REVERT: l 110 PHE cc_start: 0.8997 (t80) cc_final: 0.8701 (t80) REVERT: p 41 ASP cc_start: 0.8688 (t0) cc_final: 0.8485 (t0) REVERT: p 144 ASP cc_start: 0.7779 (t0) cc_final: 0.7377 (t0) REVERT: r 55 THR cc_start: 0.8086 (p) cc_final: 0.7882 (t) REVERT: r 90 GLU cc_start: 0.3201 (mm-30) cc_final: 0.2981 (mm-30) REVERT: r 109 GLN cc_start: 0.7380 (tt0) cc_final: 0.7171 (tt0) outliers start: 20 outliers final: 12 residues processed: 1033 average time/residue: 0.5937 time to fit residues: 1048.6845 Evaluate side-chains 872 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 860 time to evaluate : 5.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain Y residue 67 ILE Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain p residue 135 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 766 random chunks: chunk 646 optimal weight: 1.9990 chunk 580 optimal weight: 2.9990 chunk 322 optimal weight: 0.7980 chunk 198 optimal weight: 8.9990 chunk 391 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 600 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 365 optimal weight: 3.9990 chunk 446 optimal weight: 0.9980 chunk 695 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 22 HIS t 44 GLN B 131 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN D 201 GLN E 15 ASN E 55 GLN E 91 ASN E 99 HIS F 283 HIS F 398 GLN F 402 HIS G 179 ASN G 365 ASN G 629 ASN H 292 ASN I 92 GLN L 136 ASN ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 506 ASN M 144 ASN M 430 HIS N 112 HIS N 172 GLN N 273 ASN ** O 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 294 ASN P 93 ASN ** P 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 GLN S 79 ASN V 40 HIS V 82 GLN W 53 GLN W 60 GLN X 123 GLN e 44 HIS ** e 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 108 GLN l 54 GLN n 13 GLN p 58 ASN p 103 ASN p 123 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.264 65830 Z= 0.573 Angle : 1.615 51.017 89189 Z= 1.042 Chirality : 0.315 6.546 9770 Planarity : 0.005 0.061 11156 Dihedral : 12.099 177.257 9570 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 1.92 % Allowed : 16.07 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.05 (0.10), residues: 7749 helix: 1.61 (0.08), residues: 4271 sheet: -0.40 (0.27), residues: 361 loop : -0.40 (0.12), residues: 3117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 413 HIS 0.011 0.001 HIS I 67 PHE 0.040 0.001 PHE K 41 TYR 0.027 0.001 TYR I 120 ARG 0.008 0.000 ARG g 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1036 time to evaluate : 5.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 51 ILE cc_start: 0.8604 (mp) cc_final: 0.8301 (pt) REVERT: A 32 GLU cc_start: 0.7960 (mp0) cc_final: 0.7599 (mp0) REVERT: A 109 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8412 (mmtt) REVERT: C 177 ASP cc_start: 0.7606 (t0) cc_final: 0.7328 (t0) REVERT: D 410 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8696 (mtp) REVERT: E 23 PHE cc_start: 0.7937 (m-80) cc_final: 0.7679 (m-80) REVERT: E 74 GLN cc_start: 0.8116 (mp10) cc_final: 0.7882 (pm20) REVERT: E 111 ARG cc_start: 0.7253 (mmm160) cc_final: 0.6674 (mmm160) REVERT: E 153 MET cc_start: 0.7397 (ttp) cc_final: 0.6890 (tmm) REVERT: E 157 ASN cc_start: 0.7766 (m-40) cc_final: 0.7374 (m-40) REVERT: F 42 TRP cc_start: 0.6323 (m100) cc_final: 0.5938 (m100) REVERT: F 60 MET cc_start: 0.7438 (mmp) cc_final: 0.7208 (mmt) REVERT: F 110 ILE cc_start: 0.8530 (mt) cc_final: 0.8175 (mt) REVERT: F 111 MET cc_start: 0.7516 (mpp) cc_final: 0.7018 (mmm) REVERT: F 242 PHE cc_start: 0.6816 (t80) cc_final: 0.6594 (t80) REVERT: F 354 TYR cc_start: 0.9002 (m-80) cc_final: 0.8708 (m-10) REVERT: G 237 ASN cc_start: 0.8557 (m-40) cc_final: 0.8095 (m110) REVERT: G 432 ILE cc_start: 0.7296 (mt) cc_final: 0.7046 (mm) REVERT: G 450 MET cc_start: 0.7928 (ttp) cc_final: 0.7641 (ttp) REVERT: G 523 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.6667 (t80) REVERT: G 684 MET cc_start: 0.7901 (mmt) cc_final: 0.7125 (mmm) REVERT: H 140 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8349 (mt) REVERT: H 199 ASP cc_start: 0.7421 (p0) cc_final: 0.7215 (p0) REVERT: I 6 ASN cc_start: 0.7866 (t0) cc_final: 0.7277 (t0) REVERT: I 95 THR cc_start: 0.9255 (m) cc_final: 0.8896 (p) REVERT: I 111 TYR cc_start: 0.8570 (t80) cc_final: 0.8232 (t80) REVERT: I 112 ASP cc_start: 0.7876 (m-30) cc_final: 0.7164 (t0) REVERT: J 73 MET cc_start: 0.7555 (mtt) cc_final: 0.7324 (mtp) REVERT: L 180 ILE cc_start: 0.9359 (mm) cc_final: 0.9094 (tp) REVERT: L 186 MET cc_start: 0.8899 (mtp) cc_final: 0.8477 (mtt) REVERT: L 197 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7559 (mt-10) REVERT: L 338 MET cc_start: 0.8472 (ttp) cc_final: 0.8216 (ttm) REVERT: M 310 MET cc_start: 0.8262 (ttt) cc_final: 0.7965 (ttt) REVERT: M 396 MET cc_start: 0.8527 (mmm) cc_final: 0.7941 (mmm) REVERT: N 181 TYR cc_start: 0.8835 (m-10) cc_final: 0.8574 (m-10) REVERT: O 295 SER cc_start: 0.8859 (m) cc_final: 0.8582 (p) REVERT: P 41 MET cc_start: 0.7586 (tmm) cc_final: 0.7274 (ppp) REVERT: P 278 TRP cc_start: 0.7999 (m-10) cc_final: 0.6589 (m100) REVERT: U 57 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7784 (tm-30) REVERT: U 75 GLU cc_start: 0.7258 (tp30) cc_final: 0.6777 (tp30) REVERT: W 103 THR cc_start: 0.8502 (p) cc_final: 0.8173 (t) REVERT: Y 4 LYS cc_start: 0.7786 (pptt) cc_final: 0.7395 (tmmt) REVERT: Y 70 MET cc_start: 0.7373 (mtp) cc_final: 0.7140 (mtp) REVERT: Z 97 MET cc_start: 0.8744 (mmt) cc_final: 0.8303 (mmt) REVERT: a 4 GLU cc_start: 0.8396 (mp0) cc_final: 0.8168 (mp0) REVERT: b 15 GLU cc_start: 0.8486 (mp0) cc_final: 0.8270 (mp0) REVERT: c 30 TYR cc_start: 0.8061 (t80) cc_final: 0.7817 (t80) REVERT: d 49 ARG cc_start: 0.7941 (mmm-85) cc_final: 0.7620 (mmm-85) REVERT: e 67 LEU cc_start: 0.8610 (mt) cc_final: 0.8239 (mp) REVERT: f 30 ASP cc_start: 0.8078 (p0) cc_final: 0.7543 (p0) REVERT: g 116 ILE cc_start: 0.7708 (pt) cc_final: 0.7483 (pt) REVERT: h 108 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7694 (mm-40) REVERT: l 67 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6813 (mt-10) REVERT: l 110 PHE cc_start: 0.9022 (t80) cc_final: 0.8744 (t80) REVERT: m 128 TYR cc_start: 0.7314 (p90) cc_final: 0.6728 (p90) REVERT: o 69 LYS cc_start: 0.8952 (tppt) cc_final: 0.8653 (tppt) REVERT: r 55 THR cc_start: 0.8291 (p) cc_final: 0.8028 (p) outliers start: 132 outliers final: 74 residues processed: 1114 average time/residue: 0.5805 time to fit residues: 1114.5812 Evaluate side-chains 968 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 890 time to evaluate : 5.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 96 GLU Chi-restraints excluded: chain t residue 157 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 523 PHE Chi-restraints excluded: chain G residue 687 CYS Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 402 CYS Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 269 MET Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 225 MET Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 72 CYS Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 87 TYR Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 101 GLN Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain g residue 121 ASP Chi-restraints excluded: chain h residue 108 GLN Chi-restraints excluded: chain h residue 130 LYS Chi-restraints excluded: chain h residue 142 ASP Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain j residue 26 GLU Chi-restraints excluded: chain l residue 104 LEU Chi-restraints excluded: chain n residue 102 CYS Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 32 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain r residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 766 random chunks: chunk 386 optimal weight: 5.9990 chunk 215 optimal weight: 0.0770 chunk 578 optimal weight: 2.9990 chunk 473 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 696 optimal weight: 2.9990 chunk 752 optimal weight: 10.0000 chunk 620 optimal weight: 5.9990 chunk 691 optimal weight: 6.9990 chunk 237 optimal weight: 8.9990 chunk 559 optimal weight: 4.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 505 ASN M 92 GLN ** P 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN ** e 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 9 HIS f 12 HIS f 50 ASN ** h 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 103 ASN s 37 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.267 65830 Z= 0.574 Angle : 1.604 50.898 89189 Z= 1.037 Chirality : 0.316 6.531 9770 Planarity : 0.005 0.068 11156 Dihedral : 11.404 177.522 9556 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 2.73 % Allowed : 16.44 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.05 (0.10), residues: 7749 helix: 1.57 (0.08), residues: 4280 sheet: -0.34 (0.27), residues: 362 loop : -0.35 (0.12), residues: 3107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 25 HIS 0.011 0.001 HIS I 67 PHE 0.024 0.001 PHE K 41 TYR 0.025 0.001 TYR E 81 ARG 0.006 0.000 ARG t 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 936 time to evaluate : 5.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 51 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8307 (pt) REVERT: t 103 GLN cc_start: 0.7600 (tm-30) cc_final: 0.7230 (tm-30) REVERT: t 104 ASP cc_start: 0.7900 (m-30) cc_final: 0.7446 (t70) REVERT: A 87 MET cc_start: 0.9072 (tmm) cc_final: 0.8711 (tmm) REVERT: A 109 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8427 (mmtt) REVERT: B 60 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7569 (t80) REVERT: B 182 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7881 (ttmm) REVERT: C 177 ASP cc_start: 0.7657 (t0) cc_final: 0.7238 (t0) REVERT: D 48 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8042 (p) REVERT: E 23 PHE cc_start: 0.7937 (m-80) cc_final: 0.7673 (m-80) REVERT: E 111 ARG cc_start: 0.7483 (mmm160) cc_final: 0.6847 (mmm160) REVERT: E 127 LYS cc_start: 0.8257 (tttm) cc_final: 0.8030 (mmmt) REVERT: E 153 MET cc_start: 0.7357 (ttp) cc_final: 0.7105 (tmm) REVERT: F 110 ILE cc_start: 0.8469 (mt) cc_final: 0.8143 (mt) REVERT: F 111 MET cc_start: 0.7450 (mpp) cc_final: 0.6936 (mmm) REVERT: F 149 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8829 (tp) REVERT: F 242 PHE cc_start: 0.6951 (t80) cc_final: 0.6630 (t80) REVERT: F 257 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8146 (m110) REVERT: F 354 TYR cc_start: 0.8944 (m-80) cc_final: 0.8530 (m-10) REVERT: G 237 ASN cc_start: 0.8543 (m-40) cc_final: 0.8217 (m110) REVERT: G 378 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7948 (mt) REVERT: G 523 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.6515 (t80) REVERT: G 684 MET cc_start: 0.8195 (mmt) cc_final: 0.7716 (mmm) REVERT: H 199 ASP cc_start: 0.7563 (p0) cc_final: 0.7180 (p0) REVERT: I 6 ASN cc_start: 0.7817 (t0) cc_final: 0.7425 (t0) REVERT: I 95 THR cc_start: 0.9262 (m) cc_final: 0.8951 (p) REVERT: I 111 TYR cc_start: 0.8639 (t80) cc_final: 0.8395 (t80) REVERT: I 112 ASP cc_start: 0.7874 (m-30) cc_final: 0.7262 (t0) REVERT: J 73 MET cc_start: 0.7351 (mtt) cc_final: 0.7143 (mtp) REVERT: J 99 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8142 (tm-30) REVERT: J 118 ASP cc_start: 0.6022 (OUTLIER) cc_final: 0.5796 (p0) REVERT: K 69 CYS cc_start: 0.8457 (t) cc_final: 0.8135 (t) REVERT: L 186 MET cc_start: 0.8901 (mtp) cc_final: 0.8505 (mtt) REVERT: L 197 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7557 (mt-10) REVERT: L 338 MET cc_start: 0.8677 (ttp) cc_final: 0.8410 (ttm) REVERT: M 46 ASP cc_start: 0.7403 (t0) cc_final: 0.6662 (t0) REVERT: M 47 GLU cc_start: 0.7775 (tt0) cc_final: 0.7520 (tt0) REVERT: M 222 GLU cc_start: 0.7535 (mp0) cc_final: 0.6882 (mp0) REVERT: M 310 MET cc_start: 0.8163 (ttt) cc_final: 0.7933 (ttp) REVERT: M 316 MET cc_start: 0.8116 (mtp) cc_final: 0.7852 (mtp) REVERT: M 396 MET cc_start: 0.8523 (mmm) cc_final: 0.7972 (mmm) REVERT: N 164 MET cc_start: 0.8644 (mmm) cc_final: 0.8243 (mtp) REVERT: N 191 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8967 (tp) REVERT: O 295 SER cc_start: 0.8914 (m) cc_final: 0.8641 (p) REVERT: P 278 TRP cc_start: 0.8019 (m-10) cc_final: 0.6576 (m100) REVERT: P 286 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7905 (mtm180) REVERT: T 22 TYR cc_start: 0.6629 (t80) cc_final: 0.6301 (t80) REVERT: T 24 LYS cc_start: 0.5114 (mtmt) cc_final: 0.4843 (mtmt) REVERT: T 37 MET cc_start: 0.4867 (mmt) cc_final: 0.4642 (mmm) REVERT: T 55 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6594 (mt-10) REVERT: U 57 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7699 (tm-30) REVERT: W 90 MET cc_start: 0.8088 (mtt) cc_final: 0.7867 (mtt) REVERT: W 103 THR cc_start: 0.8521 (p) cc_final: 0.8162 (t) REVERT: X 154 GLU cc_start: 0.7302 (tp30) cc_final: 0.6705 (tp30) REVERT: Y 4 LYS cc_start: 0.7762 (pptt) cc_final: 0.7394 (tmmt) REVERT: Z 97 MET cc_start: 0.8735 (mmt) cc_final: 0.8388 (mmt) REVERT: Z 99 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6797 (t70) REVERT: a 4 GLU cc_start: 0.8415 (mp0) cc_final: 0.8191 (mp0) REVERT: b 15 GLU cc_start: 0.8497 (mp0) cc_final: 0.8232 (mp0) REVERT: c 30 TYR cc_start: 0.7931 (t80) cc_final: 0.7620 (t80) REVERT: d 49 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7468 (mmm-85) REVERT: e 75 MET cc_start: 0.8736 (tpp) cc_final: 0.8472 (tpp) REVERT: g 116 ILE cc_start: 0.7356 (pt) cc_final: 0.7150 (pt) REVERT: h 108 GLN cc_start: 0.8447 (mm-40) cc_final: 0.7866 (mm-40) REVERT: i 69 PHE cc_start: 0.5871 (m-80) cc_final: 0.5431 (t80) REVERT: k 25 ARG cc_start: 0.8114 (mpt180) cc_final: 0.7789 (mmt90) REVERT: l 67 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7057 (mt-10) REVERT: l 105 PHE cc_start: 0.7855 (m-80) cc_final: 0.7535 (t80) REVERT: l 110 PHE cc_start: 0.9010 (t80) cc_final: 0.8594 (t80) REVERT: n 57 MET cc_start: 0.7942 (tpp) cc_final: 0.7527 (tmm) REVERT: n 117 TYR cc_start: 0.8542 (t80) cc_final: 0.8272 (t80) REVERT: o 69 LYS cc_start: 0.8967 (tppt) cc_final: 0.8708 (tppt) REVERT: o 90 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8377 (mm-30) REVERT: r 55 THR cc_start: 0.8193 (p) cc_final: 0.7939 (p) outliers start: 187 outliers final: 112 residues processed: 1061 average time/residue: 0.5815 time to fit residues: 1068.2992 Evaluate side-chains 990 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 867 time to evaluate : 5.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 51 ILE Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 523 PHE Chi-restraints excluded: chain G residue 531 CYS Chi-restraints excluded: chain G residue 585 VAL Chi-restraints excluded: chain G residue 687 CYS Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 118 ASP Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 431 THR Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 225 MET Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 87 TYR Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain Y residue 43 SER Chi-restraints excluded: chain Y residue 48 ASP Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain b residue 61 ASN Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 121 ASP Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 130 LYS Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain h residue 142 ASP Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 26 GLU Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 104 LEU Chi-restraints excluded: chain n residue 102 CYS Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 32 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 72 ASP Chi-restraints excluded: chain p residue 135 THR Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain s residue 39 ASP Chi-restraints excluded: chain s residue 50 LEU Chi-restraints excluded: chain s residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 766 random chunks: chunk 688 optimal weight: 9.9990 chunk 523 optimal weight: 10.0000 chunk 361 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 332 optimal weight: 6.9990 chunk 467 optimal weight: 10.0000 chunk 699 optimal weight: 4.9990 chunk 740 optimal weight: 20.0000 chunk 365 optimal weight: 6.9990 chunk 662 optimal weight: 0.7980 chunk 199 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 GLN H 284 GLN L 67 HIS ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 ASN L 295 GLN ** P 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN b 10 ASN e 76 HIS ** e 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 9 HIS ** h 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 21 GLN p 103 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.262 65830 Z= 0.615 Angle : 1.624 51.033 89189 Z= 1.044 Chirality : 0.316 6.558 9770 Planarity : 0.005 0.067 11156 Dihedral : 11.245 179.290 9556 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.12 % Favored : 95.84 % Rotamer: Outliers : 3.51 % Allowed : 16.64 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.92 (0.10), residues: 7749 helix: 1.45 (0.08), residues: 4268 sheet: -0.41 (0.27), residues: 368 loop : -0.37 (0.12), residues: 3113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP M 43 HIS 0.010 0.001 HIS I 67 PHE 0.024 0.002 PHE M 151 TYR 0.025 0.002 TYR E 81 ARG 0.006 0.001 ARG t 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 895 time to evaluate : 5.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 51 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8301 (pt) REVERT: t 90 LYS cc_start: 0.7820 (tptt) cc_final: 0.7384 (tptp) REVERT: A 4 TYR cc_start: 0.8884 (m-80) cc_final: 0.8650 (m-10) REVERT: A 109 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8326 (mmtt) REVERT: B 60 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7623 (t80) REVERT: C 177 ASP cc_start: 0.7812 (t0) cc_final: 0.7472 (t0) REVERT: D 48 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8054 (p) REVERT: E 127 LYS cc_start: 0.8294 (tttm) cc_final: 0.8037 (mmmt) REVERT: E 153 MET cc_start: 0.7590 (ttp) cc_final: 0.7227 (tmm) REVERT: E 176 LEU cc_start: 0.7251 (mt) cc_final: 0.6975 (mt) REVERT: F 42 TRP cc_start: 0.6369 (m100) cc_final: 0.5479 (m100) REVERT: F 110 ILE cc_start: 0.8507 (mt) cc_final: 0.8144 (mt) REVERT: F 111 MET cc_start: 0.7521 (mpp) cc_final: 0.7168 (mmm) REVERT: F 149 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8884 (tp) REVERT: F 242 PHE cc_start: 0.7066 (t80) cc_final: 0.6612 (t80) REVERT: F 354 TYR cc_start: 0.8911 (m-80) cc_final: 0.8426 (m-10) REVERT: G 9 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7535 (tt) REVERT: G 378 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7977 (mt) REVERT: G 523 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.6513 (t80) REVERT: G 684 MET cc_start: 0.8318 (mmm) cc_final: 0.7910 (mmm) REVERT: H 181 MET cc_start: 0.8456 (mmm) cc_final: 0.8118 (mmm) REVERT: H 199 ASP cc_start: 0.7593 (p0) cc_final: 0.7164 (p0) REVERT: I 6 ASN cc_start: 0.7981 (t0) cc_final: 0.7600 (t0) REVERT: I 95 THR cc_start: 0.9262 (m) cc_final: 0.8983 (p) REVERT: I 112 ASP cc_start: 0.7904 (m-30) cc_final: 0.7396 (t0) REVERT: J 73 MET cc_start: 0.7343 (mtt) cc_final: 0.7110 (mtp) REVERT: J 127 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: K 69 CYS cc_start: 0.8579 (t) cc_final: 0.8182 (t) REVERT: L 338 MET cc_start: 0.8869 (ttp) cc_final: 0.8548 (ttp) REVERT: M 98 MET cc_start: 0.8780 (mmp) cc_final: 0.8526 (mmt) REVERT: M 222 GLU cc_start: 0.7666 (mp0) cc_final: 0.7002 (mp0) REVERT: M 316 MET cc_start: 0.8167 (mtp) cc_final: 0.7919 (mtm) REVERT: M 396 MET cc_start: 0.8503 (mmm) cc_final: 0.7967 (mmm) REVERT: M 459 MET cc_start: 0.8409 (ptm) cc_final: 0.8029 (ttp) REVERT: N 10 TYR cc_start: 0.8767 (m-80) cc_final: 0.8539 (m-80) REVERT: N 54 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7313 (tp30) REVERT: N 164 MET cc_start: 0.8745 (mmm) cc_final: 0.8264 (mtp) REVERT: N 181 TYR cc_start: 0.8979 (m-10) cc_final: 0.8583 (m-10) REVERT: O 41 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: O 295 SER cc_start: 0.8976 (m) cc_final: 0.8706 (p) REVERT: P 170 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7418 (t0) REVERT: T 8 LEU cc_start: 0.6593 (tt) cc_final: 0.5970 (mm) REVERT: T 22 TYR cc_start: 0.6560 (t80) cc_final: 0.5890 (t80) REVERT: T 24 LYS cc_start: 0.5322 (mtmt) cc_final: 0.4670 (mtmt) REVERT: U 57 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7594 (tm-30) REVERT: U 71 MET cc_start: 0.8133 (mmp) cc_final: 0.7549 (mmp) REVERT: W 90 MET cc_start: 0.8377 (mtt) cc_final: 0.7823 (mtm) REVERT: W 103 THR cc_start: 0.8547 (p) cc_final: 0.8214 (t) REVERT: X 154 GLU cc_start: 0.7336 (tp30) cc_final: 0.6709 (tp30) REVERT: Y 4 LYS cc_start: 0.7822 (pptt) cc_final: 0.7424 (tmmt) REVERT: Y 70 MET cc_start: 0.7717 (ttm) cc_final: 0.6872 (tpt) REVERT: Z 97 MET cc_start: 0.8746 (mmt) cc_final: 0.8422 (mmt) REVERT: a 4 GLU cc_start: 0.8467 (mp0) cc_final: 0.8182 (mp0) REVERT: c 30 TYR cc_start: 0.7986 (t80) cc_final: 0.7734 (t80) REVERT: e 75 MET cc_start: 0.8767 (tpp) cc_final: 0.8511 (tpp) REVERT: g 116 ILE cc_start: 0.7449 (pt) cc_final: 0.7229 (pt) REVERT: h 108 GLN cc_start: 0.8482 (mm-40) cc_final: 0.7995 (mm-40) REVERT: i 69 PHE cc_start: 0.6197 (m-80) cc_final: 0.5497 (t80) REVERT: k 25 ARG cc_start: 0.8029 (mpt180) cc_final: 0.7637 (mmt90) REVERT: l 67 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7083 (mt-10) REVERT: l 110 PHE cc_start: 0.8923 (t80) cc_final: 0.8404 (t80) REVERT: l 114 MET cc_start: 0.7859 (mmm) cc_final: 0.7269 (mmm) REVERT: n 117 TYR cc_start: 0.8568 (t80) cc_final: 0.8337 (t80) REVERT: o 46 MET cc_start: 0.8540 (ttp) cc_final: 0.8308 (ttm) REVERT: o 69 LYS cc_start: 0.9000 (tppt) cc_final: 0.8742 (tppt) REVERT: p 92 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7718 (ttm110) REVERT: r 52 TYR cc_start: 0.7364 (m-80) cc_final: 0.6944 (m-10) REVERT: r 55 THR cc_start: 0.8149 (p) cc_final: 0.7902 (p) outliers start: 241 outliers final: 163 residues processed: 1066 average time/residue: 0.5930 time to fit residues: 1102.2399 Evaluate side-chains 1017 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 842 time to evaluate : 5.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 51 ILE Chi-restraints excluded: chain t residue 66 ASP Chi-restraints excluded: chain t residue 67 ILE Chi-restraints excluded: chain t residue 96 GLU Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 523 PHE Chi-restraints excluded: chain G residue 531 CYS Chi-restraints excluded: chain G residue 585 VAL Chi-restraints excluded: chain G residue 687 CYS Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 269 THR Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 127 GLU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 431 THR Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 578 THR Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 269 MET Chi-restraints excluded: chain M residue 414 THR Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 225 MET Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 334 THR Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 170 ASP Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain P residue 284 VAL Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 101 GLN Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 43 SER Chi-restraints excluded: chain Y residue 48 ASP Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain b residue 61 ASN Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain g residue 38 LYS Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 121 ASP Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 86 ASN Chi-restraints excluded: chain h residue 130 LYS Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain h residue 142 ASP Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 112 THR Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 26 GLU Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 104 LEU Chi-restraints excluded: chain n residue 8 TYR Chi-restraints excluded: chain n residue 102 CYS Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 32 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 72 ASP Chi-restraints excluded: chain p residue 92 ARG Chi-restraints excluded: chain p residue 135 THR Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain s residue 39 ASP Chi-restraints excluded: chain s residue 49 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 766 random chunks: chunk 616 optimal weight: 0.4980 chunk 420 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 551 optimal weight: 7.9990 chunk 305 optimal weight: 6.9990 chunk 631 optimal weight: 5.9990 chunk 511 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 378 optimal weight: 4.9990 chunk 664 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS E 67 ASN E 99 HIS F 431 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN L 361 ASN P 103 ASN ** P 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN ** e 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 103 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.263 65830 Z= 0.585 Angle : 1.605 50.956 89189 Z= 1.037 Chirality : 0.315 6.520 9770 Planarity : 0.005 0.066 11156 Dihedral : 10.963 173.858 9556 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 3.40 % Allowed : 17.71 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.96 (0.10), residues: 7749 helix: 1.48 (0.08), residues: 4256 sheet: -0.29 (0.27), residues: 373 loop : -0.36 (0.12), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 25 HIS 0.009 0.001 HIS I 67 PHE 0.025 0.001 PHE N 292 TYR 0.022 0.001 TYR h 16 ARG 0.006 0.000 ARG t 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 925 time to evaluate : 5.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 51 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8300 (pt) REVERT: t 90 LYS cc_start: 0.7787 (tptt) cc_final: 0.7383 (tptp) REVERT: A 4 TYR cc_start: 0.8847 (m-80) cc_final: 0.8614 (m-10) REVERT: A 99 SER cc_start: 0.9431 (m) cc_final: 0.8978 (t) REVERT: A 109 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8242 (mmtt) REVERT: B 60 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7586 (t80) REVERT: C 177 ASP cc_start: 0.7875 (t0) cc_final: 0.7501 (t0) REVERT: D 48 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8047 (p) REVERT: D 80 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8629 (pp) REVERT: D 112 MET cc_start: 0.7812 (mmm) cc_final: 0.7472 (mmm) REVERT: E 127 LYS cc_start: 0.8272 (tttm) cc_final: 0.8041 (mmmt) REVERT: E 153 MET cc_start: 0.7733 (ttp) cc_final: 0.7374 (tmm) REVERT: E 176 LEU cc_start: 0.7418 (mt) cc_final: 0.7084 (mt) REVERT: F 110 ILE cc_start: 0.8397 (mt) cc_final: 0.8014 (mt) REVERT: F 111 MET cc_start: 0.7471 (mpp) cc_final: 0.7097 (mmm) REVERT: F 242 PHE cc_start: 0.7099 (t80) cc_final: 0.6676 (t80) REVERT: F 317 MET cc_start: 0.7506 (mmm) cc_final: 0.7151 (mpp) REVERT: G 9 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7552 (tt) REVERT: G 378 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7963 (mt) REVERT: G 437 HIS cc_start: 0.6127 (OUTLIER) cc_final: 0.5523 (t-90) REVERT: G 523 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.6522 (t80) REVERT: G 684 MET cc_start: 0.8032 (mmm) cc_final: 0.7693 (mmm) REVERT: H 181 MET cc_start: 0.8469 (mmm) cc_final: 0.8098 (mmm) REVERT: H 199 ASP cc_start: 0.7622 (p0) cc_final: 0.7205 (p0) REVERT: I 6 ASN cc_start: 0.7934 (t0) cc_final: 0.7569 (t0) REVERT: I 95 THR cc_start: 0.9265 (m) cc_final: 0.9008 (p) REVERT: I 112 ASP cc_start: 0.7883 (m-30) cc_final: 0.7215 (t0) REVERT: I 174 ASP cc_start: 0.8208 (m-30) cc_final: 0.7501 (t0) REVERT: J 73 MET cc_start: 0.7153 (mtt) cc_final: 0.6950 (mtp) REVERT: J 80 GLU cc_start: 0.7186 (pm20) cc_final: 0.6900 (pm20) REVERT: J 99 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8218 (tm-30) REVERT: J 127 GLU cc_start: 0.7578 (tt0) cc_final: 0.7269 (tm-30) REVERT: K 69 CYS cc_start: 0.8539 (t) cc_final: 0.8106 (t) REVERT: L 338 MET cc_start: 0.8950 (ttp) cc_final: 0.8621 (ttp) REVERT: M 98 MET cc_start: 0.8736 (mmp) cc_final: 0.8506 (mmt) REVERT: M 222 GLU cc_start: 0.7651 (mp0) cc_final: 0.6909 (mp0) REVERT: M 316 MET cc_start: 0.8249 (mtp) cc_final: 0.7955 (mtm) REVERT: M 396 MET cc_start: 0.8482 (mmm) cc_final: 0.7936 (mmm) REVERT: N 10 TYR cc_start: 0.8554 (m-80) cc_final: 0.8194 (m-80) REVERT: N 54 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7265 (tp30) REVERT: N 164 MET cc_start: 0.8824 (mmm) cc_final: 0.8239 (mtp) REVERT: N 181 TYR cc_start: 0.8989 (m-10) cc_final: 0.8671 (m-10) REVERT: N 191 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8969 (tp) REVERT: N 229 SER cc_start: 0.9129 (OUTLIER) cc_final: 0.8726 (p) REVERT: O 41 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7705 (tp30) REVERT: O 216 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: O 295 SER cc_start: 0.8961 (m) cc_final: 0.8691 (p) REVERT: P 170 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7448 (t0) REVERT: P 286 ARG cc_start: 0.8249 (mtm110) cc_final: 0.8023 (mtp85) REVERT: T 8 LEU cc_start: 0.6464 (tt) cc_final: 0.5907 (mm) REVERT: T 22 TYR cc_start: 0.6617 (t80) cc_final: 0.5932 (t80) REVERT: T 24 LYS cc_start: 0.5595 (mtmt) cc_final: 0.4880 (mtmt) REVERT: U 56 ASP cc_start: 0.8131 (m-30) cc_final: 0.7670 (m-30) REVERT: U 57 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7389 (tm-30) REVERT: U 69 LYS cc_start: 0.8942 (mttm) cc_final: 0.8627 (mttp) REVERT: U 71 MET cc_start: 0.8114 (mmp) cc_final: 0.7590 (mmp) REVERT: W 90 MET cc_start: 0.8414 (mtt) cc_final: 0.8053 (mtm) REVERT: W 103 THR cc_start: 0.8556 (p) cc_final: 0.8179 (t) REVERT: X 154 GLU cc_start: 0.7257 (tp30) cc_final: 0.6607 (tp30) REVERT: Y 4 LYS cc_start: 0.7769 (pptt) cc_final: 0.7370 (tmmt) REVERT: Z 49 MET cc_start: 0.8549 (tpp) cc_final: 0.8310 (tpp) REVERT: Z 97 MET cc_start: 0.8743 (mmt) cc_final: 0.8496 (mmt) REVERT: Z 129 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8293 (mmmt) REVERT: a 4 GLU cc_start: 0.8418 (mp0) cc_final: 0.8168 (mp0) REVERT: c 30 TYR cc_start: 0.7980 (t80) cc_final: 0.7703 (t80) REVERT: e 75 MET cc_start: 0.8778 (tpp) cc_final: 0.8549 (tpp) REVERT: h 108 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7976 (mm-40) REVERT: i 69 PHE cc_start: 0.6207 (m-80) cc_final: 0.5547 (t80) REVERT: k 25 ARG cc_start: 0.8040 (mpt180) cc_final: 0.7632 (mmt90) REVERT: l 67 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7048 (mt-10) REVERT: l 105 PHE cc_start: 0.7660 (m-80) cc_final: 0.7444 (t80) REVERT: l 110 PHE cc_start: 0.8886 (t80) cc_final: 0.8413 (t80) REVERT: l 114 MET cc_start: 0.7889 (mmm) cc_final: 0.7312 (mmm) REVERT: m 4 LYS cc_start: 0.6573 (tmtt) cc_final: 0.6299 (tttt) REVERT: n 57 MET cc_start: 0.7986 (tpp) cc_final: 0.7531 (tmm) REVERT: o 44 GLU cc_start: 0.8559 (mt-10) cc_final: 0.7024 (mm-30) REVERT: o 46 MET cc_start: 0.8532 (ttp) cc_final: 0.8309 (ttm) REVERT: o 69 LYS cc_start: 0.8996 (tppt) cc_final: 0.8734 (tppt) REVERT: p 92 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7654 (ttm110) REVERT: r 52 TYR cc_start: 0.7333 (m-80) cc_final: 0.7001 (m-80) REVERT: r 55 THR cc_start: 0.8149 (p) cc_final: 0.7886 (p) outliers start: 233 outliers final: 155 residues processed: 1095 average time/residue: 0.5668 time to fit residues: 1078.0246 Evaluate side-chains 1037 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 867 time to evaluate : 5.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 51 ILE Chi-restraints excluded: chain t residue 67 ILE Chi-restraints excluded: chain t residue 96 GLU Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 77 TRP Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 437 HIS Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 523 PHE Chi-restraints excluded: chain G residue 585 VAL Chi-restraints excluded: chain G residue 687 CYS Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 361 ASN Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 431 THR Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain N residue 27 MET Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 225 MET Chi-restraints excluded: chain N residue 229 SER Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 216 GLU Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 170 ASP Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain P residue 284 VAL Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 101 GLN Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 43 SER Chi-restraints excluded: chain Y residue 48 ASP Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain b residue 61 ASN Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain g residue 32 ASP Chi-restraints excluded: chain g residue 38 LYS Chi-restraints excluded: chain g residue 121 ASP Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 86 ASN Chi-restraints excluded: chain h residue 130 LYS Chi-restraints excluded: chain h residue 142 ASP Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 26 GLU Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain l residue 7 MET Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 104 LEU Chi-restraints excluded: chain n residue 102 CYS Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 32 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 72 ASP Chi-restraints excluded: chain p residue 92 ARG Chi-restraints excluded: chain p residue 135 THR Chi-restraints excluded: chain s residue 39 ASP Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 766 random chunks: chunk 249 optimal weight: 4.9990 chunk 666 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 434 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 741 optimal weight: 5.9990 chunk 615 optimal weight: 9.9990 chunk 343 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 389 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 ASN ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN P 58 HIS ** P 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN W 110 HIS X 108 GLN a 31 ASN ** e 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 9 HIS h 108 GLN p 103 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.262 65830 Z= 0.632 Angle : 1.629 51.102 89189 Z= 1.046 Chirality : 0.316 6.581 9770 Planarity : 0.005 0.066 11156 Dihedral : 10.946 175.537 9556 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 3.98 % Allowed : 18.07 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.84 (0.10), residues: 7749 helix: 1.38 (0.08), residues: 4237 sheet: -0.37 (0.27), residues: 374 loop : -0.40 (0.11), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 25 HIS 0.013 0.001 HIS C 160 PHE 0.026 0.002 PHE N 292 TYR 0.020 0.002 TYR h 16 ARG 0.008 0.001 ARG G 436 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1141 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 868 time to evaluate : 5.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 51 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8300 (pt) REVERT: t 90 LYS cc_start: 0.7821 (tptt) cc_final: 0.7387 (tptp) REVERT: t 106 TYR cc_start: 0.4677 (m-80) cc_final: 0.3796 (m-10) REVERT: A 4 TYR cc_start: 0.8901 (m-80) cc_final: 0.8666 (m-10) REVERT: A 99 SER cc_start: 0.9470 (m) cc_final: 0.9007 (t) REVERT: A 109 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8301 (mmtt) REVERT: B 60 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7601 (t80) REVERT: C 73 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7572 (mtpt) REVERT: C 79 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8139 (t) REVERT: C 177 ASP cc_start: 0.7885 (t0) cc_final: 0.7558 (t0) REVERT: D 48 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8092 (p) REVERT: E 127 LYS cc_start: 0.8254 (tttm) cc_final: 0.8046 (mmmt) REVERT: E 153 MET cc_start: 0.7815 (ttp) cc_final: 0.7183 (tmm) REVERT: E 176 LEU cc_start: 0.7347 (mt) cc_final: 0.7042 (mt) REVERT: F 80 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8635 (p) REVERT: F 110 ILE cc_start: 0.8587 (mt) cc_final: 0.8218 (mt) REVERT: F 111 MET cc_start: 0.7490 (mpp) cc_final: 0.7115 (mmm) REVERT: F 149 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8859 (tp) REVERT: G 9 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7668 (tt) REVERT: G 378 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7861 (mt) REVERT: G 523 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.6519 (t80) REVERT: G 556 MET cc_start: 0.7744 (mpp) cc_final: 0.6124 (ppp) REVERT: G 684 MET cc_start: 0.8226 (mmm) cc_final: 0.7908 (mmm) REVERT: H 181 MET cc_start: 0.8516 (mmm) cc_final: 0.8074 (mmm) REVERT: H 199 ASP cc_start: 0.7783 (p0) cc_final: 0.7346 (p0) REVERT: I 6 ASN cc_start: 0.7865 (t0) cc_final: 0.7596 (t0) REVERT: I 95 THR cc_start: 0.9235 (m) cc_final: 0.8992 (p) REVERT: I 112 ASP cc_start: 0.7889 (m-30) cc_final: 0.7181 (t0) REVERT: J 73 MET cc_start: 0.7034 (mtt) cc_final: 0.6749 (mtp) REVERT: J 127 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: K 69 CYS cc_start: 0.8616 (t) cc_final: 0.8223 (t) REVERT: L 175 ASN cc_start: 0.8584 (m110) cc_final: 0.8350 (m-40) REVERT: L 338 MET cc_start: 0.8933 (ttp) cc_final: 0.8594 (ttp) REVERT: M 98 MET cc_start: 0.8764 (mmp) cc_final: 0.8545 (mmt) REVERT: M 222 GLU cc_start: 0.7661 (mp0) cc_final: 0.6941 (mp0) REVERT: M 316 MET cc_start: 0.8146 (mtp) cc_final: 0.7899 (mtm) REVERT: M 396 MET cc_start: 0.8495 (mmm) cc_final: 0.8075 (mmm) REVERT: N 54 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7371 (tp30) REVERT: N 164 MET cc_start: 0.8849 (mmm) cc_final: 0.8158 (mtp) REVERT: N 181 TYR cc_start: 0.9028 (m-10) cc_final: 0.8614 (m-10) REVERT: N 229 SER cc_start: 0.9146 (OUTLIER) cc_final: 0.8774 (p) REVERT: O 41 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7763 (tp30) REVERT: O 216 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: O 295 SER cc_start: 0.9033 (m) cc_final: 0.8806 (p) REVERT: P 170 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7474 (t0) REVERT: T 8 LEU cc_start: 0.6604 (tt) cc_final: 0.6192 (mp) REVERT: T 22 TYR cc_start: 0.6488 (t80) cc_final: 0.6106 (t80) REVERT: T 24 LYS cc_start: 0.6149 (mtmt) cc_final: 0.5733 (mtmt) REVERT: T 37 MET cc_start: 0.4992 (mmt) cc_final: 0.4780 (mmm) REVERT: U 57 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7421 (tm-30) REVERT: U 69 LYS cc_start: 0.8963 (mttm) cc_final: 0.8650 (mttp) REVERT: U 71 MET cc_start: 0.8135 (mmp) cc_final: 0.7617 (mmp) REVERT: U 88 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6488 (pm20) REVERT: W 23 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.7109 (m-10) REVERT: W 90 MET cc_start: 0.8459 (mtt) cc_final: 0.7972 (mtm) REVERT: W 103 THR cc_start: 0.8561 (p) cc_final: 0.8214 (t) REVERT: Y 4 LYS cc_start: 0.7784 (pptt) cc_final: 0.7400 (tmmt) REVERT: Y 70 MET cc_start: 0.7645 (ttm) cc_final: 0.6904 (tpt) REVERT: Z 97 MET cc_start: 0.8741 (mmt) cc_final: 0.8526 (mmt) REVERT: Z 129 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8361 (mmmt) REVERT: a 4 GLU cc_start: 0.8457 (mp0) cc_final: 0.8154 (mp0) REVERT: c 30 TYR cc_start: 0.8041 (t80) cc_final: 0.7770 (t80) REVERT: e 75 MET cc_start: 0.8779 (tpp) cc_final: 0.8565 (tpp) REVERT: f 7 ARG cc_start: 0.6748 (mtm-85) cc_final: 0.5539 (ttm110) REVERT: h 97 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6874 (mm-30) REVERT: h 108 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7974 (mm-40) REVERT: i 69 PHE cc_start: 0.6287 (m-80) cc_final: 0.5394 (t80) REVERT: k 25 ARG cc_start: 0.7868 (mpt180) cc_final: 0.7408 (mmt90) REVERT: l 67 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7012 (mt-10) REVERT: l 110 PHE cc_start: 0.8874 (t80) cc_final: 0.8514 (t80) REVERT: l 114 MET cc_start: 0.7908 (mmm) cc_final: 0.7425 (mmm) REVERT: m 4 LYS cc_start: 0.6591 (tmtt) cc_final: 0.6321 (tttt) REVERT: m 54 LYS cc_start: 0.8654 (mtpp) cc_final: 0.8420 (mttp) REVERT: o 44 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8346 (mp0) REVERT: o 69 LYS cc_start: 0.8982 (tppt) cc_final: 0.8723 (tppt) REVERT: p 92 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7821 (ttm110) REVERT: r 52 TYR cc_start: 0.7412 (m-80) cc_final: 0.7143 (m-80) REVERT: r 55 THR cc_start: 0.8108 (p) cc_final: 0.7847 (p) outliers start: 273 outliers final: 196 residues processed: 1066 average time/residue: 0.5897 time to fit residues: 1086.4461 Evaluate side-chains 1051 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 835 time to evaluate : 5.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 51 ILE Chi-restraints excluded: chain t residue 66 ASP Chi-restraints excluded: chain t residue 67 ILE Chi-restraints excluded: chain t residue 96 GLU Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 77 TRP Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 523 PHE Chi-restraints excluded: chain G residue 531 CYS Chi-restraints excluded: chain G residue 541 CYS Chi-restraints excluded: chain G residue 585 VAL Chi-restraints excluded: chain G residue 687 CYS Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 269 THR Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 127 GLU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 201 ILE Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 285 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 431 THR Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 578 THR Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 269 MET Chi-restraints excluded: chain M residue 308 SER Chi-restraints excluded: chain M residue 414 THR Chi-restraints excluded: chain N residue 27 MET Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 225 MET Chi-restraints excluded: chain N residue 229 SER Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 216 GLU Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 170 ASP Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 284 VAL Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain W residue 23 PHE Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 101 GLN Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 156 ASP Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 43 SER Chi-restraints excluded: chain Y residue 48 ASP Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain Z residue 123 MET Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain b residue 61 ASN Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain g residue 121 ASP Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 86 ASN Chi-restraints excluded: chain h residue 108 GLN Chi-restraints excluded: chain h residue 130 LYS Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain h residue 142 ASP Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 112 THR Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain k residue 59 MET Chi-restraints excluded: chain l residue 7 MET Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 104 LEU Chi-restraints excluded: chain n residue 8 TYR Chi-restraints excluded: chain n residue 102 CYS Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 98 MET Chi-restraints excluded: chain p residue 32 LEU Chi-restraints excluded: chain p residue 63 TYR Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 72 ASP Chi-restraints excluded: chain p residue 92 ARG Chi-restraints excluded: chain p residue 135 THR Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain s residue 39 ASP Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 766 random chunks: chunk 714 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 422 optimal weight: 5.9990 chunk 541 optimal weight: 0.1980 chunk 419 optimal weight: 0.9990 chunk 623 optimal weight: 3.9990 chunk 413 optimal weight: 4.9990 chunk 738 optimal weight: 6.9990 chunk 462 optimal weight: 10.0000 chunk 450 optimal weight: 0.0980 chunk 340 optimal weight: 0.0570 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS E 150 ASN ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 GLN ** P 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 79 ASN W 53 GLN ** e 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 55 ASN n 32 HIS ** p 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 123 ASN p 160 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.263 65830 Z= 0.558 Angle : 1.595 50.811 89189 Z= 1.033 Chirality : 0.315 6.466 9770 Planarity : 0.004 0.063 11156 Dihedral : 10.558 173.731 9556 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.42 % Favored : 96.57 % Rotamer: Outliers : 2.89 % Allowed : 19.21 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.05 (0.10), residues: 7749 helix: 1.54 (0.08), residues: 4248 sheet: -0.22 (0.27), residues: 373 loop : -0.30 (0.12), residues: 3128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 60 HIS 0.008 0.001 HIS C 160 PHE 0.025 0.001 PHE N 292 TYR 0.021 0.001 TYR Y 91 ARG 0.006 0.000 ARG t 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 965 time to evaluate : 5.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 51 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8202 (pt) REVERT: t 90 LYS cc_start: 0.7934 (tptt) cc_final: 0.7668 (tptp) REVERT: t 106 TYR cc_start: 0.4761 (m-80) cc_final: 0.4060 (m-10) REVERT: A 67 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8376 (mm) REVERT: A 99 SER cc_start: 0.9465 (m) cc_final: 0.8894 (t) REVERT: A 109 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8371 (mmtt) REVERT: B 60 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7591 (t80) REVERT: C 49 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7799 (tp30) REVERT: C 79 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7779 (t) REVERT: C 137 MET cc_start: 0.8775 (mmm) cc_final: 0.8311 (mmm) REVERT: C 177 ASP cc_start: 0.7882 (t0) cc_final: 0.7543 (t0) REVERT: D 40 LYS cc_start: 0.6914 (tmtt) cc_final: 0.6700 (mttp) REVERT: D 112 MET cc_start: 0.7815 (mmm) cc_final: 0.7522 (mmm) REVERT: E 153 MET cc_start: 0.7709 (ttp) cc_final: 0.7077 (tmm) REVERT: E 176 LEU cc_start: 0.7249 (mt) cc_final: 0.6779 (mt) REVERT: E 182 PRO cc_start: 0.5296 (Cg_endo) cc_final: 0.5082 (Cg_exo) REVERT: F 60 MET cc_start: 0.7321 (mmp) cc_final: 0.7020 (mmm) REVERT: F 80 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8602 (p) REVERT: F 110 ILE cc_start: 0.8452 (mt) cc_final: 0.8073 (mt) REVERT: F 111 MET cc_start: 0.7433 (mpp) cc_final: 0.7048 (mmm) REVERT: F 149 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8848 (tp) REVERT: G 9 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7693 (tt) REVERT: G 378 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7881 (mt) REVERT: G 523 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.6447 (t80) REVERT: G 673 MET cc_start: 0.6909 (mmm) cc_final: 0.6678 (mmp) REVERT: G 684 MET cc_start: 0.7980 (mmm) cc_final: 0.7569 (mmm) REVERT: H 140 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8155 (mt) REVERT: H 199 ASP cc_start: 0.7705 (p0) cc_final: 0.7253 (p0) REVERT: I 6 ASN cc_start: 0.7776 (t0) cc_final: 0.7505 (t0) REVERT: I 95 THR cc_start: 0.9225 (m) cc_final: 0.8988 (p) REVERT: I 112 ASP cc_start: 0.7822 (m-30) cc_final: 0.7089 (t0) REVERT: I 174 ASP cc_start: 0.8106 (m-30) cc_final: 0.7439 (t0) REVERT: J 134 MET cc_start: 0.7784 (mtm) cc_final: 0.7251 (mtm) REVERT: J 168 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7146 (tp30) REVERT: L 75 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7616 (mt-10) REVERT: L 175 ASN cc_start: 0.8540 (m110) cc_final: 0.8300 (m110) REVERT: L 338 MET cc_start: 0.8929 (ttp) cc_final: 0.8568 (ttp) REVERT: L 340 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8195 (m-10) REVERT: L 358 LYS cc_start: 0.8854 (mttt) cc_final: 0.8510 (mtpt) REVERT: L 537 THR cc_start: 0.9505 (m) cc_final: 0.9253 (p) REVERT: M 222 GLU cc_start: 0.7628 (mp0) cc_final: 0.6839 (mp0) REVERT: M 316 MET cc_start: 0.8149 (mtp) cc_final: 0.7872 (mtm) REVERT: M 396 MET cc_start: 0.8435 (mmm) cc_final: 0.8014 (mmm) REVERT: N 10 TYR cc_start: 0.8594 (m-80) cc_final: 0.8138 (m-80) REVERT: N 54 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7210 (tp30) REVERT: N 164 MET cc_start: 0.8762 (mmm) cc_final: 0.8109 (mtp) REVERT: N 181 TYR cc_start: 0.8967 (m-10) cc_final: 0.8668 (m-10) REVERT: N 191 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8921 (tp) REVERT: O 41 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7639 (tp30) REVERT: O 110 ASP cc_start: 0.8116 (m-30) cc_final: 0.7664 (m-30) REVERT: O 216 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: O 233 LYS cc_start: 0.8510 (mmtt) cc_final: 0.7938 (ptmm) REVERT: O 295 SER cc_start: 0.8940 (m) cc_final: 0.8666 (p) REVERT: P 102 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6772 (ptm160) REVERT: P 170 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7459 (t0) REVERT: P 286 ARG cc_start: 0.8255 (mtm110) cc_final: 0.8047 (mtp85) REVERT: T 8 LEU cc_start: 0.6620 (tt) cc_final: 0.6013 (mm) REVERT: T 9 ASP cc_start: 0.5585 (t0) cc_final: 0.5298 (t0) REVERT: T 22 TYR cc_start: 0.6452 (t80) cc_final: 0.6033 (t80) REVERT: T 24 LYS cc_start: 0.6282 (mtmt) cc_final: 0.5945 (mtmt) REVERT: T 37 MET cc_start: 0.5127 (mmt) cc_final: 0.4925 (mmm) REVERT: U 56 ASP cc_start: 0.8053 (m-30) cc_final: 0.7461 (m-30) REVERT: U 57 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7316 (tm-30) REVERT: U 69 LYS cc_start: 0.8922 (mttm) cc_final: 0.8617 (mttp) REVERT: W 90 MET cc_start: 0.8399 (mtt) cc_final: 0.8176 (mtm) REVERT: W 103 THR cc_start: 0.8520 (p) cc_final: 0.8145 (t) REVERT: Y 4 LYS cc_start: 0.7648 (pptt) cc_final: 0.7217 (tmmt) REVERT: Y 70 MET cc_start: 0.7606 (ttm) cc_final: 0.6844 (tpt) REVERT: Z 49 MET cc_start: 0.8541 (tpp) cc_final: 0.8331 (tpp) REVERT: a 3 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.6233 (m-80) REVERT: a 4 GLU cc_start: 0.8333 (mp0) cc_final: 0.8113 (mp0) REVERT: b 50 TYR cc_start: 0.7737 (m-80) cc_final: 0.7501 (m-80) REVERT: c 30 TYR cc_start: 0.7990 (t80) cc_final: 0.7696 (t80) REVERT: d 44 MET cc_start: 0.8323 (tpt) cc_final: 0.8080 (tpt) REVERT: e 67 LEU cc_start: 0.8529 (mt) cc_final: 0.8241 (mp) REVERT: e 75 MET cc_start: 0.8742 (tpp) cc_final: 0.8541 (tpp) REVERT: f 7 ARG cc_start: 0.6728 (mtm-85) cc_final: 0.5531 (ttm110) REVERT: f 24 TYR cc_start: 0.8197 (t80) cc_final: 0.7911 (t80) REVERT: i 69 PHE cc_start: 0.6050 (m-80) cc_final: 0.5694 (t80) REVERT: k 25 ARG cc_start: 0.8059 (mpt180) cc_final: 0.7681 (mmt90) REVERT: l 67 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6910 (mt-10) REVERT: l 105 PHE cc_start: 0.8065 (t80) cc_final: 0.7713 (m-80) REVERT: l 110 PHE cc_start: 0.8805 (t80) cc_final: 0.8441 (t80) REVERT: l 114 MET cc_start: 0.7854 (mmm) cc_final: 0.7406 (mmm) REVERT: m 4 LYS cc_start: 0.6640 (tmtt) cc_final: 0.6355 (tttt) REVERT: o 44 GLU cc_start: 0.8232 (mt-10) cc_final: 0.6774 (mm-30) REVERT: o 69 LYS cc_start: 0.9008 (tppt) cc_final: 0.8729 (tppt) REVERT: p 92 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7792 (ttm110) REVERT: r 52 TYR cc_start: 0.7192 (m-80) cc_final: 0.6895 (m-80) REVERT: r 55 THR cc_start: 0.8136 (p) cc_final: 0.7876 (p) REVERT: r 72 GLN cc_start: 0.6719 (pp30) cc_final: 0.6479 (pt0) REVERT: s 32 TYR cc_start: 0.3296 (t80) cc_final: 0.3086 (t80) outliers start: 198 outliers final: 131 residues processed: 1101 average time/residue: 0.5825 time to fit residues: 1109.4020 Evaluate side-chains 1042 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 890 time to evaluate : 5.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 51 ILE Chi-restraints excluded: chain t residue 67 ILE Chi-restraints excluded: chain t residue 96 GLU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 77 TRP Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 523 PHE Chi-restraints excluded: chain G residue 541 CYS Chi-restraints excluded: chain G residue 585 VAL Chi-restraints excluded: chain G residue 687 CYS Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 281 ASP Chi-restraints excluded: chain M residue 424 ILE Chi-restraints excluded: chain N residue 27 MET Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 216 GLU Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 102 ARG Chi-restraints excluded: chain P residue 170 ASP Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 284 VAL Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 86 VAL Chi-restraints excluded: chain U residue 87 TYR Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 101 GLN Chi-restraints excluded: chain X residue 156 ASP Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 48 ASP Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain g residue 38 LYS Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 105 ILE Chi-restraints excluded: chain g residue 121 ASP Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 86 ASN Chi-restraints excluded: chain h residue 130 LYS Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain h residue 142 ASP Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 26 GLU Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain n residue 102 CYS Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 32 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 72 ASP Chi-restraints excluded: chain p residue 92 ARG Chi-restraints excluded: chain p residue 135 THR Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain r residue 100 MET Chi-restraints excluded: chain s residue 39 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 766 random chunks: chunk 456 optimal weight: 8.9990 chunk 294 optimal weight: 6.9990 chunk 440 optimal weight: 0.9990 chunk 222 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 143 optimal weight: 0.0040 chunk 469 optimal weight: 2.9990 chunk 503 optimal weight: 9.9990 chunk 365 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 580 optimal weight: 6.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 HIS O 97 GLN ** O 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 79 ASN V 110 GLN W 53 GLN Z 75 GLN ** e 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 HIS p 103 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.260 65830 Z= 0.562 Angle : 1.600 50.949 89189 Z= 1.034 Chirality : 0.315 6.497 9770 Planarity : 0.004 0.062 11156 Dihedral : 10.353 174.222 9553 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.78 % Favored : 96.21 % Rotamer: Outliers : 2.89 % Allowed : 19.59 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.09 (0.10), residues: 7749 helix: 1.55 (0.08), residues: 4242 sheet: -0.21 (0.28), residues: 367 loop : -0.23 (0.12), residues: 3140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP M 43 HIS 0.008 0.001 HIS C 160 PHE 0.029 0.001 PHE K 41 TYR 0.027 0.001 TYR W 125 ARG 0.007 0.000 ARG t 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 917 time to evaluate : 5.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 51 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8235 (pt) REVERT: t 90 LYS cc_start: 0.7925 (tptt) cc_final: 0.7663 (tptp) REVERT: t 106 TYR cc_start: 0.4810 (m-80) cc_final: 0.4094 (m-10) REVERT: A 38 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7532 (mt-10) REVERT: A 67 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8487 (mm) REVERT: A 99 SER cc_start: 0.9445 (m) cc_final: 0.8896 (t) REVERT: A 109 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8382 (mmtt) REVERT: B 60 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7588 (t80) REVERT: C 49 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7847 (tp30) REVERT: C 79 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7642 (t) REVERT: C 177 ASP cc_start: 0.7881 (t0) cc_final: 0.7428 (t0) REVERT: D 72 MET cc_start: 0.8103 (mmp) cc_final: 0.7619 (mmp) REVERT: D 112 MET cc_start: 0.7790 (mmm) cc_final: 0.7502 (mmm) REVERT: E 10 ARG cc_start: 0.6995 (mtt-85) cc_final: 0.6793 (mtm-85) REVERT: E 153 MET cc_start: 0.7674 (ttp) cc_final: 0.7076 (tmm) REVERT: E 176 LEU cc_start: 0.7276 (mt) cc_final: 0.6912 (mt) REVERT: E 182 PRO cc_start: 0.5262 (Cg_endo) cc_final: 0.5054 (Cg_exo) REVERT: F 60 MET cc_start: 0.7394 (mmp) cc_final: 0.7137 (mmm) REVERT: F 110 ILE cc_start: 0.8464 (mt) cc_final: 0.8078 (mt) REVERT: F 111 MET cc_start: 0.7440 (mpp) cc_final: 0.7047 (mmm) REVERT: G 378 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7862 (mt) REVERT: G 523 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.6601 (t80) REVERT: G 684 MET cc_start: 0.7941 (mmm) cc_final: 0.7525 (mmm) REVERT: H 140 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8151 (mt) REVERT: H 199 ASP cc_start: 0.7623 (p0) cc_final: 0.7175 (p0) REVERT: H 225 MET cc_start: 0.8223 (mtp) cc_final: 0.7921 (mtp) REVERT: I 6 ASN cc_start: 0.7766 (t0) cc_final: 0.7377 (t0) REVERT: I 95 THR cc_start: 0.9220 (m) cc_final: 0.8981 (p) REVERT: I 112 ASP cc_start: 0.7812 (m-30) cc_final: 0.7116 (t0) REVERT: I 174 ASP cc_start: 0.8072 (m-30) cc_final: 0.7403 (t0) REVERT: J 134 MET cc_start: 0.7914 (mtm) cc_final: 0.7127 (mtm) REVERT: J 168 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7130 (tp30) REVERT: K 69 CYS cc_start: 0.8231 (t) cc_final: 0.7918 (t) REVERT: L 75 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7556 (mt-10) REVERT: L 175 ASN cc_start: 0.8531 (m110) cc_final: 0.8312 (m110) REVERT: L 338 MET cc_start: 0.8923 (ttp) cc_final: 0.8606 (ttp) REVERT: L 340 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8286 (m-10) REVERT: L 358 LYS cc_start: 0.8865 (mttt) cc_final: 0.8566 (mmmt) REVERT: L 447 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7528 (t70) REVERT: L 513 MET cc_start: 0.6824 (tpp) cc_final: 0.6618 (tpt) REVERT: L 537 THR cc_start: 0.9491 (m) cc_final: 0.9257 (p) REVERT: M 98 MET cc_start: 0.8748 (mmt) cc_final: 0.8540 (mmt) REVERT: M 222 GLU cc_start: 0.7622 (mp0) cc_final: 0.6823 (mp0) REVERT: M 316 MET cc_start: 0.8152 (mtp) cc_final: 0.7907 (mtm) REVERT: M 396 MET cc_start: 0.8441 (mmm) cc_final: 0.7901 (mmm) REVERT: N 10 TYR cc_start: 0.8605 (m-80) cc_final: 0.8168 (m-80) REVERT: N 54 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7318 (tp30) REVERT: N 164 MET cc_start: 0.8778 (mmm) cc_final: 0.8088 (mtp) REVERT: N 181 TYR cc_start: 0.8968 (m-10) cc_final: 0.8662 (m-10) REVERT: N 191 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8924 (tp) REVERT: N 271 MET cc_start: 0.8393 (mmm) cc_final: 0.8028 (mmp) REVERT: O 41 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7656 (tp30) REVERT: O 110 ASP cc_start: 0.8136 (m-30) cc_final: 0.7683 (m-30) REVERT: O 216 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: O 233 LYS cc_start: 0.8411 (mmtt) cc_final: 0.7947 (ptmm) REVERT: O 295 SER cc_start: 0.8942 (m) cc_final: 0.8667 (p) REVERT: P 102 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6772 (ptm160) REVERT: P 286 ARG cc_start: 0.8238 (mtm110) cc_final: 0.8017 (mtp85) REVERT: T 8 LEU cc_start: 0.6937 (tt) cc_final: 0.6300 (mm) REVERT: T 22 TYR cc_start: 0.6377 (t80) cc_final: 0.5951 (t80) REVERT: T 24 LYS cc_start: 0.6116 (mtmt) cc_final: 0.5744 (mtmt) REVERT: T 52 MET cc_start: 0.7973 (mtp) cc_final: 0.7760 (mtp) REVERT: U 56 ASP cc_start: 0.8069 (m-30) cc_final: 0.7499 (m-30) REVERT: U 57 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7366 (tm-30) REVERT: U 69 LYS cc_start: 0.8915 (mttm) cc_final: 0.8631 (mttp) REVERT: W 90 MET cc_start: 0.8434 (mtt) cc_final: 0.7997 (mtm) REVERT: W 103 THR cc_start: 0.8514 (p) cc_final: 0.8148 (t) REVERT: Y 4 LYS cc_start: 0.7860 (pptt) cc_final: 0.7434 (tmmt) REVERT: Y 15 ASP cc_start: 0.5795 (m-30) cc_final: 0.5428 (m-30) REVERT: Y 70 MET cc_start: 0.7611 (ttm) cc_final: 0.6896 (tpt) REVERT: Z 49 MET cc_start: 0.8536 (tpp) cc_final: 0.8311 (tpp) REVERT: Z 97 MET cc_start: 0.8701 (mmt) cc_final: 0.8091 (mmm) REVERT: a 3 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.6244 (m-80) REVERT: a 4 GLU cc_start: 0.8374 (mp0) cc_final: 0.8123 (mp0) REVERT: b 9 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8155 (mtmt) REVERT: b 50 TYR cc_start: 0.7828 (m-80) cc_final: 0.7613 (m-80) REVERT: c 30 TYR cc_start: 0.8013 (t80) cc_final: 0.7707 (t80) REVERT: e 36 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: f 7 ARG cc_start: 0.6950 (mtm-85) cc_final: 0.5550 (ttm110) REVERT: f 24 TYR cc_start: 0.8189 (t80) cc_final: 0.7904 (t80) REVERT: i 69 PHE cc_start: 0.6245 (m-80) cc_final: 0.5825 (t80) REVERT: k 25 ARG cc_start: 0.8013 (mpt180) cc_final: 0.7642 (mmt90) REVERT: k 47 ARG cc_start: 0.7880 (mtp180) cc_final: 0.7515 (ptm160) REVERT: l 67 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6927 (mt-10) REVERT: l 105 PHE cc_start: 0.8072 (t80) cc_final: 0.7872 (t80) REVERT: l 110 PHE cc_start: 0.8802 (t80) cc_final: 0.8422 (t80) REVERT: l 114 MET cc_start: 0.7864 (mmm) cc_final: 0.7331 (mmm) REVERT: m 4 LYS cc_start: 0.6635 (tmtt) cc_final: 0.6354 (tttt) REVERT: o 69 LYS cc_start: 0.9005 (tppt) cc_final: 0.8756 (tppt) REVERT: p 92 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7838 (ttm110) REVERT: r 52 TYR cc_start: 0.7148 (m-80) cc_final: 0.6851 (m-80) REVERT: r 55 THR cc_start: 0.8123 (p) cc_final: 0.7870 (p) REVERT: s 32 TYR cc_start: 0.3580 (t80) cc_final: 0.3350 (t80) outliers start: 198 outliers final: 156 residues processed: 1057 average time/residue: 0.5646 time to fit residues: 1033.5633 Evaluate side-chains 1054 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 878 time to evaluate : 5.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 51 ILE Chi-restraints excluded: chain t residue 67 ILE Chi-restraints excluded: chain t residue 96 GLU Chi-restraints excluded: chain t residue 97 GLU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 77 TRP Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 523 PHE Chi-restraints excluded: chain G residue 541 CYS Chi-restraints excluded: chain G residue 585 VAL Chi-restraints excluded: chain G residue 687 CYS Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 285 THR Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 281 ASP Chi-restraints excluded: chain M residue 424 ILE Chi-restraints excluded: chain N residue 27 MET Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 216 GLU Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 274 THR Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 102 ARG Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 284 VAL Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 86 VAL Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 101 GLN Chi-restraints excluded: chain X residue 156 ASP Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 48 ASP Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 61 ASN Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 36 GLU Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 105 ILE Chi-restraints excluded: chain g residue 121 ASP Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 86 ASN Chi-restraints excluded: chain h residue 130 LYS Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain h residue 142 ASP Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 26 GLU Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain n residue 102 CYS Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 32 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 72 ASP Chi-restraints excluded: chain p residue 92 ARG Chi-restraints excluded: chain p residue 135 THR Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 100 MET Chi-restraints excluded: chain s residue 39 ASP Chi-restraints excluded: chain s residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 766 random chunks: chunk 671 optimal weight: 4.9990 chunk 707 optimal weight: 9.9990 chunk 645 optimal weight: 7.9990 chunk 688 optimal weight: 7.9990 chunk 414 optimal weight: 3.9990 chunk 299 optimal weight: 4.9990 chunk 540 optimal weight: 6.9990 chunk 211 optimal weight: 20.0000 chunk 621 optimal weight: 5.9990 chunk 650 optimal weight: 10.0000 chunk 685 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN G 43 HIS G 100 ASN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 HIS O 97 GLN ** P 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 79 ASN W 53 GLN X 30 HIS d 117 HIS ** e 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 HIS ** s 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.259 65830 Z= 0.644 Angle : 1.641 51.140 89189 Z= 1.050 Chirality : 0.316 6.589 9770 Planarity : 0.005 0.062 11156 Dihedral : 10.616 173.703 9553 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 3.07 % Allowed : 19.80 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.84 (0.10), residues: 7749 helix: 1.37 (0.08), residues: 4237 sheet: -0.27 (0.28), residues: 355 loop : -0.38 (0.11), residues: 3157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 43 HIS 0.012 0.001 HIS g 43 PHE 0.030 0.002 PHE K 41 TYR 0.027 0.002 TYR Y 91 ARG 0.007 0.001 ARG N 295 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 850 time to evaluate : 5.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 51 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8211 (pt) REVERT: t 90 LYS cc_start: 0.8100 (tptt) cc_final: 0.7699 (tptp) REVERT: t 106 TYR cc_start: 0.4836 (m-80) cc_final: 0.4152 (m-10) REVERT: A 99 SER cc_start: 0.9488 (m) cc_final: 0.8975 (t) REVERT: A 109 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8377 (mmtt) REVERT: B 60 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7582 (t80) REVERT: C 49 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: C 73 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7681 (mtpt) REVERT: C 79 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.7910 (t) REVERT: C 177 ASP cc_start: 0.8020 (t0) cc_final: 0.7806 (t0) REVERT: D 112 MET cc_start: 0.7792 (mmm) cc_final: 0.7486 (mmm) REVERT: E 153 MET cc_start: 0.7821 (ttp) cc_final: 0.7547 (tmm) REVERT: E 176 LEU cc_start: 0.7320 (mt) cc_final: 0.6961 (mt) REVERT: E 182 PRO cc_start: 0.5218 (Cg_endo) cc_final: 0.4994 (Cg_exo) REVERT: F 110 ILE cc_start: 0.8555 (mt) cc_final: 0.8240 (mt) REVERT: F 111 MET cc_start: 0.7434 (mpp) cc_final: 0.7049 (mmm) REVERT: G 9 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7435 (tt) REVERT: G 378 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7945 (mt) REVERT: G 523 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.6419 (t80) REVERT: G 684 MET cc_start: 0.8243 (mmm) cc_final: 0.8014 (mmm) REVERT: H 199 ASP cc_start: 0.7802 (p0) cc_final: 0.7357 (p0) REVERT: H 318 MET cc_start: 0.7748 (tmm) cc_final: 0.7513 (tmm) REVERT: I 6 ASN cc_start: 0.7854 (t0) cc_final: 0.7600 (t0) REVERT: I 95 THR cc_start: 0.9165 (m) cc_final: 0.8960 (p) REVERT: I 112 ASP cc_start: 0.7858 (m-30) cc_final: 0.7181 (t0) REVERT: I 174 ASP cc_start: 0.8164 (m-30) cc_final: 0.7472 (t0) REVERT: I 175 TYR cc_start: 0.8061 (p90) cc_final: 0.7850 (p90) REVERT: J 134 MET cc_start: 0.7738 (mtm) cc_final: 0.6982 (mtm) REVERT: K 69 CYS cc_start: 0.8431 (t) cc_final: 0.8023 (t) REVERT: L 75 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7601 (mt-10) REVERT: L 338 MET cc_start: 0.8948 (ttp) cc_final: 0.8592 (ttp) REVERT: L 340 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.7994 (m-10) REVERT: L 358 LYS cc_start: 0.8925 (mttt) cc_final: 0.8616 (mmmt) REVERT: M 222 GLU cc_start: 0.7584 (mp0) cc_final: 0.6943 (mp0) REVERT: M 396 MET cc_start: 0.8428 (mmm) cc_final: 0.7987 (mmm) REVERT: N 54 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7309 (tp30) REVERT: N 164 MET cc_start: 0.8872 (mmm) cc_final: 0.7983 (mmm) REVERT: N 229 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8777 (p) REVERT: N 271 MET cc_start: 0.8514 (mmm) cc_final: 0.8294 (mmt) REVERT: O 41 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7789 (tp30) REVERT: O 216 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: O 233 LYS cc_start: 0.8511 (mmtt) cc_final: 0.8006 (ptmm) REVERT: O 295 SER cc_start: 0.9013 (m) cc_final: 0.8794 (p) REVERT: P 102 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6800 (ptm160) REVERT: P 170 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7443 (t0) REVERT: T 8 LEU cc_start: 0.7002 (tt) cc_final: 0.6467 (mp) REVERT: T 22 TYR cc_start: 0.6483 (t80) cc_final: 0.6043 (t80) REVERT: T 24 LYS cc_start: 0.6442 (mtmt) cc_final: 0.5981 (mtmt) REVERT: U 56 ASP cc_start: 0.8154 (m-30) cc_final: 0.7580 (m-30) REVERT: U 57 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7489 (tm-30) REVERT: U 69 LYS cc_start: 0.8984 (mttm) cc_final: 0.8674 (mttp) REVERT: U 88 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.6781 (pm20) REVERT: W 90 MET cc_start: 0.8490 (mtt) cc_final: 0.8038 (mtm) REVERT: W 103 THR cc_start: 0.8578 (p) cc_final: 0.8223 (t) REVERT: Y 4 LYS cc_start: 0.7957 (pptt) cc_final: 0.7540 (tmmt) REVERT: Y 70 MET cc_start: 0.7723 (ttm) cc_final: 0.6930 (tpt) REVERT: Z 49 MET cc_start: 0.8589 (tpp) cc_final: 0.8350 (tpp) REVERT: a 3 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.6243 (m-80) REVERT: a 4 GLU cc_start: 0.8540 (mp0) cc_final: 0.8241 (mp0) REVERT: c 30 TYR cc_start: 0.8067 (t80) cc_final: 0.7772 (t80) REVERT: e 36 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: f 7 ARG cc_start: 0.7049 (mtm-85) cc_final: 0.5740 (ttm110) REVERT: g 120 GLU cc_start: 0.6782 (tm-30) cc_final: 0.6423 (tm-30) REVERT: h 25 MET cc_start: 0.8314 (ttt) cc_final: 0.7928 (ttp) REVERT: h 97 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6806 (mm-30) REVERT: i 69 PHE cc_start: 0.6365 (m-80) cc_final: 0.5909 (t80) REVERT: k 25 ARG cc_start: 0.7903 (mpt180) cc_final: 0.7439 (mmt90) REVERT: l 67 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7131 (mt-10) REVERT: l 105 PHE cc_start: 0.8063 (t80) cc_final: 0.7806 (t80) REVERT: l 110 PHE cc_start: 0.8881 (t80) cc_final: 0.8630 (t80) REVERT: l 114 MET cc_start: 0.7906 (mmm) cc_final: 0.7558 (mmm) REVERT: m 4 LYS cc_start: 0.6714 (tmtt) cc_final: 0.6458 (tttt) REVERT: o 69 LYS cc_start: 0.8936 (tppt) cc_final: 0.8680 (tppt) REVERT: p 92 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7820 (ttm110) REVERT: r 55 THR cc_start: 0.8099 (p) cc_final: 0.7757 (t) REVERT: s 32 TYR cc_start: 0.3867 (t80) cc_final: 0.3644 (t80) outliers start: 211 outliers final: 176 residues processed: 1007 average time/residue: 0.5719 time to fit residues: 1000.1589 Evaluate side-chains 1024 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 829 time to evaluate : 6.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 51 ILE Chi-restraints excluded: chain t residue 66 ASP Chi-restraints excluded: chain t residue 67 ILE Chi-restraints excluded: chain t residue 96 GLU Chi-restraints excluded: chain t residue 97 GLU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 77 TRP Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 523 PHE Chi-restraints excluded: chain G residue 541 CYS Chi-restraints excluded: chain G residue 585 VAL Chi-restraints excluded: chain G residue 636 ILE Chi-restraints excluded: chain G residue 687 CYS Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 285 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain M residue 18 SER Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 281 ASP Chi-restraints excluded: chain M residue 308 SER Chi-restraints excluded: chain M residue 376 MET Chi-restraints excluded: chain M residue 424 ILE Chi-restraints excluded: chain N residue 27 MET Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 229 SER Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 299 SER Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 216 GLU Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 274 THR Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 102 ARG Chi-restraints excluded: chain P residue 170 ASP Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 284 VAL Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 71 MET Chi-restraints excluded: chain U residue 86 VAL Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 101 GLN Chi-restraints excluded: chain X residue 156 ASP Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 43 SER Chi-restraints excluded: chain Y residue 48 ASP Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 61 ASN Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain e residue 36 GLU Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain g residue 121 ASP Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 34 ILE Chi-restraints excluded: chain h residue 86 ASN Chi-restraints excluded: chain h residue 130 LYS Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain h residue 142 ASP Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain l residue 7 MET Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain n residue 102 CYS Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 98 MET Chi-restraints excluded: chain p residue 32 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 72 ASP Chi-restraints excluded: chain p residue 89 MET Chi-restraints excluded: chain p residue 92 ARG Chi-restraints excluded: chain p residue 135 THR Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 100 MET Chi-restraints excluded: chain s residue 39 ASP Chi-restraints excluded: chain s residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 766 random chunks: chunk 451 optimal weight: 0.9990 chunk 727 optimal weight: 20.0000 chunk 444 optimal weight: 9.9990 chunk 345 optimal weight: 2.9990 chunk 505 optimal weight: 4.9990 chunk 763 optimal weight: 20.0000 chunk 702 optimal weight: 6.9990 chunk 607 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 469 optimal weight: 4.9990 chunk 372 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 494 HIS ** G 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 HIS L 361 ASN O 97 GLN ** P 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 79 ASN W 53 GLN ** Y 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 HIS n 32 HIS ** s 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.262 65830 Z= 0.608 Angle : 1.628 51.052 89189 Z= 1.045 Chirality : 0.315 6.550 9770 Planarity : 0.005 0.062 11156 Dihedral : 10.592 173.386 9553 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.10 % Favored : 95.87 % Rotamer: Outliers : 2.90 % Allowed : 20.17 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.83 (0.10), residues: 7749 helix: 1.35 (0.08), residues: 4243 sheet: -0.30 (0.28), residues: 358 loop : -0.38 (0.11), residues: 3148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP M 43 HIS 0.011 0.001 HIS C 160 PHE 0.028 0.002 PHE K 41 TYR 0.032 0.002 TYR Y 91 ARG 0.008 0.000 ARG N 295 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 854 time to evaluate : 5.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 51 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8298 (pt) REVERT: t 90 LYS cc_start: 0.8108 (tptt) cc_final: 0.7707 (tptp) REVERT: t 106 TYR cc_start: 0.4936 (m-80) cc_final: 0.4405 (m-10) REVERT: A 87 MET cc_start: 0.9160 (tmm) cc_final: 0.8882 (tmm) REVERT: A 99 SER cc_start: 0.9487 (m) cc_final: 0.8979 (t) REVERT: A 109 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8374 (mmtt) REVERT: B 44 ASP cc_start: 0.7665 (t70) cc_final: 0.7433 (t0) REVERT: B 60 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7640 (t80) REVERT: C 49 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7984 (tp30) REVERT: C 73 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7735 (mtpt) REVERT: C 79 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7867 (t) REVERT: C 177 ASP cc_start: 0.8058 (t0) cc_final: 0.7747 (t0) REVERT: D 40 LYS cc_start: 0.6796 (tmtt) cc_final: 0.6533 (mttp) REVERT: D 72 MET cc_start: 0.8129 (mmp) cc_final: 0.7864 (mmp) REVERT: D 112 MET cc_start: 0.7812 (mmm) cc_final: 0.7460 (mmm) REVERT: E 153 MET cc_start: 0.7801 (ttp) cc_final: 0.7498 (tmm) REVERT: E 176 LEU cc_start: 0.7348 (mt) cc_final: 0.6968 (mt) REVERT: E 182 PRO cc_start: 0.5174 (Cg_endo) cc_final: 0.4947 (Cg_exo) REVERT: F 110 ILE cc_start: 0.8494 (mt) cc_final: 0.8153 (mt) REVERT: F 111 MET cc_start: 0.7453 (mpp) cc_final: 0.7063 (mmm) REVERT: G 9 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7457 (tt) REVERT: G 378 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7879 (mt) REVERT: G 490 MET cc_start: 0.7650 (tmm) cc_final: 0.7165 (ppp) REVERT: G 523 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.6270 (t80) REVERT: G 684 MET cc_start: 0.8206 (mmm) cc_final: 0.7950 (mmm) REVERT: H 199 ASP cc_start: 0.7735 (p0) cc_final: 0.7339 (p0) REVERT: I 6 ASN cc_start: 0.7959 (t0) cc_final: 0.7670 (t0) REVERT: I 95 THR cc_start: 0.9172 (m) cc_final: 0.8953 (p) REVERT: I 112 ASP cc_start: 0.7840 (m-30) cc_final: 0.7203 (t0) REVERT: J 134 MET cc_start: 0.7620 (mtm) cc_final: 0.6924 (mtm) REVERT: J 168 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7138 (tp30) REVERT: L 75 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7511 (mt-10) REVERT: L 101 MET cc_start: 0.8884 (mmm) cc_final: 0.8591 (mmt) REVERT: L 338 MET cc_start: 0.8913 (ttp) cc_final: 0.8566 (ttp) REVERT: L 340 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.7929 (m-10) REVERT: L 358 LYS cc_start: 0.8894 (mttt) cc_final: 0.8571 (mmmt) REVERT: M 222 GLU cc_start: 0.7636 (mp0) cc_final: 0.6948 (mp0) REVERT: M 350 MET cc_start: 0.8290 (mmt) cc_final: 0.8032 (mmt) REVERT: M 396 MET cc_start: 0.8453 (mmm) cc_final: 0.8012 (mmm) REVERT: N 10 TYR cc_start: 0.8658 (m-80) cc_final: 0.8197 (m-80) REVERT: N 54 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7332 (tp30) REVERT: N 164 MET cc_start: 0.8850 (mmm) cc_final: 0.7944 (mmm) REVERT: N 187 MET cc_start: 0.8406 (mmm) cc_final: 0.8030 (mtm) REVERT: N 271 MET cc_start: 0.8475 (mmm) cc_final: 0.8108 (mmp) REVERT: O 41 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7782 (tp30) REVERT: O 110 ASP cc_start: 0.8104 (m-30) cc_final: 0.7583 (m-30) REVERT: O 126 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.5904 (mtt90) REVERT: O 216 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: O 233 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8009 (ptmm) REVERT: O 295 SER cc_start: 0.8968 (m) cc_final: 0.8697 (p) REVERT: P 170 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7501 (t0) REVERT: P 286 ARG cc_start: 0.8309 (mtm110) cc_final: 0.8041 (mtp85) REVERT: T 8 LEU cc_start: 0.7044 (tt) cc_final: 0.6542 (mp) REVERT: T 22 TYR cc_start: 0.6496 (t80) cc_final: 0.6080 (t80) REVERT: T 24 LYS cc_start: 0.6465 (mtmt) cc_final: 0.5993 (mtmt) REVERT: U 56 ASP cc_start: 0.8140 (m-30) cc_final: 0.7565 (m-30) REVERT: U 57 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7429 (tm-30) REVERT: U 69 LYS cc_start: 0.8962 (mttm) cc_final: 0.8658 (mttp) REVERT: U 88 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.6759 (pm20) REVERT: W 90 MET cc_start: 0.8480 (mtt) cc_final: 0.8019 (mtm) REVERT: W 103 THR cc_start: 0.8565 (p) cc_final: 0.8202 (t) REVERT: Y 4 LYS cc_start: 0.7965 (pptt) cc_final: 0.7587 (tmmt) REVERT: Y 70 MET cc_start: 0.7709 (ttm) cc_final: 0.6930 (tpt) REVERT: Z 49 MET cc_start: 0.8605 (tpp) cc_final: 0.8361 (tpp) REVERT: a 3 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7488 (p90) REVERT: a 4 GLU cc_start: 0.8528 (mp0) cc_final: 0.7677 (mp0) REVERT: c 30 TYR cc_start: 0.8057 (t80) cc_final: 0.7759 (t80) REVERT: e 36 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: f 7 ARG cc_start: 0.7097 (mtm-85) cc_final: 0.5775 (ttm110) REVERT: g 120 GLU cc_start: 0.6814 (tm-30) cc_final: 0.6458 (tm-30) REVERT: h 25 MET cc_start: 0.8303 (ttt) cc_final: 0.7930 (ttp) REVERT: h 59 TYR cc_start: 0.7653 (t80) cc_final: 0.7215 (t80) REVERT: h 97 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6788 (mm-30) REVERT: k 25 ARG cc_start: 0.7913 (mpt180) cc_final: 0.7443 (mmt90) REVERT: l 67 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7142 (mt-10) REVERT: l 105 PHE cc_start: 0.8059 (t80) cc_final: 0.7816 (t80) REVERT: l 110 PHE cc_start: 0.8878 (t80) cc_final: 0.8450 (t80) REVERT: l 114 MET cc_start: 0.7940 (mmm) cc_final: 0.7450 (mmm) REVERT: m 4 LYS cc_start: 0.6560 (tmtt) cc_final: 0.6317 (tttt) REVERT: o 69 LYS cc_start: 0.8934 (tppt) cc_final: 0.8681 (tppt) REVERT: p 92 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7780 (ttm110) REVERT: r 55 THR cc_start: 0.8034 (p) cc_final: 0.7688 (t) REVERT: s 32 TYR cc_start: 0.3517 (t80) cc_final: 0.3244 (t80) outliers start: 199 outliers final: 169 residues processed: 1003 average time/residue: 0.5734 time to fit residues: 998.7834 Evaluate side-chains 1025 residues out of total 6892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 837 time to evaluate : 5.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 51 ILE Chi-restraints excluded: chain t residue 66 ASP Chi-restraints excluded: chain t residue 67 ILE Chi-restraints excluded: chain t residue 96 GLU Chi-restraints excluded: chain t residue 97 GLU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 77 TRP Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 452 VAL Chi-restraints excluded: chain G residue 523 PHE Chi-restraints excluded: chain G residue 541 CYS Chi-restraints excluded: chain G residue 585 VAL Chi-restraints excluded: chain G residue 687 CYS Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 285 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 361 ASN Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 281 ASP Chi-restraints excluded: chain M residue 376 MET Chi-restraints excluded: chain M residue 424 ILE Chi-restraints excluded: chain N residue 27 MET Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 299 SER Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 126 ARG Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 216 GLU Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain O residue 274 THR Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 170 ASP Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 284 VAL Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 86 VAL Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 101 GLN Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 156 ASP Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 43 SER Chi-restraints excluded: chain Y residue 48 ASP Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 61 ASN Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 36 GLU Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain g residue 105 ILE Chi-restraints excluded: chain g residue 121 ASP Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 34 ILE Chi-restraints excluded: chain h residue 41 THR Chi-restraints excluded: chain h residue 86 ASN Chi-restraints excluded: chain h residue 130 LYS Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain h residue 142 ASP Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain l residue 7 MET Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain n residue 8 TYR Chi-restraints excluded: chain n residue 102 CYS Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 32 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 72 ASP Chi-restraints excluded: chain p residue 92 ARG Chi-restraints excluded: chain p residue 135 THR Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 100 MET Chi-restraints excluded: chain s residue 39 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 766 random chunks: chunk 482 optimal weight: 0.6980 chunk 647 optimal weight: 7.9990 chunk 186 optimal weight: 0.7980 chunk 560 optimal weight: 8.9990 chunk 89 optimal weight: 0.0770 chunk 168 optimal weight: 10.0000 chunk 608 optimal weight: 0.0570 chunk 254 optimal weight: 8.9990 chunk 624 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 103 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 494 HIS ** G 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 HIS L 361 ASN ** P 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN ** Y 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 HIS ** s 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.076721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.062853 restraints weight = 175841.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.064455 restraints weight = 90977.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.065460 restraints weight = 57110.595| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.270 65830 Z= 0.609 Angle : 1.656 59.189 89189 Z= 1.064 Chirality : 0.315 6.561 9770 Planarity : 0.005 0.204 11156 Dihedral : 10.590 173.382 9553 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 2.89 % Allowed : 20.29 % Favored : 76.83 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.16 % 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: 0.83 (0.10), residues: 7749 helix: 1.36 (0.08), residues: 4243 sheet: -0.31 (0.28), residues: 358 loop : -0.39 (0.11), residues: 3148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 43 HIS 0.013 0.001 HIS g 43 PHE 0.026 0.002 PHE N 292 TYR 0.021 0.001 TYR Y 91 ARG 0.010 0.000 ARG N 295 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15302.02 seconds wall clock time: 270 minutes 18.95 seconds (16218.95 seconds total)