Starting phenix.real_space_refine on Thu Feb 15 04:40:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca3_16516/02_2024/8ca3_16516_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca3_16516/02_2024/8ca3_16516.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca3_16516/02_2024/8ca3_16516_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/8ca3_16516/02_2024/8ca3_16516_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca3_16516/02_2024/8ca3_16516_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca3_16516/02_2024/8ca3_16516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca3_16516/02_2024/8ca3_16516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca3_16516/02_2024/8ca3_16516_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca3_16516/02_2024/8ca3_16516_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= 0.422 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 30 5.49 5 S 483 5.16 5 C 41230 2.51 5 N 10513 2.21 5 O 11427 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 66": "OD1" <-> "OD2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ASP 94": "OD1" <-> "OD2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D ASP 422": "OD1" <-> "OD2" Residue "E TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F ASP 174": "OD1" <-> "OD2" Residue "F ASP 212": "OD1" <-> "OD2" Residue "F ASP 318": "OD1" <-> "OD2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G ASP 139": "OD1" <-> "OD2" Residue "G PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 403": "OD1" <-> "OD2" Residue "G PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 76": "OE1" <-> "OE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 127": "OE1" <-> "OE2" Residue "J GLU 168": "OE1" <-> "OE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 75": "OE1" <-> "OE2" Residue "L PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 297": "OD1" <-> "OD2" Residue "L ASP 447": "OD1" <-> "OD2" Residue "L ASP 449": "OD1" <-> "OD2" Residue "M ASP 251": "OD1" <-> "OD2" Residue "N TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S GLU 56": "OE1" <-> "OE2" Residue "T GLU 49": "OE1" <-> "OE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T GLU 68": "OE1" <-> "OE2" Residue "U GLU 28": "OE1" <-> "OE2" Residue "U ASP 39": "OD1" <-> "OD2" Residue "U ASP 43": "OD1" <-> "OD2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "V ASP 32": "OD1" <-> "OD2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "W ASP 26": "OD1" <-> "OD2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W GLU 44": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 111": "OE1" <-> "OE2" Residue "X ASP 156": "OD1" <-> "OD2" Residue "Y ASP 15": "OD1" <-> "OD2" Residue "Z ASP 8": "OD1" <-> "OD2" Residue "b GLU 15": "OE1" <-> "OE2" Residue "b TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 37": "OE1" <-> "OE2" Residue "d GLU 9": "OE1" <-> "OE2" Residue "d ASP 87": "OD1" <-> "OD2" Residue "e GLU 102": "OE1" <-> "OE2" Residue "f ASP 29": "OD1" <-> "OD2" Residue "f GLU 31": "OE1" <-> "OE2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "g PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 99": "OE1" <-> "OE2" Residue "g GLU 120": "OE1" <-> "OE2" Residue "h ASP 81": "OD1" <-> "OD2" Residue "i GLU 16": "OE1" <-> "OE2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "i GLU 114": "OE1" <-> "OE2" Residue "k GLU 35": "OE1" <-> "OE2" Residue "k ASP 48": "OD1" <-> "OD2" Residue "k TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 6": "OD1" <-> "OD2" Residue "l GLU 34": "OE1" <-> "OE2" Residue "l ASP 39": "OD1" <-> "OD2" Residue "l GLU 150": "OE1" <-> "OE2" Residue "m GLU 21": "OE1" <-> "OE2" Residue "m GLU 60": "OE1" <-> "OE2" Residue "m ASP 109": "OD1" <-> "OD2" Residue "n PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 146": "OD1" <-> "OD2" Residue "n GLU 175": "OE1" <-> "OE2" Residue "o GLU 32": "OE1" <-> "OE2" Residue "p ASP 72": "OD1" <-> "OD2" Residue "p GLU 118": "OE1" <-> "OE2" Residue "p GLU 129": "OE1" <-> "OE2" Residue "r GLU 61": "OE1" <-> "OE2" 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: 63712 Number of models: 1 Model: "" Number of chains: 63 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: {'PCIS': 1, 'PTRANS': 30, '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: "R" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 413 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} 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: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 787 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 12, 'TRANS': 81} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 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: "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: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 138 Unusual residues: {'3PE': 1, 'PC1': 1, 'UQ9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 34 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: 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: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 59 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 128 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 72 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: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 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: "Z" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "d" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "h" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 70 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "i" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1688 SG CYS B 129 67.965 106.788 93.830 1.00 28.77 S ATOM 1191 SG CYS B 65 67.171 100.411 91.804 1.00 38.23 S ATOM 1185 SG CYS B 64 62.185 103.825 93.682 1.00 37.54 S ATOM 1918 SG CYS B 159 65.880 105.941 88.428 1.00 33.58 S ATOM 8166 SG CYS E 103 41.565 141.580 31.293 1.00 65.71 S ATOM 8200 SG CYS E 108 38.467 140.943 29.119 1.00 53.16 S ATOM 8484 SG CYS E 144 39.389 145.357 34.133 1.00 42.44 S ATOM 8507 SG CYS E 148 36.697 145.447 32.968 1.00 71.90 S ATOM 11708 SG CYS F 362 46.958 144.965 55.868 1.00 43.49 S ATOM 11728 SG CYS F 365 45.720 142.068 50.994 1.00 24.74 S ATOM 12050 SG CYS F 405 43.803 148.157 51.099 1.00 42.67 S ATOM 11689 SG CYS F 359 50.149 146.935 50.380 1.00 23.71 S ATOM 13128 SG CYS G 114 59.755 133.304 67.814 1.00 31.30 S ATOM 13067 SG CYS G 105 59.527 127.021 66.248 1.00 33.66 S ATOM 13088 SG CYS G 108 64.632 130.696 64.735 1.00 28.19 S ATOM 13460 SG CYS G 156 59.486 143.344 61.919 1.00 19.81 S ATOM 13437 SG CYS G 153 60.626 139.264 56.803 1.00 19.00 S ATOM 13484 SG CYS G 159 64.377 144.418 58.106 1.00 36.98 S ATOM 13813 SG CYS G 203 64.238 139.421 62.265 1.00 26.08 S ATOM 12574 SG CYS G 41 53.557 147.086 63.520 1.00 29.11 S ATOM 12660 SG CYS G 52 51.795 143.487 64.442 1.00 32.68 S ATOM 12685 SG CYS G 55 48.470 147.335 67.228 1.00 44.56 S ATOM 12786 SG CYS G 69 50.496 149.623 65.896 1.00 22.90 S ATOM 21112 SG CYS I 128 65.472 113.926 68.892 1.00 61.06 S ATOM 20759 SG CYS I 82 67.243 118.924 70.508 1.00 56.63 S ATOM 20782 SG CYS I 85 68.775 117.088 73.561 1.00 56.86 S ATOM 20740 SG CYS I 79 71.990 115.948 68.574 1.00 51.65 S ATOM 20759 SG CYS I 82 67.243 118.924 70.508 1.00 56.63 S ATOM 21062 SG CYS I 121 62.497 110.965 81.619 1.00 40.28 S ATOM 21036 SG CYS I 118 68.484 108.137 82.063 1.00 33.11 S ATOM 21083 SG CYS I 124 66.059 110.911 76.630 1.00 43.80 S ATOM 20810 SG CYS I 89 67.963 114.448 81.798 1.00 33.10 S ATOM 40075 SG CYS R 59 64.386 116.990 53.021 1.00 37.50 S ATOM 40251 SG CYS R 84 66.242 119.302 55.352 1.00 28.06 S ATOM 40273 SG CYS R 87 67.448 115.985 54.847 1.00 47.48 S Time building chain proxies: 24.32, per 1000 atoms: 0.38 Number of scatterers: 63712 At special positions: 0 Unit cell: (141.96, 196.04, 297.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 483 16.00 P 30 15.00 O 11427 8.00 N 10513 7.00 C 41230 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=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.01 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " 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=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 365 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 359 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 405 " 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="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " 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="FE3 SF4 I 202 " - pdb=" SG CYS I 124 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 118 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 89 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 121 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14694 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 340 helices and 23 sheets defined 55.2% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.46 Creating SS restraints... 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 removed outlier: 3.738A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.651A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 108 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 16 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.778A pdb=" N VAL C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 4.900A 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 125 through 138 removed outlier: 3.880A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE C 138 " --> pdb=" O TRP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 8 through 14 removed outlier: 4.027A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.715A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 106 Proline residue: D 101 - end of helix removed outlier: 3.963A 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: 3.859A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.693A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.723A 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: 4.075A 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 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 293 through 317 removed outlier: 3.554A pdb=" N ARG D 305 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) 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: 3.642A pdb=" N ALA D 400 " --> pdb=" O PHE D 396 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 3.662A pdb=" N GLY D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.664A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.331A 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 73 Processing helix chain 'E' and resid 77 through 86 Processing helix chain 'E' and resid 106 through 110 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: 4.380A 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 184 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: 3.621A pdb=" N GLU F 313 " --> pdb=" O LYS F 309 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 309 through 314' 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: 4.305A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 400 removed outlier: 3.770A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 435 Proline residue: F 414 - end of helix removed outlier: 3.693A pdb=" N ARG F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) 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 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' 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 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 196 through 202 Processing helix chain 'G' and resid 265 through 275 removed outlier: 3.546A pdb=" N ALA G 270 " --> pdb=" O LYS G 266 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 removed outlier: 3.709A pdb=" N ARG G 302 " --> pdb=" O ASP G 298 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL G 303 " --> pdb=" O ALA G 299 " (cutoff:3.500A) 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 355 through 357 No H-bonds generated for 'chain 'G' and resid 355 through 357' 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: 4.039A pdb=" N VAL G 371 " --> pdb=" O THR G 367 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU G 372 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU G 373 " --> pdb=" O ALA G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 367 through 373' Processing helix chain 'G' and resid 389 through 400 Processing helix chain 'G' and resid 426 through 434 removed outlier: 3.910A pdb=" N LEU G 429 " --> pdb=" O PRO G 426 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN G 430 " --> pdb=" O LYS G 427 " (cutoff:3.500A) 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 removed outlier: 3.881A pdb=" N VAL G 479 " --> pdb=" O GLN G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 505 removed outlier: 4.316A pdb=" N VAL G 500 " --> pdb=" O ALA G 497 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 554 through 556 No H-bonds generated for 'chain 'G' and resid 554 through 556' Processing helix chain 'G' and resid 596 through 606 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 628 through 631 removed outlier: 3.646A pdb=" N VAL G 631 " --> pdb=" O PRO G 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 628 through 631' Processing helix chain 'G' and resid 642 through 651 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: 3.803A 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: 4.214A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 122 removed outlier: 3.771A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 4.249A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 removed outlier: 3.535A 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: 3.627A pdb=" N TYR H 228 " --> pdb=" O PHE H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 276 Processing helix chain 'H' and resid 282 through 291 removed outlier: 4.065A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 311 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: 3.716A 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 147 through 149 No H-bonds generated for 'chain 'I' and resid 147 through 149' Processing helix chain 'I' and resid 153 through 162 Processing helix chain 'I' and resid 164 through 177 removed outlier: 5.112A pdb=" N LEU I 176 " --> pdb=" O GLN I 172 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 50 through 72 Processing helix chain 'J' and resid 86 through 109 removed outlier: 3.746A pdb=" N CYS J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 145 removed outlier: 4.485A pdb=" N MET J 144 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N TYR J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 170 removed outlier: 3.636A pdb=" N ILE J 163 " --> pdb=" O LEU J 159 " (cutoff:3.500A) removed outlier: 3.989A 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: 3.553A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (cutoff:3.500A) 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: 3.909A pdb=" N PHE L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix removed outlier: 3.750A pdb=" N MET L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 32 through 57 removed outlier: 4.107A 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: 3.580A pdb=" N SER L 91 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 3.895A 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 removed outlier: 3.579A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 192 removed outlier: 3.912A pdb=" N GLY L 178 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 removed outlier: 4.223A pdb=" N PHE L 203 " --> pdb=" O GLN L 199 " (cutoff:3.500A) removed outlier: 4.516A 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: 4.331A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 3.596A pdb=" N HIS L 248 " --> pdb=" O SER L 244 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 262 removed outlier: 4.270A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.606A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) 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: 4.092A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.021A 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 389 through 400 removed outlier: 5.102A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.837A 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: 5.831A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N PHE L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 508 removed outlier: 5.054A pdb=" N ALA L 490 " --> pdb=" O LEU L 486 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU L 491 " --> pdb=" O LYS L 487 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 removed outlier: 3.627A pdb=" N PHE L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 4.900A pdb=" N HIS L 534 " --> pdb=" O SER L 531 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.506A pdb=" N LEU L 542 " --> pdb=" O MET L 539 " (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: 4.055A 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: 3.816A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 81 Proline residue: M 64 - end of helix removed outlier: 3.659A 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: 4.758A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 171 removed outlier: 4.055A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE M 158 " --> pdb=" O ILE M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.561A pdb=" N VAL M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 181 Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.738A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.991A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 234 Processing helix chain 'M' and resid 237 through 249 removed outlier: 4.399A pdb=" N ILE M 248 " --> pdb=" O ILE M 244 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 Processing helix chain 'M' and resid 259 through 277 removed outlier: 3.894A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE M 275 " --> pdb=" O MET M 271 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.768A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.508A pdb=" N MET M 310 " --> pdb=" O PRO M 306 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER M 324 " --> pdb=" O GLY M 320 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN M 333 " --> pdb=" O LEU M 329 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) 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 392 through 414 removed outlier: 3.518A pdb=" N ILE M 411 " --> pdb=" O SER M 407 " (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 removed outlier: 3.509A pdb=" N THR N 12 " --> pdb=" O ILE N 8 " (cutoff:3.500A) Proline residue: N 17 - end of helix Processing helix chain 'N' and resid 26 through 44 removed outlier: 3.726A pdb=" N ILE N 41 " --> pdb=" O LEU N 37 " (cutoff:3.500A) 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: 4.087A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 148 removed outlier: 3.929A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.620A pdb=" N ILE N 141 " --> pdb=" O ALA N 137 " (cutoff:3.500A) removed outlier: 3.561A 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: 3.717A pdb=" N LEU N 170 " --> pdb=" O ALA N 166 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 193 removed outlier: 3.799A pdb=" N ILE N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 Proline residue: N 214 - end of helix removed outlier: 4.130A pdb=" N ASN N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 236 removed outlier: 3.705A pdb=" N LEU N 232 " --> pdb=" O ASN N 228 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP N 234 " --> pdb=" O ILE N 230 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 252 removed outlier: 4.212A pdb=" N THR N 242 " --> pdb=" O ALA N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 276 through 300 removed outlier: 4.461A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN N 289 " --> pdb=" O MET N 285 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU N 290 " --> pdb=" O ALA N 286 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 316 Processing helix chain 'N' and resid 324 through 334 removed outlier: 3.643A pdb=" N THR N 328 " --> pdb=" O LEU N 324 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 343 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 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 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 141 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: 3.670A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) removed outlier: 4.092A 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 removed outlier: 3.669A pdb=" N TYR O 240 " --> pdb=" O GLU O 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 247 through 249 No H-bonds generated for 'chain 'O' and resid 247 through 249' Processing helix chain 'O' and resid 253 through 264 removed outlier: 4.581A pdb=" N TYR O 258 " --> pdb=" O TRP O 254 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 274 removed outlier: 4.841A pdb=" N TYR O 272 " --> pdb=" O GLU O 268 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N THR O 273 " --> pdb=" O VAL O 269 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR O 274 " --> pdb=" O LEU O 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 297 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 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' 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 31 through 41 Processing helix chain 'P' and resid 53 through 62 removed outlier: 3.575A pdb=" N MET P 57 " --> pdb=" O TYR P 54 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N HIS P 58 " --> pdb=" O ASP P 55 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU P 61 " --> pdb=" O HIS P 58 " (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 188 removed outlier: 3.702A pdb=" N TYR P 185 " --> pdb=" O HIS P 181 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE P 188 " --> pdb=" O ASN P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 197 Processing helix chain 'P' and resid 207 through 217 Processing helix chain 'P' and resid 221 through 223 No H-bonds generated for 'chain 'P' and resid 221 through 223' Processing helix chain 'P' and resid 238 through 248 Processing helix chain 'P' and resid 260 through 272 removed outlier: 3.616A pdb=" N LEU P 272 " --> pdb=" O LYS P 268 " (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 313 No H-bonds generated for 'chain 'P' and resid 310 through 313' Processing helix chain 'P' and resid 315 through 321 removed outlier: 6.013A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 324 through 326 No H-bonds generated for 'chain 'P' and resid 324 through 326' Processing helix chain 'P' and resid 331 through 333 No H-bonds generated for 'chain 'P' and resid 331 through 333' Processing helix chain 'R' and resid 41 through 45 removed outlier: 3.746A pdb=" N ALA R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 41 through 45' Processing helix chain 'S' and resid 27 through 46 removed outlier: 4.534A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR S 40 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL S 41 " --> pdb=" O GLN S 38 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA S 46 " --> pdb=" O LEU S 43 " (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 44 through 58 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.671A 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 20 Processing helix chain 'U' and resid 44 through 58 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.177A pdb=" N LYS U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'V' and resid 19 through 36 removed outlier: 4.058A 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 removed outlier: 3.758A pdb=" N LYS V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) 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: 3.977A pdb=" N ASN W 72 " --> pdb=" O MET W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 96 Processing helix chain 'W' and resid 102 through 108 removed outlier: 3.790A pdb=" N ARG W 107 " --> pdb=" O THR W 103 " (cutoff:3.500A) removed outlier: 4.694A 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 removed outlier: 3.680A pdb=" N ALA X 33 " --> pdb=" O HIS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 52 through 54 No H-bonds generated for 'chain 'X' and resid 52 through 54' Processing helix chain 'X' and resid 56 through 76 Processing helix chain 'X' and resid 78 through 90 removed outlier: 3.656A pdb=" N TYR X 90 " --> pdb=" O THR X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 98 No H-bonds generated for 'chain 'X' and resid 96 through 98' Processing helix chain 'X' and resid 100 through 113 Processing helix chain 'Y' and resid 4 through 11 removed outlier: 3.540A pdb=" N SER Y 9 " --> pdb=" O PHE Y 6 " (cutoff:3.500A) 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 removed outlier: 3.556A pdb=" N ILE Z 95 " --> pdb=" O GLU Z 91 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 124 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: 4.131A pdb=" N ALA a 10 " --> pdb=" O PRO a 7 " (cutoff:3.500A) removed outlier: 3.650A 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: 4.495A pdb=" N SER b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET b 43 " --> pdb=" O LYS b 39 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN b 45 " --> pdb=" O ALA b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 81 No H-bonds generated for 'chain 'b' and resid 78 through 81' Processing helix chain 'c' and resid 14 through 46 Processing helix chain 'd' and resid 2 through 4 No H-bonds generated for 'chain 'd' and resid 2 through 4' Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 49 Processing helix chain 'd' and resid 58 through 96 Processing helix chain 'd' and resid 98 through 100 No H-bonds generated for 'chain 'd' and resid 98 through 100' 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 50 through 54 removed outlier: 4.265A pdb=" N GLU e 54 " --> pdb=" O ALA e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 through 88 Processing helix chain 'e' and resid 95 through 98 No H-bonds generated for 'chain 'e' and resid 95 through 98' Processing helix chain 'f' and resid 6 through 32 removed outlier: 5.635A pdb=" N VAL f 11 " --> pdb=" O ARG f 7 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N HIS f 12 " --> pdb=" O GLU f 8 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE f 13 " --> pdb=" O HIS f 9 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU f 14 " --> pdb=" O TRP f 10 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL f 15 " --> pdb=" O VAL f 11 " (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 Processing helix chain 'g' and resid 81 through 101 removed outlier: 5.719A pdb=" N GLU g 85 " --> pdb=" O ARG g 82 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP g 86 " --> pdb=" O MET g 83 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA g 87 " --> pdb=" O GLN g 84 " (cutoff:3.500A) Processing helix chain 'h' and resid 16 through 45 removed outlier: 4.157A 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 63 through 66 Processing helix chain 'h' and resid 70 through 79 Processing helix chain 'h' and resid 83 through 117 removed outlier: 3.760A pdb=" N ALA h 92 " --> pdb=" O GLU h 88 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN h 108 " --> pdb=" O ARG h 104 " (cutoff:3.500A) Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 24 Processing helix chain 'i' and resid 68 through 73 Processing helix chain 'i' and resid 76 through 88 Processing helix chain 'j' and resid 19 through 42 Processing helix chain 'j' and resid 44 through 48 Processing helix chain 'j' and resid 61 through 64 No H-bonds generated for 'chain 'j' and resid 61 through 64' Processing helix chain 'k' and resid 24 through 26 No H-bonds generated for 'chain 'k' and resid 24 through 26' Processing helix chain 'k' and resid 33 through 43 Processing helix chain 'k' and resid 51 through 58 removed outlier: 4.879A pdb=" N TRP k 56 " --> pdb=" O ARG k 52 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG k 57 " --> pdb=" O ASN k 53 " (cutoff:3.500A) removed outlier: 4.091A 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 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 19 through 21 No H-bonds generated for 'chain 'm' and resid 19 through 21' Processing helix chain 'm' and resid 26 through 51 Processing helix chain 'm' and resid 62 through 72 Processing helix chain 'm' and resid 83 through 117 Proline residue: m 96 - end of helix Processing helix chain 'n' and resid 11 through 29 Processing helix chain 'n' and resid 33 through 50 removed outlier: 4.031A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 73 removed outlier: 3.584A pdb=" N THR n 60 " --> pdb=" O MET n 56 " (cutoff:3.500A) Processing helix chain 'n' and resid 92 through 94 No H-bonds generated for 'chain 'n' and resid 92 through 94' Processing helix chain 'n' and resid 100 through 105 Processing helix chain 'n' and resid 108 through 113 removed outlier: 3.917A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) Processing helix chain 'n' and resid 115 through 142 removed outlier: 4.658A pdb=" N ASP n 133 " --> pdb=" O MET n 129 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 9 Processing helix chain 'o' and resid 12 through 14 No H-bonds generated for 'chain 'o' and resid 12 through 14' Processing helix chain 'o' and resid 18 through 20 No H-bonds generated for 'chain 'o' and resid 18 through 20' Processing helix chain 'o' and resid 42 through 48 Processing helix chain 'o' and resid 59 through 72 removed outlier: 3.574A pdb=" N ARG o 64 " --> pdb=" O HIS o 60 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 110 Processing helix chain 'p' and resid 28 through 56 removed outlier: 4.022A pdb=" N ASP p 41 " --> pdb=" O ASP p 37 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP p 42 " --> pdb=" O LEU p 38 " (cutoff:3.500A) Proline residue: p 43 - end of helix Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 123 removed outlier: 6.070A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLN p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 142 Processing helix chain 'p' and resid 151 through 170 Processing helix chain 'r' and resid 53 through 56 No H-bonds generated for 'chain 'r' and resid 53 through 56' 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 38 No H-bonds generated for 'chain 's' and resid 36 through 38' Processing helix chain 's' and resid 44 through 54 removed outlier: 3.995A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.634A pdb=" N TYR B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL B 98 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B 154 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 74 through 82 removed outlier: 6.473A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 48 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LYS C 108 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE C 50 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N TYR C 110 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ILE C 52 " --> pdb=" O TYR C 110 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= D, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.388A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 361 through 369 Processing sheet with id= F, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.491A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N MET E 153 " --> pdb=" O CYS E 103 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 220 through 224 removed outlier: 7.116A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'F' and resid 266 through 271 removed outlier: 5.869A pdb=" N VAL F 334 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 8 through 13 Processing sheet with id= J, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= K, first strand: chain 'G' and resid 223 through 228 removed outlier: 3.504A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 315 through 319 removed outlier: 6.262A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 490 through 493 removed outlier: 6.139A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASP G 420 " --> pdb=" O LEU G 408 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= O, first strand: chain 'I' and resid 67 through 69 Processing sheet with id= P, first strand: chain 'I' and resid 94 through 100 removed outlier: 5.946A pdb=" N GLU I 99 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR I 108 " --> pdb=" O GLU I 99 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.730A pdb=" N MET L 78 " --> pdb=" O THR L 65 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'O' and resid 219 through 224 removed outlier: 6.386A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N TYR O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'P' and resid 164 through 166 removed outlier: 3.502A pdb=" N VAL P 132 " --> pdb=" O ASN P 93 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'P' and resid 191 through 193 Processing sheet with id= U, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= V, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= W, first strand: chain 'S' and resid 51 through 54 removed outlier: 6.503A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS S 63 " --> pdb=" O VAL S 20 " (cutoff:3.500A) 2833 hydrogen bonds defined for protein. 7755 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: 18.62 Time building geometry restraints manager: 21.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 26252 1.40 - 1.63: 38153 1.63 - 1.85: 841 1.85 - 2.08: 0 2.08 - 2.30: 80 Bond restraints: 65326 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.390 1.665 -0.275 2.00e-02 2.50e+03 1.90e+02 bond pdb=" C5A FMN F 502 " pdb=" C9A FMN F 502 " ideal model delta sigma weight residual 1.390 1.579 -0.189 2.00e-02 2.50e+03 8.95e+01 bond pdb=" C5A FMN F 502 " pdb=" C6 FMN F 502 " ideal model delta sigma weight residual 1.390 1.577 -0.187 2.00e-02 2.50e+03 8.72e+01 bond pdb=" C2 FMN F 502 " pdb=" O2 FMN F 502 " ideal model delta sigma weight residual 1.230 1.398 -0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" C6 GTP O 401 " pdb=" O6 GTP O 401 " ideal model delta sigma weight residual 1.230 1.396 -0.166 2.00e-02 2.50e+03 6.90e+01 ... (remaining 65321 not shown) Histogram of bond angle deviations from ideal: 73.03 - 87.47: 76 87.47 - 101.91: 284 101.91 - 116.35: 43664 116.35 - 130.78: 44139 130.78 - 145.22: 343 Bond angle restraints: 88506 Sorted by residual: angle pdb=" C6 FMN F 502 " pdb=" C5A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 120.00 145.22 -25.22 3.00e+00 1.11e-01 7.07e+01 angle pdb=" C11 CDL d 201 " pdb=" CA5 CDL d 201 " pdb=" OA6 CDL d 201 " ideal model delta sigma weight residual 111.33 121.69 -10.36 1.32e+00 5.72e-01 6.14e+01 angle pdb=" C51 CDL M 501 " pdb=" CB5 CDL M 501 " pdb=" OB6 CDL M 501 " ideal model delta sigma weight residual 111.33 120.90 -9.57 1.32e+00 5.72e-01 5.24e+01 angle pdb=" C11 CDL L 702 " pdb=" CA5 CDL L 702 " pdb=" OA6 CDL L 702 " ideal model delta sigma weight residual 111.33 120.63 -9.30 1.32e+00 5.72e-01 4.94e+01 angle pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 120.00 140.02 -20.02 3.00e+00 1.11e-01 4.45e+01 ... (remaining 88501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 38371 35.08 - 70.15: 1071 70.15 - 105.23: 63 105.23 - 140.31: 16 140.31 - 175.38: 3 Dihedral angle restraints: 39524 sinusoidal: 16753 harmonic: 22771 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 82.21 175.38 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O3A GTP O 401 " pdb=" O3B GTP O 401 " pdb=" PB GTP O 401 " pdb=" PG GTP O 401 " ideal model delta sinusoidal sigma weight residual -56.21 83.97 -140.18 1 2.00e+01 2.50e-03 4.24e+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 -27.52 132.11 1 2.00e+01 2.50e-03 4.01e+01 ... (remaining 39521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.282: 9683 4.282 - 8.564: 0 8.564 - 12.846: 0 12.846 - 17.128: 0 17.128 - 21.410: 24 Chirality restraints: 9707 Sorted by residual: chirality pdb="FE2 SF4 B 201 " pdb=" S1 SF4 B 201 " pdb=" S3 SF4 B 201 " pdb=" S4 SF4 B 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.86 21.41 2.00e-01 2.50e+01 1.15e+04 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 10.71 -21.27 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE4 SF4 F 501 " pdb=" S1 SF4 F 501 " pdb=" S2 SF4 F 501 " pdb=" S3 SF4 F 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.71 21.26 2.00e-01 2.50e+01 1.13e+04 ... (remaining 9704 not shown) Planarity restraints: 11070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG m 29 " -0.350 9.50e-02 1.11e+02 1.57e-01 1.67e+01 pdb=" NE ARG m 29 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG m 29 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG m 29 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG m 29 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 662 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO G 663 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO G 663 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 663 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 59 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO K 60 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO K 60 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO K 60 " 0.029 5.00e-02 4.00e+02 ... (remaining 11067 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 239 2.43 - 3.05: 43405 3.05 - 3.66: 96474 3.66 - 4.28: 154547 4.28 - 4.90: 256554 Nonbonded interactions: 551219 Sorted by model distance: nonbonded pdb=" O PHE p 131 " pdb=" OG1 THR p 135 " model vdw 1.812 2.440 nonbonded pdb=" O VAL P 215 " pdb=" OG1 THR P 218 " model vdw 1.927 2.440 nonbonded pdb=" OG SER O 22 " pdb=" O GLY O 119 " model vdw 1.944 2.440 nonbonded pdb=" OG SER F 303 " pdb=" OH TYR F 354 " model vdw 1.944 2.440 nonbonded pdb=" OG SER H 110 " pdb=" OE2 GLU H 143 " model vdw 2.007 2.440 ... (remaining 551214 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 21.680 Check model and map are aligned: 0.740 Set scattering table: 0.460 Process input model: 140.870 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 0.275 65326 Z= 0.378 Angle : 0.751 25.222 88506 Z= 0.362 Chirality : 1.055 21.410 9707 Planarity : 0.004 0.157 11070 Dihedral : 15.808 175.385 24806 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.85 % Favored : 95.12 % Rotamer: Outliers : 0.06 % Allowed : 10.82 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % 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: 0.98 (0.10), residues: 7698 helix: 1.67 (0.08), residues: 4300 sheet: -1.06 (0.25), residues: 372 loop : -0.56 (0.12), residues: 3026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 254 HIS 0.005 0.001 HIS D 27 PHE 0.023 0.001 PHE N 292 TYR 0.021 0.001 TYR H 282 ARG 0.022 0.000 ARG m 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1072 time to evaluate : 5.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8561 (tp40) cc_final: 0.7984 (tp-100) REVERT: A 85 SER cc_start: 0.8933 (m) cc_final: 0.8548 (p) REVERT: E 15 ASN cc_start: 0.8391 (t0) cc_final: 0.7758 (t0) REVERT: E 56 ARG cc_start: 0.7485 (mtt90) cc_final: 0.7244 (mtt-85) REVERT: E 67 ASN cc_start: 0.8143 (m-40) cc_final: 0.7429 (m110) REVERT: F 79 TRP cc_start: 0.8886 (m-10) cc_final: 0.8583 (m-10) REVERT: F 317 MET cc_start: 0.8167 (mmm) cc_final: 0.7746 (mmm) REVERT: F 430 MET cc_start: 0.7957 (mtt) cc_final: 0.7705 (mtt) REVERT: G 229 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8123 (t0) REVERT: G 460 ARG cc_start: 0.5929 (mtm110) cc_final: 0.5083 (ttp80) REVERT: H 277 TYR cc_start: 0.8403 (m-80) cc_final: 0.7929 (m-80) REVERT: H 318 MET cc_start: 0.7885 (tmm) cc_final: 0.7325 (tmm) REVERT: J 69 TYR cc_start: 0.7708 (m-80) cc_final: 0.7384 (m-10) REVERT: J 78 TYR cc_start: 0.7515 (m-80) cc_final: 0.7016 (m-10) REVERT: J 130 ASP cc_start: 0.8270 (m-30) cc_final: 0.7838 (m-30) REVERT: L 116 ARG cc_start: 0.7982 (ttm110) cc_final: 0.7770 (ttm110) REVERT: L 277 MET cc_start: 0.8593 (mtm) cc_final: 0.8369 (mtp) REVERT: M 102 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8336 (tp) REVERT: M 376 MET cc_start: 0.7931 (mmm) cc_final: 0.7497 (mmm) REVERT: M 458 THR cc_start: 0.8772 (p) cc_final: 0.8560 (p) REVERT: N 284 MET cc_start: 0.8289 (tpt) cc_final: 0.7984 (tpt) REVERT: O 65 ASP cc_start: 0.7338 (t0) cc_final: 0.7016 (t0) REVERT: O 261 MET cc_start: 0.8330 (mmm) cc_final: 0.7905 (mmm) REVERT: P 41 MET cc_start: 0.7947 (mtm) cc_final: 0.7670 (mmm) REVERT: R 81 THR cc_start: 0.8826 (p) cc_final: 0.8569 (p) REVERT: R 92 LYS cc_start: 0.8442 (ttmm) cc_final: 0.7579 (tttp) REVERT: S 30 GLN cc_start: 0.6727 (tp40) cc_final: 0.6511 (tp40) REVERT: S 81 LEU cc_start: 0.6650 (mp) cc_final: 0.6416 (mp) REVERT: T 47 GLN cc_start: 0.7394 (tm-30) cc_final: 0.6568 (tm-30) REVERT: T 69 LYS cc_start: 0.7806 (mtmm) cc_final: 0.7531 (ptpp) REVERT: T 71 MET cc_start: 0.6666 (mmm) cc_final: 0.6174 (mtt) REVERT: U 49 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7723 (mt-10) REVERT: W 126 MET cc_start: 0.5851 (ptm) cc_final: 0.5641 (ptt) REVERT: Z 21 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7666 (mtmt) REVERT: a 43 TYR cc_start: 0.8516 (t80) cc_final: 0.8157 (t80) REVERT: b 51 ASN cc_start: 0.8631 (m-40) cc_final: 0.8407 (m-40) REVERT: b 81 LYS cc_start: 0.8429 (ttmt) cc_final: 0.7953 (tttm) REVERT: c 11 LYS cc_start: 0.8785 (mtmm) cc_final: 0.8578 (mtmm) REVERT: d 3 ASN cc_start: 0.7710 (m110) cc_final: 0.7338 (m-40) REVERT: e 75 MET cc_start: 0.8671 (mmm) cc_final: 0.8385 (mmm) REVERT: f 28 LYS cc_start: 0.7014 (mmpt) cc_final: 0.6736 (mmtp) REVERT: g 112 ASP cc_start: 0.8973 (t70) cc_final: 0.8641 (t0) REVERT: h 41 THR cc_start: 0.8795 (m) cc_final: 0.8352 (t) REVERT: h 106 LYS cc_start: 0.8206 (mttm) cc_final: 0.7904 (mttp) REVERT: i 111 GLU cc_start: 0.7865 (mp0) cc_final: 0.7630 (mp0) REVERT: l 7 MET cc_start: 0.8576 (mtt) cc_final: 0.8145 (mtt) REVERT: l 17 GLU cc_start: 0.7882 (mp0) cc_final: 0.7513 (mp0) REVERT: l 100 MET cc_start: 0.8395 (mtm) cc_final: 0.8020 (mtm) REVERT: l 102 LYS cc_start: 0.8221 (mttm) cc_final: 0.7773 (mtpt) REVERT: m 4 LYS cc_start: 0.7833 (ttmt) cc_final: 0.7434 (ttmm) REVERT: m 18 ASP cc_start: 0.8457 (t0) cc_final: 0.8247 (t0) REVERT: m 21 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7290 (mm-30) REVERT: m 52 ASP cc_start: 0.8873 (t70) cc_final: 0.8593 (t0) REVERT: m 112 GLU cc_start: 0.8300 (tp30) cc_final: 0.8082 (tp30) REVERT: o 17 ASP cc_start: 0.8466 (t0) cc_final: 0.8174 (t0) REVERT: p 38 LEU cc_start: 0.8183 (mm) cc_final: 0.7926 (tp) REVERT: s 35 LEU cc_start: 0.7213 (mm) cc_final: 0.6984 (mm) outliers start: 4 outliers final: 1 residues processed: 1076 average time/residue: 0.6108 time to fit residues: 1102.0150 Evaluate side-chains 978 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 975 time to evaluate : 5.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain Y residue 3 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 642 optimal weight: 5.9990 chunk 576 optimal weight: 4.9990 chunk 320 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 389 optimal weight: 0.8980 chunk 308 optimal weight: 0.8980 chunk 596 optimal weight: 0.8980 chunk 230 optimal weight: 3.9990 chunk 362 optimal weight: 0.0270 chunk 443 optimal weight: 0.9990 chunk 691 optimal weight: 7.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 HIS ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN E 91 ASN F 113 HIS F 264 HIS G 308 GLN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 494 HIS G 665 GLN H 5 ASN H 138 GLN H 235 ASN K 7 ASN K 25 HIS M 51 ASN M 82 ASN M 92 GLN M 304 GLN M 427 GLN N 63 GLN O 89 ASN O 141 GLN O 288 GLN P 67 GLN P 181 HIS P 184 ASN P 240 HIS S 92 ASN W 60 GLN X 72 GLN b 10 ASN b 70 GLN b 82 ASN g 84 GLN g 101 ASN g 117 GLN j 21 GLN j 58 GLN k 38 GLN l 71 ASN o 109 GLN s 59 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.267 65326 Z= 0.547 Angle : 1.593 51.253 88506 Z= 1.035 Chirality : 0.317 6.478 9707 Planarity : 0.004 0.066 11070 Dihedral : 11.575 173.380 9489 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.59 % Favored : 97.39 % Rotamer: Outliers : 1.59 % Allowed : 11.00 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % 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: 1.18 (0.10), residues: 7698 helix: 1.77 (0.08), residues: 4265 sheet: -0.73 (0.26), residues: 354 loop : -0.39 (0.11), residues: 3079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 254 HIS 0.007 0.001 HIS R 68 PHE 0.023 0.001 PHE N 292 TYR 0.020 0.001 TYR s 32 ARG 0.006 0.000 ARG s 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1055 time to evaluate : 5.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8518 (tp40) cc_final: 0.7921 (tp-100) REVERT: A 85 SER cc_start: 0.8900 (m) cc_final: 0.8558 (p) REVERT: B 79 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7769 (ptm) REVERT: B 135 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7081 (t80) REVERT: C 113 GLU cc_start: 0.6444 (mp0) cc_final: 0.6198 (mp0) REVERT: D 105 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.6050 (mtt-85) REVERT: E 15 ASN cc_start: 0.8444 (t0) cc_final: 0.7765 (t0) REVERT: E 112 ASP cc_start: 0.7898 (t0) cc_final: 0.7649 (t0) REVERT: E 163 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7613 (t70) REVERT: E 187 ARG cc_start: 0.7217 (mtt90) cc_final: 0.6981 (mtt90) REVERT: F 43 TYR cc_start: 0.7828 (t80) cc_final: 0.7530 (t80) REVERT: F 212 ASP cc_start: 0.7816 (t0) cc_final: 0.7446 (t0) REVERT: F 409 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8455 (m-30) REVERT: F 430 MET cc_start: 0.7635 (mtt) cc_final: 0.7408 (mtt) REVERT: G 229 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8018 (t0) REVERT: G 418 ARG cc_start: 0.7058 (tpp-160) cc_final: 0.6591 (mtm110) REVERT: G 473 MET cc_start: 0.8012 (ttp) cc_final: 0.7650 (tmm) REVERT: G 491 ASN cc_start: 0.6968 (OUTLIER) cc_final: 0.6460 (p0) REVERT: H 68 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7559 (mmm) REVERT: H 181 MET cc_start: 0.8929 (mtm) cc_final: 0.8649 (mtm) REVERT: H 277 TYR cc_start: 0.8504 (m-80) cc_final: 0.8070 (m-80) REVERT: J 78 TYR cc_start: 0.7450 (m-80) cc_final: 0.6795 (m-10) REVERT: J 122 ASP cc_start: 0.7063 (m-30) cc_final: 0.6844 (m-30) REVERT: J 130 ASP cc_start: 0.8417 (m-30) cc_final: 0.7980 (m-30) REVERT: J 152 MET cc_start: 0.8580 (ttm) cc_final: 0.8331 (tpp) REVERT: K 23 ARG cc_start: 0.8162 (ttt-90) cc_final: 0.7787 (ttt90) REVERT: L 100 ILE cc_start: 0.8391 (mt) cc_final: 0.8177 (mm) REVERT: L 140 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8467 (tt) REVERT: L 352 ASP cc_start: 0.6868 (t0) cc_final: 0.6498 (t0) REVERT: M 168 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: M 310 MET cc_start: 0.8051 (ttp) cc_final: 0.7580 (ttp) REVERT: M 376 MET cc_start: 0.7756 (mmm) cc_final: 0.7189 (mmm) REVERT: N 126 MET cc_start: 0.7850 (mmm) cc_final: 0.7640 (mmp) REVERT: N 284 MET cc_start: 0.8415 (tpt) cc_final: 0.8208 (mmm) REVERT: O 65 ASP cc_start: 0.7463 (t0) cc_final: 0.7149 (t0) REVERT: O 261 MET cc_start: 0.8408 (mmm) cc_final: 0.8167 (mmp) REVERT: P 211 SER cc_start: 0.8628 (t) cc_final: 0.8386 (p) REVERT: R 81 THR cc_start: 0.8777 (p) cc_final: 0.8416 (p) REVERT: R 92 LYS cc_start: 0.8433 (ttmm) cc_final: 0.7586 (tttp) REVERT: S 55 ARG cc_start: 0.7513 (mmt180) cc_final: 0.6955 (mmt180) REVERT: T 47 GLN cc_start: 0.7015 (tm-30) cc_final: 0.6395 (tm-30) REVERT: T 69 LYS cc_start: 0.7654 (mtmm) cc_final: 0.7423 (ptpp) REVERT: V 109 ASN cc_start: 0.8257 (m-40) cc_final: 0.7971 (m110) REVERT: W 101 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7295 (mm-40) REVERT: W 126 MET cc_start: 0.6004 (ptm) cc_final: 0.5568 (ptt) REVERT: Z 9 MET cc_start: 0.8299 (mmm) cc_final: 0.7720 (mmm) REVERT: Z 99 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7960 (m-30) REVERT: a 43 TYR cc_start: 0.8583 (t80) cc_final: 0.8274 (t80) REVERT: b 81 LYS cc_start: 0.8380 (ttmt) cc_final: 0.7900 (tttm) REVERT: d 3 ASN cc_start: 0.7637 (m110) cc_final: 0.7234 (m-40) REVERT: e 39 TRP cc_start: 0.7948 (t60) cc_final: 0.7737 (t60) REVERT: e 75 MET cc_start: 0.8778 (mmm) cc_final: 0.8353 (mmm) REVERT: f 28 LYS cc_start: 0.7045 (mmpt) cc_final: 0.6677 (mmmm) REVERT: g 84 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7951 (mm-40) REVERT: g 112 ASP cc_start: 0.8999 (t70) cc_final: 0.8607 (t70) REVERT: h 106 LYS cc_start: 0.8257 (mttm) cc_final: 0.7933 (mttp) REVERT: h 143 ASN cc_start: 0.7710 (m110) cc_final: 0.7462 (m-40) REVERT: i 111 GLU cc_start: 0.7933 (mp0) cc_final: 0.7690 (mp0) REVERT: l 7 MET cc_start: 0.8143 (mtt) cc_final: 0.7869 (mtt) REVERT: l 17 GLU cc_start: 0.7894 (mp0) cc_final: 0.7660 (mp0) REVERT: l 100 MET cc_start: 0.8428 (mtm) cc_final: 0.8034 (mtm) REVERT: l 102 LYS cc_start: 0.8177 (mttm) cc_final: 0.7728 (mtpt) REVERT: m 4 LYS cc_start: 0.7663 (ttmt) cc_final: 0.6531 (ttpp) REVERT: m 21 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7315 (mm-30) REVERT: n 54 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8228 (mmtt) REVERT: n 65 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7791 (mt-10) REVERT: o 17 ASP cc_start: 0.8314 (t0) cc_final: 0.7920 (t0) REVERT: o 83 GLN cc_start: 0.8318 (tt0) cc_final: 0.8009 (tt0) REVERT: p 38 LEU cc_start: 0.8186 (mm) cc_final: 0.7916 (tp) REVERT: p 144 ASP cc_start: 0.8598 (m-30) cc_final: 0.8203 (m-30) REVERT: p 170 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6904 (mtt180) REVERT: s 32 TYR cc_start: 0.7036 (t80) cc_final: 0.6712 (t80) outliers start: 108 outliers final: 57 residues processed: 1119 average time/residue: 0.6658 time to fit residues: 1270.0911 Evaluate side-chains 1043 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 974 time to evaluate : 5.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 409 ASP Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 491 ASN Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 109 TYR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain P residue 341 ASN Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 52 ILE Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 68 GLU Chi-restraints excluded: chain U residue 87 TYR Chi-restraints excluded: chain W residue 119 ASP Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 86 ASP Chi-restraints excluded: chain Z residue 7 GLN Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain Z residue 143 THR Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain g residue 99 GLU Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 142 ASP Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain l residue 152 VAL Chi-restraints excluded: chain o residue 46 MET Chi-restraints excluded: chain o residue 85 ASP Chi-restraints excluded: chain p residue 25 LEU Chi-restraints excluded: chain p residue 170 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 384 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 chunk 575 optimal weight: 0.9980 chunk 470 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 692 optimal weight: 5.9990 chunk 747 optimal weight: 6.9990 chunk 616 optimal weight: 4.9990 chunk 686 optimal weight: 6.9990 chunk 236 optimal weight: 0.8980 chunk 555 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 HIS ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN H 5 ASN J 3 ASN W 60 GLN X 72 GLN b 10 ASN b 51 ASN f 12 HIS g 101 ASN ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 GLN s 59 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.249 65326 Z= 0.564 Angle : 1.582 50.819 88506 Z= 1.030 Chirality : 0.316 6.415 9707 Planarity : 0.004 0.063 11070 Dihedral : 10.691 172.956 9487 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.63 % Allowed : 12.07 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % 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: 1.22 (0.10), residues: 7698 helix: 1.77 (0.08), residues: 4267 sheet: -0.51 (0.27), residues: 342 loop : -0.35 (0.11), residues: 3089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 85 HIS 0.006 0.001 HIS R 68 PHE 0.028 0.001 PHE G 439 TYR 0.018 0.001 TYR s 40 ARG 0.007 0.000 ARG E 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1124 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1013 time to evaluate : 6.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8535 (tp40) cc_final: 0.7970 (tp-100) REVERT: A 85 SER cc_start: 0.8876 (m) cc_final: 0.8546 (p) REVERT: B 135 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7377 (t80) REVERT: D 105 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.6308 (mtt-85) REVERT: E 15 ASN cc_start: 0.8488 (t0) cc_final: 0.7804 (t0) REVERT: E 112 ASP cc_start: 0.7733 (t0) cc_final: 0.7377 (t0) REVERT: E 163 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7521 (t70) REVERT: E 176 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7050 (tp) REVERT: F 79 TRP cc_start: 0.8748 (m-10) cc_final: 0.8446 (m-10) REVERT: F 212 ASP cc_start: 0.7883 (t0) cc_final: 0.7517 (t0) REVERT: F 248 GLU cc_start: 0.6684 (mp0) cc_final: 0.6364 (mt-10) REVERT: F 409 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8408 (m-30) REVERT: F 430 MET cc_start: 0.7617 (mtt) cc_final: 0.7396 (mtt) REVERT: G 418 ARG cc_start: 0.7046 (tpp-160) cc_final: 0.6593 (mtm110) REVERT: G 439 PHE cc_start: 0.7553 (t80) cc_final: 0.7193 (t80) REVERT: G 444 LYS cc_start: 0.7192 (mmtm) cc_final: 0.6886 (mttp) REVERT: G 491 ASN cc_start: 0.6907 (OUTLIER) cc_final: 0.6170 (p0) REVERT: G 592 LEU cc_start: 0.7510 (mp) cc_final: 0.6900 (mt) REVERT: H 181 MET cc_start: 0.8935 (mtm) cc_final: 0.8648 (mtm) REVERT: H 277 TYR cc_start: 0.8495 (m-80) cc_final: 0.8059 (m-80) REVERT: H 302 MET cc_start: 0.8298 (ttm) cc_final: 0.8050 (ttm) REVERT: H 318 MET cc_start: 0.7728 (ppp) cc_final: 0.7492 (ppp) REVERT: I 16 MET cc_start: 0.8145 (tpp) cc_final: 0.7854 (tpp) REVERT: J 78 TYR cc_start: 0.7388 (m-80) cc_final: 0.6846 (m-10) REVERT: J 130 ASP cc_start: 0.8487 (m-30) cc_final: 0.8144 (m-30) REVERT: J 152 MET cc_start: 0.8605 (ttm) cc_final: 0.8379 (tpp) REVERT: L 71 MET cc_start: 0.8142 (tpp) cc_final: 0.7840 (mmp) REVERT: L 100 ILE cc_start: 0.8384 (mt) cc_final: 0.8152 (mm) REVERT: L 352 ASP cc_start: 0.7014 (t0) cc_final: 0.6607 (t0) REVERT: L 513 MET cc_start: 0.7425 (tpt) cc_final: 0.7147 (tpt) REVERT: M 168 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: M 376 MET cc_start: 0.7849 (mmm) cc_final: 0.7304 (mmm) REVERT: N 323 ASN cc_start: 0.7705 (m-40) cc_final: 0.7473 (m110) REVERT: O 65 ASP cc_start: 0.7503 (t0) cc_final: 0.7185 (t0) REVERT: O 261 MET cc_start: 0.8421 (mmm) cc_final: 0.8163 (mmp) REVERT: P 211 SER cc_start: 0.8567 (t) cc_final: 0.8324 (p) REVERT: P 263 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7464 (t80) REVERT: R 81 THR cc_start: 0.8645 (p) cc_final: 0.8329 (p) REVERT: R 92 LYS cc_start: 0.8439 (ttmm) cc_final: 0.7530 (tttp) REVERT: T 47 GLN cc_start: 0.7182 (tm-30) cc_final: 0.6449 (tm-30) REVERT: T 69 LYS cc_start: 0.7573 (mtmm) cc_final: 0.7345 (ptpp) REVERT: T 71 MET cc_start: 0.7273 (mmm) cc_final: 0.6827 (mtm) REVERT: V 109 ASN cc_start: 0.8264 (m-40) cc_final: 0.8010 (m110) REVERT: Z 9 MET cc_start: 0.8287 (mmm) cc_final: 0.8031 (mmm) REVERT: a 43 TYR cc_start: 0.8569 (t80) cc_final: 0.8243 (t80) REVERT: b 51 ASN cc_start: 0.8775 (m-40) cc_final: 0.8567 (m-40) REVERT: d 3 ASN cc_start: 0.7685 (m110) cc_final: 0.7272 (m-40) REVERT: e 39 TRP cc_start: 0.7953 (t60) cc_final: 0.7744 (t60) REVERT: e 75 MET cc_start: 0.8785 (mmm) cc_final: 0.8387 (mmm) REVERT: f 8 GLU cc_start: 0.7917 (pm20) cc_final: 0.7512 (pm20) REVERT: f 13 ILE cc_start: 0.8915 (tp) cc_final: 0.8569 (tp) REVERT: f 28 LYS cc_start: 0.7045 (mmpt) cc_final: 0.6588 (mmmm) REVERT: g 56 MET cc_start: 0.7879 (tmm) cc_final: 0.7613 (tmm) REVERT: g 84 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8046 (mm-40) REVERT: g 112 ASP cc_start: 0.9001 (t70) cc_final: 0.8594 (t70) REVERT: h 106 LYS cc_start: 0.8307 (mttm) cc_final: 0.7980 (mttt) REVERT: i 111 GLU cc_start: 0.7952 (mp0) cc_final: 0.7732 (mp0) REVERT: l 7 MET cc_start: 0.8182 (mtt) cc_final: 0.7789 (mtt) REVERT: l 17 GLU cc_start: 0.7886 (mp0) cc_final: 0.7679 (mp0) REVERT: l 93 THR cc_start: 0.8762 (m) cc_final: 0.8221 (p) REVERT: l 100 MET cc_start: 0.8428 (mtm) cc_final: 0.8072 (mtm) REVERT: l 102 LYS cc_start: 0.8151 (mttm) cc_final: 0.7914 (mttt) REVERT: m 4 LYS cc_start: 0.7651 (ttmt) cc_final: 0.6450 (ttpp) REVERT: m 27 GLU cc_start: 0.8135 (mp0) cc_final: 0.7727 (tm-30) REVERT: m 111 LYS cc_start: 0.7781 (ttpp) cc_final: 0.6774 (ttmt) REVERT: n 54 LYS cc_start: 0.8697 (mmmt) cc_final: 0.8165 (mmtt) REVERT: n 65 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7469 (mt-10) REVERT: o 17 ASP cc_start: 0.8327 (t0) cc_final: 0.7880 (t0) REVERT: o 28 LEU cc_start: 0.7253 (mt) cc_final: 0.6886 (mp) REVERT: o 83 GLN cc_start: 0.8308 (tt0) cc_final: 0.7968 (tt0) REVERT: p 38 LEU cc_start: 0.8220 (mm) cc_final: 0.7835 (tp) REVERT: p 42 TRP cc_start: 0.8431 (t60) cc_final: 0.8188 (t60) REVERT: p 144 ASP cc_start: 0.8556 (m-30) cc_final: 0.8330 (m-30) REVERT: p 170 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7104 (mtt180) REVERT: s 32 TYR cc_start: 0.7035 (t80) cc_final: 0.6729 (t80) REVERT: s 55 PHE cc_start: 0.7923 (m-80) cc_final: 0.7175 (m-10) outliers start: 111 outliers final: 68 residues processed: 1081 average time/residue: 0.6097 time to fit residues: 1112.5570 Evaluate side-chains 1046 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 969 time to evaluate : 5.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 409 ASP Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 491 ASN Chi-restraints excluded: chain G residue 544 VAL Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 399 ILE Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 325 MET Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain P residue 341 ASN Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 52 ILE Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain W residue 119 ASP Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 86 ASP Chi-restraints excluded: chain Z residue 7 GLN Chi-restraints excluded: chain Z residue 19 ASP Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain Z residue 143 THR Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 49 THR Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 50 ASN Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 30 MET Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain o residue 46 MET Chi-restraints excluded: chain o residue 85 ASP Chi-restraints excluded: chain p residue 25 LEU Chi-restraints excluded: chain p residue 170 ARG Chi-restraints excluded: chain s residue 30 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 684 optimal weight: 8.9990 chunk 520 optimal weight: 7.9990 chunk 359 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 330 optimal weight: 0.7980 chunk 464 optimal weight: 0.0020 chunk 694 optimal weight: 4.9990 chunk 735 optimal weight: 9.9990 chunk 363 optimal weight: 1.9990 chunk 658 optimal weight: 0.1980 chunk 198 optimal weight: 20.0000 overall best weight: 0.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 HIS H 5 ASN P 89 ASN S 30 GLN W 60 GLN X 72 GLN b 10 ASN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 59 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.248 65326 Z= 0.554 Angle : 1.574 50.748 88506 Z= 1.027 Chirality : 0.316 6.395 9707 Planarity : 0.004 0.065 11070 Dihedral : 10.214 171.770 9485 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.04 % Allowed : 12.22 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.10), residues: 7698 helix: 1.84 (0.08), residues: 4264 sheet: -0.43 (0.27), residues: 352 loop : -0.33 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 85 HIS 0.006 0.001 HIS R 68 PHE 0.026 0.001 PHE N 292 TYR 0.032 0.001 TYR F 43 ARG 0.009 0.000 ARG E 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1023 time to evaluate : 5.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8493 (tp40) cc_final: 0.7960 (tp40) REVERT: A 85 SER cc_start: 0.8877 (m) cc_final: 0.8559 (p) REVERT: C 113 GLU cc_start: 0.6341 (mp0) cc_final: 0.6081 (mp0) REVERT: D 105 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.6305 (mtt-85) REVERT: E 15 ASN cc_start: 0.8576 (t0) cc_final: 0.7721 (t0) REVERT: E 112 ASP cc_start: 0.7787 (t0) cc_final: 0.7381 (t0) REVERT: E 163 ASP cc_start: 0.7902 (t70) cc_final: 0.7332 (t70) REVERT: E 176 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7061 (tp) REVERT: F 212 ASP cc_start: 0.7891 (t0) cc_final: 0.7520 (t0) REVERT: F 248 GLU cc_start: 0.6606 (mp0) cc_final: 0.6362 (mt-10) REVERT: F 409 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8391 (m-30) REVERT: F 430 MET cc_start: 0.7592 (mtt) cc_final: 0.7376 (mtt) REVERT: G 135 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7107 (ptt90) REVERT: G 418 ARG cc_start: 0.7047 (tpp-160) cc_final: 0.6583 (mtm110) REVERT: G 439 PHE cc_start: 0.7118 (t80) cc_final: 0.6814 (t80) REVERT: G 444 LYS cc_start: 0.7197 (mmtm) cc_final: 0.6872 (mttp) REVERT: H 181 MET cc_start: 0.8913 (mtm) cc_final: 0.8627 (mtm) REVERT: H 277 TYR cc_start: 0.8497 (m-80) cc_final: 0.8047 (m-80) REVERT: H 302 MET cc_start: 0.8376 (ttm) cc_final: 0.8066 (ttm) REVERT: H 318 MET cc_start: 0.7659 (ppp) cc_final: 0.7406 (ppp) REVERT: I 16 MET cc_start: 0.8140 (tpp) cc_final: 0.7926 (tpp) REVERT: J 78 TYR cc_start: 0.7366 (m-80) cc_final: 0.6853 (m-10) REVERT: J 130 ASP cc_start: 0.8522 (m-30) cc_final: 0.8069 (m-30) REVERT: J 152 MET cc_start: 0.8629 (ttm) cc_final: 0.8396 (tpp) REVERT: L 71 MET cc_start: 0.8078 (tpp) cc_final: 0.7806 (mmp) REVERT: L 124 PHE cc_start: 0.7114 (t80) cc_final: 0.6718 (t80) REVERT: L 140 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8497 (tt) REVERT: L 340 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7027 (m-80) REVERT: L 352 ASP cc_start: 0.7166 (t0) cc_final: 0.6830 (t0) REVERT: L 397 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7257 (mt-10) REVERT: L 513 MET cc_start: 0.7306 (tpt) cc_final: 0.7062 (tpt) REVERT: M 168 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: M 376 MET cc_start: 0.7797 (mmm) cc_final: 0.7277 (mmm) REVERT: N 190 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6903 (mtp) REVERT: N 323 ASN cc_start: 0.7584 (m-40) cc_final: 0.7374 (m110) REVERT: O 65 ASP cc_start: 0.7501 (t0) cc_final: 0.7195 (t0) REVERT: P 211 SER cc_start: 0.8539 (t) cc_final: 0.8309 (p) REVERT: P 263 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7415 (t80) REVERT: R 81 THR cc_start: 0.8594 (p) cc_final: 0.8361 (p) REVERT: R 92 LYS cc_start: 0.8413 (ttmm) cc_final: 0.7337 (tttp) REVERT: T 47 GLN cc_start: 0.7158 (tm-30) cc_final: 0.6367 (tm-30) REVERT: T 71 MET cc_start: 0.7227 (mmm) cc_final: 0.6654 (mtm) REVERT: U 22 TYR cc_start: 0.7218 (t80) cc_final: 0.6663 (t80) REVERT: V 109 ASN cc_start: 0.8175 (m-40) cc_final: 0.7915 (m110) REVERT: W 126 MET cc_start: 0.5916 (ptm) cc_final: 0.5471 (ptt) REVERT: Y 48 ASP cc_start: 0.7275 (m-30) cc_final: 0.6752 (p0) REVERT: Z 9 MET cc_start: 0.8301 (mmm) cc_final: 0.8031 (mmm) REVERT: a 43 TYR cc_start: 0.8524 (t80) cc_final: 0.8186 (t80) REVERT: b 46 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8130 (ttmt) REVERT: b 81 LYS cc_start: 0.8368 (ttmt) cc_final: 0.7913 (tttm) REVERT: d 2 MET cc_start: 0.8708 (mtp) cc_final: 0.8294 (mtm) REVERT: d 3 ASN cc_start: 0.7877 (m110) cc_final: 0.7436 (m-40) REVERT: e 75 MET cc_start: 0.8789 (mmm) cc_final: 0.8343 (mmm) REVERT: f 8 GLU cc_start: 0.7908 (pm20) cc_final: 0.7673 (pm20) REVERT: f 13 ILE cc_start: 0.8908 (tp) cc_final: 0.8554 (tp) REVERT: f 28 LYS cc_start: 0.6981 (mmpt) cc_final: 0.6508 (mmmm) REVERT: f 31 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6837 (mt-10) REVERT: f 46 GLU cc_start: 0.7592 (mp0) cc_final: 0.7375 (mp0) REVERT: g 56 MET cc_start: 0.7890 (tmm) cc_final: 0.7608 (tmm) REVERT: g 84 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8092 (mm-40) REVERT: g 112 ASP cc_start: 0.8995 (t70) cc_final: 0.8644 (t70) REVERT: h 106 LYS cc_start: 0.8254 (mttm) cc_final: 0.7907 (mttt) REVERT: i 111 GLU cc_start: 0.7984 (mp0) cc_final: 0.7781 (mp0) REVERT: l 7 MET cc_start: 0.8134 (mtt) cc_final: 0.7866 (mtt) REVERT: l 93 THR cc_start: 0.8719 (m) cc_final: 0.8199 (p) REVERT: l 100 MET cc_start: 0.8370 (mtm) cc_final: 0.8016 (mtm) REVERT: l 102 LYS cc_start: 0.8118 (mttm) cc_final: 0.7886 (mtmm) REVERT: m 4 LYS cc_start: 0.7588 (ttmt) cc_final: 0.6429 (ttpp) REVERT: m 27 GLU cc_start: 0.8123 (mp0) cc_final: 0.7669 (tm-30) REVERT: m 111 LYS cc_start: 0.7782 (ttpp) cc_final: 0.6803 (ttmt) REVERT: n 54 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8170 (mmtt) REVERT: n 65 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7552 (mt-10) REVERT: o 17 ASP cc_start: 0.8318 (t0) cc_final: 0.7818 (t0) REVERT: o 28 LEU cc_start: 0.7253 (mt) cc_final: 0.7038 (tt) REVERT: o 100 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7829 (mm-30) REVERT: o 109 GLN cc_start: 0.8741 (pt0) cc_final: 0.8468 (pt0) REVERT: p 38 LEU cc_start: 0.8194 (mm) cc_final: 0.7804 (tp) REVERT: p 42 TRP cc_start: 0.8373 (t60) cc_final: 0.7989 (t60) REVERT: p 170 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7151 (mtt180) REVERT: s 36 GLN cc_start: 0.7239 (mp10) cc_final: 0.6971 (mp10) REVERT: s 43 TYR cc_start: 0.8393 (m-10) cc_final: 0.8069 (m-10) outliers start: 139 outliers final: 75 residues processed: 1112 average time/residue: 0.6041 time to fit residues: 1134.4298 Evaluate side-chains 1062 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 976 time to evaluate : 5.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 409 ASP Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 455 SER Chi-restraints excluded: chain G residue 544 VAL Chi-restraints excluded: chain G residue 587 VAL Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 109 TYR Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 190 MET Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain P residue 341 ASN Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 52 ILE Chi-restraints excluded: chain T residue 56 ASP Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 87 TYR Chi-restraints excluded: chain W residue 119 ASP Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 86 ASP Chi-restraints excluded: chain Z residue 23 ASN Chi-restraints excluded: chain Z residue 143 THR Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 49 THR Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 31 GLU Chi-restraints excluded: chain f residue 50 ASN Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 30 MET Chi-restraints excluded: chain h residue 142 ASP Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 146 THR Chi-restraints excluded: chain l residue 152 VAL Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 46 MET Chi-restraints excluded: chain p residue 25 LEU Chi-restraints excluded: chain p residue 170 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 612 optimal weight: 4.9990 chunk 417 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 547 optimal weight: 6.9990 chunk 303 optimal weight: 4.9990 chunk 627 optimal weight: 4.9990 chunk 508 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 375 optimal weight: 4.9990 chunk 660 optimal weight: 4.9990 chunk 185 optimal weight: 20.0000 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 ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 ASN F 264 HIS G 255 HIS G 437 HIS ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN L 58 ASN L 175 ASN M 430 HIS U 74 GLN X 72 GLN Z 7 GLN b 10 ASN b 51 ASN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 GLN m 85 ASN ** s 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 59 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.244 65326 Z= 0.699 Angle : 1.630 50.820 88506 Z= 1.049 Chirality : 0.318 6.460 9707 Planarity : 0.005 0.069 11070 Dihedral : 10.560 175.241 9485 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.26 % Allowed : 13.13 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % 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: 7698 helix: 1.41 (0.08), residues: 4255 sheet: -0.53 (0.27), residues: 341 loop : -0.45 (0.11), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 254 HIS 0.009 0.002 HIS R 68 PHE 0.030 0.002 PHE M 151 TYR 0.035 0.002 TYR s 40 ARG 0.008 0.001 ARG E 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 959 time to evaluate : 5.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8524 (tp40) cc_final: 0.8026 (tp40) REVERT: B 135 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.7575 (t80) REVERT: C 113 GLU cc_start: 0.6259 (mp0) cc_final: 0.5819 (mp0) REVERT: D 105 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.6931 (mtt-85) REVERT: E 15 ASN cc_start: 0.8520 (t0) cc_final: 0.7795 (t0) REVERT: F 79 TRP cc_start: 0.8749 (m-10) cc_final: 0.8398 (m-10) REVERT: F 157 TYR cc_start: 0.7933 (m-80) cc_final: 0.7705 (m-80) REVERT: F 212 ASP cc_start: 0.7919 (t0) cc_final: 0.7515 (t0) REVERT: F 248 GLU cc_start: 0.6675 (mp0) cc_final: 0.6420 (mt-10) REVERT: F 279 LEU cc_start: 0.8428 (tt) cc_final: 0.8164 (mt) REVERT: F 409 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8375 (m-30) REVERT: F 430 MET cc_start: 0.7716 (mtt) cc_final: 0.7374 (mtt) REVERT: G 418 ARG cc_start: 0.7313 (tpp-160) cc_final: 0.6599 (mtm110) REVERT: G 439 PHE cc_start: 0.7301 (t80) cc_final: 0.6906 (t80) REVERT: H 277 TYR cc_start: 0.8598 (m-80) cc_final: 0.8149 (m-80) REVERT: H 318 MET cc_start: 0.7605 (ppp) cc_final: 0.7346 (ppp) REVERT: I 16 MET cc_start: 0.8232 (tpp) cc_final: 0.7955 (tpp) REVERT: J 130 ASP cc_start: 0.8427 (m-30) cc_final: 0.8037 (m-30) REVERT: L 71 MET cc_start: 0.8036 (tpp) cc_final: 0.7641 (mmt) REVERT: L 140 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8505 (tt) REVERT: L 352 ASP cc_start: 0.7381 (t0) cc_final: 0.7105 (t0) REVERT: L 397 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7434 (mt-10) REVERT: M 168 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: M 408 MET cc_start: 0.8631 (mmp) cc_final: 0.8422 (mmp) REVERT: O 65 ASP cc_start: 0.7492 (t0) cc_final: 0.7202 (t0) REVERT: P 211 SER cc_start: 0.8631 (t) cc_final: 0.8400 (p) REVERT: P 263 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7517 (t80) REVERT: R 51 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7453 (mm-30) REVERT: R 81 THR cc_start: 0.8694 (p) cc_final: 0.8456 (p) REVERT: R 92 LYS cc_start: 0.8439 (ttmm) cc_final: 0.7556 (tttp) REVERT: T 47 GLN cc_start: 0.7488 (tm-30) cc_final: 0.6489 (tm-30) REVERT: T 71 MET cc_start: 0.7174 (mmm) cc_final: 0.6530 (mtm) REVERT: V 4 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6190 (tt) REVERT: V 109 ASN cc_start: 0.8373 (m-40) cc_final: 0.8164 (m110) REVERT: W 126 MET cc_start: 0.6070 (ptm) cc_final: 0.5810 (ptt) REVERT: Z 9 MET cc_start: 0.8229 (mmm) cc_final: 0.7880 (mmm) REVERT: Z 78 LYS cc_start: 0.8795 (ttmt) cc_final: 0.8577 (ttpt) REVERT: d 2 MET cc_start: 0.8712 (mtp) cc_final: 0.8321 (mtm) REVERT: d 3 ASN cc_start: 0.7716 (m110) cc_final: 0.7317 (m-40) REVERT: e 75 MET cc_start: 0.8615 (mmm) cc_final: 0.8350 (mmm) REVERT: f 13 ILE cc_start: 0.8900 (tp) cc_final: 0.8595 (tp) REVERT: f 28 LYS cc_start: 0.6878 (mmpt) cc_final: 0.6562 (mmtp) REVERT: g 56 MET cc_start: 0.7846 (tmm) cc_final: 0.7615 (tmm) REVERT: g 84 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7990 (mm-40) REVERT: g 112 ASP cc_start: 0.9034 (t70) cc_final: 0.8737 (t0) REVERT: h 106 LYS cc_start: 0.8431 (mttm) cc_final: 0.8167 (mttp) REVERT: l 7 MET cc_start: 0.8508 (mtt) cc_final: 0.8091 (mtt) REVERT: l 17 GLU cc_start: 0.7635 (mp0) cc_final: 0.7075 (mp0) REVERT: l 100 MET cc_start: 0.8482 (mtm) cc_final: 0.8103 (mtm) REVERT: l 102 LYS cc_start: 0.8256 (mttm) cc_final: 0.8048 (mttt) REVERT: m 4 LYS cc_start: 0.7710 (ttmt) cc_final: 0.6647 (ttpp) REVERT: m 27 GLU cc_start: 0.8117 (mp0) cc_final: 0.7851 (tm-30) REVERT: m 111 LYS cc_start: 0.7831 (ttpp) cc_final: 0.6874 (ttmt) REVERT: n 54 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8202 (mmtt) REVERT: n 65 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7468 (mt-10) REVERT: o 17 ASP cc_start: 0.8417 (t0) cc_final: 0.7976 (t0) REVERT: p 11 GLU cc_start: 0.7434 (tp30) cc_final: 0.7075 (tm-30) REVERT: p 38 LEU cc_start: 0.8214 (mm) cc_final: 0.7797 (tp) REVERT: p 170 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7152 (mtt180) REVERT: s 32 TYR cc_start: 0.7128 (t80) cc_final: 0.6552 (t80) REVERT: s 36 GLN cc_start: 0.7245 (mp10) cc_final: 0.6880 (mp10) REVERT: s 40 TYR cc_start: 0.8055 (m-80) cc_final: 0.7314 (m-80) outliers start: 154 outliers final: 112 residues processed: 1051 average time/residue: 0.6317 time to fit residues: 1122.8334 Evaluate side-chains 1052 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 932 time to evaluate : 5.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 409 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 455 SER Chi-restraints excluded: chain G residue 521 MET Chi-restraints excluded: chain G residue 587 VAL Chi-restraints excluded: chain H residue 5 ASN Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 267 THR Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 325 MET Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 341 ASN Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain S residue 52 ILE Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 56 ASP Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 87 TYR Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain W residue 119 ASP Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 86 ASP Chi-restraints excluded: chain Z residue 19 ASP Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain Z residue 143 THR Chi-restraints excluded: chain b residue 14 LYS Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 49 THR Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 29 ASP Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 50 ASN Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 30 MET Chi-restraints excluded: chain i residue 95 THR Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 6 ASP Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 53 SER Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain l residue 152 VAL Chi-restraints excluded: chain m residue 85 ASN Chi-restraints excluded: chain m residue 119 LYS Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain n residue 56 MET Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain o residue 32 GLU Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 25 LEU Chi-restraints excluded: chain p residue 39 VAL Chi-restraints excluded: chain p residue 58 ASN Chi-restraints excluded: chain p residue 170 ARG Chi-restraints excluded: chain s residue 30 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 247 optimal weight: 1.9990 chunk 662 optimal weight: 0.0870 chunk 145 optimal weight: 5.9990 chunk 431 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 736 optimal weight: 0.0470 chunk 611 optimal weight: 4.9990 chunk 340 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 243 optimal weight: 0.9980 chunk 386 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 ASN F 264 HIS ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 273 ASN b 10 ASN b 51 ASN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 8 GLN m 85 ASN s 37 HIS s 59 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.249 65326 Z= 0.554 Angle : 1.578 50.770 88506 Z= 1.029 Chirality : 0.316 6.396 9707 Planarity : 0.004 0.066 11070 Dihedral : 9.895 172.021 9485 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.79 % Allowed : 13.92 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % 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: 1.16 (0.10), residues: 7698 helix: 1.70 (0.08), residues: 4257 sheet: -0.42 (0.27), residues: 343 loop : -0.34 (0.11), residues: 3098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 254 HIS 0.005 0.001 HIS R 68 PHE 0.027 0.001 PHE N 292 TYR 0.032 0.001 TYR F 43 ARG 0.009 0.000 ARG E 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 998 time to evaluate : 5.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8491 (tp40) cc_final: 0.7963 (tp40) REVERT: A 85 SER cc_start: 0.8928 (m) cc_final: 0.8563 (p) REVERT: B 135 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7484 (t80) REVERT: C 113 GLU cc_start: 0.6384 (mp0) cc_final: 0.6150 (mp0) REVERT: D 105 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.6725 (mtt-85) REVERT: E 15 ASN cc_start: 0.8614 (t0) cc_final: 0.8271 (t0) REVERT: E 112 ASP cc_start: 0.7747 (t0) cc_final: 0.7389 (t0) REVERT: E 176 LEU cc_start: 0.7335 (mm) cc_final: 0.6988 (tt) REVERT: F 79 TRP cc_start: 0.8758 (m-10) cc_final: 0.8548 (m-10) REVERT: F 212 ASP cc_start: 0.7932 (t0) cc_final: 0.7533 (t0) REVERT: F 224 ASN cc_start: 0.8428 (t0) cc_final: 0.8228 (t0) REVERT: F 248 GLU cc_start: 0.6630 (mp0) cc_final: 0.6347 (mt-10) REVERT: F 279 LEU cc_start: 0.8399 (tt) cc_final: 0.8143 (mt) REVERT: F 409 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8368 (m-30) REVERT: F 430 MET cc_start: 0.7599 (mtt) cc_final: 0.7317 (mtt) REVERT: G 135 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.6943 (ptt90) REVERT: G 418 ARG cc_start: 0.7078 (tpp-160) cc_final: 0.6528 (mtm110) REVERT: G 439 PHE cc_start: 0.7195 (t80) cc_final: 0.6970 (t80) REVERT: G 592 LEU cc_start: 0.6804 (mt) cc_final: 0.6228 (mt) REVERT: G 636 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7255 (pt) REVERT: H 181 MET cc_start: 0.8860 (mtm) cc_final: 0.8597 (mtm) REVERT: H 277 TYR cc_start: 0.8610 (m-80) cc_final: 0.8147 (m-80) REVERT: H 318 MET cc_start: 0.7715 (ppp) cc_final: 0.7447 (ppp) REVERT: J 130 ASP cc_start: 0.8459 (m-30) cc_final: 0.8112 (m-30) REVERT: J 152 MET cc_start: 0.8802 (ttm) cc_final: 0.8427 (tpp) REVERT: L 140 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8516 (tt) REVERT: L 340 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7071 (m-80) REVERT: L 352 ASP cc_start: 0.7288 (t0) cc_final: 0.7020 (t0) REVERT: L 397 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7360 (mt-10) REVERT: L 513 MET cc_start: 0.7322 (tpt) cc_final: 0.7107 (tpt) REVERT: M 168 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: M 310 MET cc_start: 0.7957 (ttp) cc_final: 0.7622 (ttp) REVERT: N 323 ASN cc_start: 0.7696 (m-40) cc_final: 0.7475 (m110) REVERT: O 65 ASP cc_start: 0.7548 (t0) cc_final: 0.7263 (t0) REVERT: P 27 THR cc_start: 0.8585 (m) cc_final: 0.8339 (p) REVERT: P 211 SER cc_start: 0.8552 (t) cc_final: 0.8339 (p) REVERT: P 248 MET cc_start: 0.7926 (mmt) cc_final: 0.7570 (tpp) REVERT: P 263 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7394 (t80) REVERT: P 275 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: R 81 THR cc_start: 0.8669 (p) cc_final: 0.8424 (p) REVERT: R 92 LYS cc_start: 0.8388 (ttmm) cc_final: 0.7440 (tttp) REVERT: T 47 GLN cc_start: 0.7313 (tm-30) cc_final: 0.6621 (tm-30) REVERT: T 71 MET cc_start: 0.7074 (mmm) cc_final: 0.6442 (mtm) REVERT: V 109 ASN cc_start: 0.8268 (m-40) cc_final: 0.8061 (m110) REVERT: W 126 MET cc_start: 0.6358 (ptm) cc_final: 0.6118 (ptt) REVERT: Z 9 MET cc_start: 0.8434 (mmm) cc_final: 0.8130 (mmm) REVERT: a 43 TYR cc_start: 0.8517 (t80) cc_final: 0.8196 (t80) REVERT: b 46 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8096 (ttmt) REVERT: b 81 LYS cc_start: 0.8342 (ttmt) cc_final: 0.7893 (tttm) REVERT: c 11 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8248 (mtpp) REVERT: d 2 MET cc_start: 0.8700 (mtp) cc_final: 0.8290 (mtm) REVERT: d 3 ASN cc_start: 0.7721 (m110) cc_final: 0.7286 (m-40) REVERT: e 75 MET cc_start: 0.8771 (mmm) cc_final: 0.8374 (mmm) REVERT: f 13 ILE cc_start: 0.8868 (tp) cc_final: 0.8526 (tp) REVERT: f 28 LYS cc_start: 0.6954 (mmpt) cc_final: 0.6565 (mmtp) REVERT: f 31 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6620 (mt-10) REVERT: g 56 MET cc_start: 0.7886 (tmm) cc_final: 0.7627 (tmm) REVERT: g 84 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8087 (mm-40) REVERT: g 112 ASP cc_start: 0.8977 (t70) cc_final: 0.8548 (t70) REVERT: h 106 LYS cc_start: 0.8344 (mttm) cc_final: 0.8017 (mttt) REVERT: i 111 GLU cc_start: 0.7923 (mp0) cc_final: 0.7671 (mp0) REVERT: l 7 MET cc_start: 0.8443 (mtt) cc_final: 0.8087 (mtt) REVERT: l 17 GLU cc_start: 0.7564 (mp0) cc_final: 0.6973 (mp0) REVERT: l 100 MET cc_start: 0.8437 (mtm) cc_final: 0.8034 (mtm) REVERT: l 102 LYS cc_start: 0.8137 (mttm) cc_final: 0.7742 (mtpt) REVERT: m 4 LYS cc_start: 0.7645 (ttmt) cc_final: 0.6609 (ttpp) REVERT: m 27 GLU cc_start: 0.8068 (mp0) cc_final: 0.7657 (tm-30) REVERT: m 111 LYS cc_start: 0.7768 (ttpp) cc_final: 0.6788 (ttmt) REVERT: n 54 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8154 (mmtp) REVERT: n 65 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7499 (mt-10) REVERT: o 17 ASP cc_start: 0.8337 (t0) cc_final: 0.7840 (t0) REVERT: o 100 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7937 (mm-30) REVERT: p 38 LEU cc_start: 0.8221 (mm) cc_final: 0.7772 (tp) REVERT: p 42 TRP cc_start: 0.8408 (t60) cc_final: 0.8099 (t60) REVERT: p 98 ASP cc_start: 0.7603 (m-30) cc_final: 0.7396 (m-30) REVERT: p 170 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7115 (mtt180) REVERT: s 40 TYR cc_start: 0.7976 (m-80) cc_final: 0.7606 (m-80) REVERT: s 43 TYR cc_start: 0.8410 (m-10) cc_final: 0.8136 (m-10) outliers start: 122 outliers final: 77 residues processed: 1079 average time/residue: 0.6042 time to fit residues: 1101.4153 Evaluate side-chains 1057 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 968 time to evaluate : 5.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 409 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 437 HIS Chi-restraints excluded: chain G residue 455 SER Chi-restraints excluded: chain G residue 521 MET Chi-restraints excluded: chain G residue 587 VAL Chi-restraints excluded: chain G residue 636 ILE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 109 TYR Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain P residue 275 PHE Chi-restraints excluded: chain P residue 341 ASN Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 52 ILE Chi-restraints excluded: chain T residue 56 ASP Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain W residue 119 ASP Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 86 ASP Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain b residue 14 LYS Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 108 THR Chi-restraints excluded: chain e residue 49 THR Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 31 GLU Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain i residue 95 THR Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain l residue 152 VAL Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain p residue 25 LEU Chi-restraints excluded: chain p residue 170 ARG Chi-restraints excluded: chain s residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 709 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 419 optimal weight: 1.9990 chunk 537 optimal weight: 7.9990 chunk 416 optimal weight: 5.9990 chunk 619 optimal weight: 1.9990 chunk 411 optimal weight: 4.9990 chunk 733 optimal weight: 7.9990 chunk 459 optimal weight: 0.0980 chunk 447 optimal weight: 0.8980 chunk 338 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 HIS ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN N 273 ASN X 72 GLN b 10 ASN ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 59 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 65326 Z= 0.559 Angle : 1.579 50.767 88506 Z= 1.029 Chirality : 0.316 6.406 9707 Planarity : 0.004 0.065 11070 Dihedral : 9.561 172.615 9485 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.97 % Allowed : 14.20 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % 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: 1.23 (0.10), residues: 7698 helix: 1.74 (0.08), residues: 4260 sheet: -0.34 (0.27), residues: 355 loop : -0.30 (0.11), residues: 3083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 487 HIS 0.005 0.001 HIS R 68 PHE 0.029 0.001 PHE k 92 TYR 0.031 0.001 TYR F 43 ARG 0.008 0.000 ARG E 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 983 time to evaluate : 5.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8472 (tp40) cc_final: 0.7958 (tp40) REVERT: A 85 SER cc_start: 0.8891 (m) cc_final: 0.8546 (p) REVERT: D 105 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.6468 (mtt-85) REVERT: E 15 ASN cc_start: 0.8684 (t0) cc_final: 0.8215 (t0) REVERT: E 18 ASP cc_start: 0.7200 (m-30) cc_final: 0.6802 (m-30) REVERT: E 112 ASP cc_start: 0.7720 (t0) cc_final: 0.7396 (t0) REVERT: E 176 LEU cc_start: 0.7448 (mm) cc_final: 0.6877 (tt) REVERT: F 212 ASP cc_start: 0.7917 (t0) cc_final: 0.7536 (t0) REVERT: F 279 LEU cc_start: 0.8391 (tt) cc_final: 0.8128 (mt) REVERT: F 409 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8325 (m-30) REVERT: F 430 MET cc_start: 0.7762 (mtt) cc_final: 0.7504 (mtt) REVERT: G 135 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.6953 (ptt90) REVERT: G 418 ARG cc_start: 0.7092 (tpp-160) cc_final: 0.6561 (mtm110) REVERT: G 439 PHE cc_start: 0.7260 (t80) cc_final: 0.6927 (t80) REVERT: G 592 LEU cc_start: 0.6705 (mt) cc_final: 0.6156 (mt) REVERT: H 181 MET cc_start: 0.8853 (mtm) cc_final: 0.8604 (mtm) REVERT: H 277 TYR cc_start: 0.8620 (m-80) cc_final: 0.8173 (m-80) REVERT: J 130 ASP cc_start: 0.8443 (m-30) cc_final: 0.8022 (m-30) REVERT: J 152 MET cc_start: 0.8807 (ttm) cc_final: 0.8425 (tpp) REVERT: L 140 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8526 (tt) REVERT: L 340 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7114 (m-80) REVERT: L 352 ASP cc_start: 0.7326 (t0) cc_final: 0.7029 (t0) REVERT: L 397 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7249 (mt-10) REVERT: M 86 LYS cc_start: 0.7978 (mmtm) cc_final: 0.7712 (mmmt) REVERT: M 168 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: N 323 ASN cc_start: 0.7695 (m-40) cc_final: 0.7476 (m110) REVERT: O 65 ASP cc_start: 0.7553 (t0) cc_final: 0.7273 (t0) REVERT: P 211 SER cc_start: 0.8568 (t) cc_final: 0.8364 (p) REVERT: P 248 MET cc_start: 0.8039 (mmt) cc_final: 0.7621 (mmm) REVERT: P 263 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7411 (t80) REVERT: R 92 LYS cc_start: 0.8450 (ttmm) cc_final: 0.7537 (tttp) REVERT: T 47 GLN cc_start: 0.7206 (tm-30) cc_final: 0.6583 (tm-30) REVERT: T 71 MET cc_start: 0.7047 (mmm) cc_final: 0.6443 (mtm) REVERT: V 4 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.6047 (tt) REVERT: W 36 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7380 (mt-10) REVERT: W 126 MET cc_start: 0.6396 (ptm) cc_final: 0.5890 (ptt) REVERT: Y 48 ASP cc_start: 0.7288 (m-30) cc_final: 0.6745 (p0) REVERT: Y 116 CYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7774 (t) REVERT: Z 9 MET cc_start: 0.8430 (mmm) cc_final: 0.8205 (mmm) REVERT: a 43 TYR cc_start: 0.8521 (t80) cc_final: 0.8216 (t80) REVERT: b 46 LYS cc_start: 0.8411 (ttmm) cc_final: 0.8104 (ttmt) REVERT: b 81 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7911 (tttm) REVERT: c 11 LYS cc_start: 0.8418 (mtmm) cc_final: 0.8189 (mtpp) REVERT: d 2 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8257 (mtm) REVERT: e 75 MET cc_start: 0.8774 (mmm) cc_final: 0.8397 (mmm) REVERT: e 102 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7364 (pp20) REVERT: f 13 ILE cc_start: 0.8868 (tp) cc_final: 0.8536 (tp) REVERT: f 28 LYS cc_start: 0.6974 (mmpt) cc_final: 0.6544 (mmtp) REVERT: f 31 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6872 (mt-10) REVERT: g 56 MET cc_start: 0.7866 (tmm) cc_final: 0.7439 (tmm) REVERT: g 112 ASP cc_start: 0.8978 (t70) cc_final: 0.8610 (t70) REVERT: h 106 LYS cc_start: 0.8385 (mttm) cc_final: 0.8057 (mttt) REVERT: i 111 GLU cc_start: 0.7940 (mp0) cc_final: 0.7658 (mp0) REVERT: l 7 MET cc_start: 0.8411 (mtt) cc_final: 0.8063 (mtt) REVERT: l 17 GLU cc_start: 0.7635 (mp0) cc_final: 0.7076 (mp0) REVERT: l 93 THR cc_start: 0.8689 (m) cc_final: 0.8177 (p) REVERT: l 100 MET cc_start: 0.8420 (mtm) cc_final: 0.8064 (mtm) REVERT: l 102 LYS cc_start: 0.8135 (mttm) cc_final: 0.7930 (mtmt) REVERT: m 4 LYS cc_start: 0.7648 (ttmt) cc_final: 0.6579 (ttpp) REVERT: m 27 GLU cc_start: 0.8142 (mp0) cc_final: 0.7780 (tm-30) REVERT: m 111 LYS cc_start: 0.7803 (ttpp) cc_final: 0.6859 (ttmt) REVERT: m 123 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7054 (mtmm) REVERT: n 54 LYS cc_start: 0.8687 (mmmt) cc_final: 0.8208 (mmtp) REVERT: n 65 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7484 (mt-10) REVERT: o 17 ASP cc_start: 0.8346 (t0) cc_final: 0.7853 (t0) REVERT: o 100 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7922 (mm-30) REVERT: p 11 GLU cc_start: 0.7423 (tp30) cc_final: 0.7092 (tm-30) REVERT: p 38 LEU cc_start: 0.8175 (mm) cc_final: 0.7752 (tp) REVERT: p 42 TRP cc_start: 0.8408 (t60) cc_final: 0.8123 (t60) REVERT: p 98 ASP cc_start: 0.7590 (m-30) cc_final: 0.7250 (m-30) REVERT: p 170 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7093 (mtt180) outliers start: 134 outliers final: 99 residues processed: 1065 average time/residue: 0.6038 time to fit residues: 1082.2582 Evaluate side-chains 1072 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 959 time to evaluate : 5.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 409 ASP Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 437 HIS Chi-restraints excluded: chain G residue 455 SER Chi-restraints excluded: chain G residue 521 MET Chi-restraints excluded: chain G residue 587 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 109 TYR Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 577 THR Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain P residue 341 ASN Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain S residue 52 ILE Chi-restraints excluded: chain T residue 56 ASP Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain W residue 119 ASP Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 86 ASP Chi-restraints excluded: chain Y residue 116 CYS Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain b residue 14 LYS Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 MET Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain d residue 108 THR Chi-restraints excluded: chain e residue 49 THR Chi-restraints excluded: chain e residue 102 GLU Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 31 GLU Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 30 MET Chi-restraints excluded: chain h residue 32 THR Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 51 ASN Chi-restraints excluded: chain l residue 53 SER Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain l residue 152 VAL Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 119 LYS Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain o residue 32 GLU Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 25 LEU Chi-restraints excluded: chain p residue 170 ARG Chi-restraints excluded: chain r residue 109 GLN Chi-restraints excluded: chain s residue 30 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 453 optimal weight: 8.9990 chunk 292 optimal weight: 0.6980 chunk 438 optimal weight: 0.0060 chunk 220 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 466 optimal weight: 0.9990 chunk 499 optimal weight: 4.9990 chunk 362 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 576 optimal weight: 3.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 HIS ** G 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 273 ASN X 72 GLN b 10 ASN d 3 ASN i 13 GLN m 85 ASN ** r 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 59 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 65326 Z= 0.561 Angle : 1.580 50.763 88506 Z= 1.029 Chirality : 0.316 6.403 9707 Planarity : 0.004 0.064 11070 Dihedral : 9.396 172.702 9485 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.01 % Allowed : 14.50 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % 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: 1.25 (0.10), residues: 7698 helix: 1.75 (0.08), residues: 4259 sheet: -0.30 (0.27), residues: 367 loop : -0.28 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 85 HIS 0.005 0.001 HIS R 68 PHE 0.029 0.001 PHE L 124 TYR 0.031 0.001 TYR F 43 ARG 0.009 0.000 ARG S 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 982 time to evaluate : 5.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8446 (tp40) cc_final: 0.7939 (tp40) REVERT: A 85 SER cc_start: 0.8919 (m) cc_final: 0.8565 (p) REVERT: B 126 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7962 (ttp) REVERT: C 113 GLU cc_start: 0.6279 (mp0) cc_final: 0.6054 (mp0) REVERT: D 105 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.6502 (mtt-85) REVERT: E 15 ASN cc_start: 0.8631 (t0) cc_final: 0.8265 (t0) REVERT: E 112 ASP cc_start: 0.7751 (t0) cc_final: 0.7496 (t0) REVERT: E 187 ARG cc_start: 0.7000 (mtt90) cc_final: 0.6620 (mtt90) REVERT: F 79 TRP cc_start: 0.8627 (m-10) cc_final: 0.8382 (m-10) REVERT: F 212 ASP cc_start: 0.7922 (t0) cc_final: 0.7541 (t0) REVERT: F 248 GLU cc_start: 0.7231 (mp0) cc_final: 0.6586 (mt-10) REVERT: F 279 LEU cc_start: 0.8401 (tt) cc_final: 0.8131 (mt) REVERT: F 409 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8309 (m-30) REVERT: F 430 MET cc_start: 0.7756 (mtt) cc_final: 0.7510 (mtt) REVERT: G 418 ARG cc_start: 0.7085 (tpp-160) cc_final: 0.6565 (mtm110) REVERT: G 439 PHE cc_start: 0.7286 (t80) cc_final: 0.6850 (t80) REVERT: G 592 LEU cc_start: 0.6622 (mt) cc_final: 0.6132 (mt) REVERT: H 181 MET cc_start: 0.8897 (mtm) cc_final: 0.8660 (mtm) REVERT: H 277 TYR cc_start: 0.8625 (m-80) cc_final: 0.8099 (m-80) REVERT: I 16 MET cc_start: 0.8202 (tpp) cc_final: 0.7912 (tpp) REVERT: J 130 ASP cc_start: 0.8425 (m-30) cc_final: 0.8007 (m-30) REVERT: J 152 MET cc_start: 0.8811 (ttm) cc_final: 0.8434 (tpp) REVERT: L 140 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8530 (tt) REVERT: L 340 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7098 (m-80) REVERT: L 352 ASP cc_start: 0.7405 (t0) cc_final: 0.7068 (t0) REVERT: L 397 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7214 (mt-10) REVERT: M 168 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: N 323 ASN cc_start: 0.7704 (m-40) cc_final: 0.7490 (m110) REVERT: O 65 ASP cc_start: 0.7559 (t0) cc_final: 0.7279 (t0) REVERT: P 57 MET cc_start: 0.8582 (mmt) cc_final: 0.8248 (mmp) REVERT: P 248 MET cc_start: 0.8044 (mmt) cc_final: 0.7639 (mmm) REVERT: P 263 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7393 (t80) REVERT: P 275 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: R 92 LYS cc_start: 0.8318 (ttmm) cc_final: 0.7432 (tttp) REVERT: T 47 GLN cc_start: 0.7200 (tm-30) cc_final: 0.6588 (tm-30) REVERT: T 71 MET cc_start: 0.7046 (mmm) cc_final: 0.6443 (mtm) REVERT: W 36 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7378 (mt-10) REVERT: W 126 MET cc_start: 0.6231 (ptm) cc_final: 0.5721 (ptt) REVERT: Y 12 GLU cc_start: 0.6307 (mm-30) cc_final: 0.5855 (mt-10) REVERT: Y 48 ASP cc_start: 0.7286 (m-30) cc_final: 0.6748 (p0) REVERT: Z 9 MET cc_start: 0.8387 (mmm) cc_final: 0.8158 (mmm) REVERT: a 43 TYR cc_start: 0.8499 (t80) cc_final: 0.8187 (t80) REVERT: b 46 LYS cc_start: 0.8449 (ttmm) cc_final: 0.8151 (ttmt) REVERT: b 81 LYS cc_start: 0.8356 (ttmt) cc_final: 0.7936 (tttm) REVERT: c 11 LYS cc_start: 0.8414 (mtmm) cc_final: 0.8194 (mtpp) REVERT: d 2 MET cc_start: 0.8701 (mtp) cc_final: 0.8256 (mtm) REVERT: e 75 MET cc_start: 0.8777 (mmm) cc_final: 0.8397 (mmm) REVERT: e 102 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7301 (pp20) REVERT: f 13 ILE cc_start: 0.8888 (tp) cc_final: 0.8536 (tp) REVERT: f 28 LYS cc_start: 0.6975 (mmpt) cc_final: 0.6556 (mmtp) REVERT: f 31 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6880 (mt-10) REVERT: g 56 MET cc_start: 0.7853 (tmm) cc_final: 0.7443 (tmm) REVERT: g 112 ASP cc_start: 0.8971 (t70) cc_final: 0.8619 (t70) REVERT: h 106 LYS cc_start: 0.8389 (mttm) cc_final: 0.8056 (mttt) REVERT: i 111 GLU cc_start: 0.7962 (mp0) cc_final: 0.7663 (mp0) REVERT: l 7 MET cc_start: 0.8414 (mtt) cc_final: 0.8054 (mtt) REVERT: l 17 GLU cc_start: 0.7704 (mp0) cc_final: 0.7130 (mp0) REVERT: l 93 THR cc_start: 0.8726 (m) cc_final: 0.8214 (p) REVERT: l 100 MET cc_start: 0.8416 (mtm) cc_final: 0.8079 (mtm) REVERT: l 102 LYS cc_start: 0.8128 (mttm) cc_final: 0.7880 (mtmm) REVERT: m 4 LYS cc_start: 0.7651 (ttmt) cc_final: 0.6586 (ttpp) REVERT: m 27 GLU cc_start: 0.8118 (mp0) cc_final: 0.7803 (tm-30) REVERT: m 111 LYS cc_start: 0.7804 (ttpp) cc_final: 0.6858 (ttmt) REVERT: m 123 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7063 (mtmm) REVERT: n 54 LYS cc_start: 0.8438 (mmmt) cc_final: 0.7841 (mmtp) REVERT: n 65 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7481 (mt-10) REVERT: o 17 ASP cc_start: 0.8360 (t0) cc_final: 0.7850 (t0) REVERT: o 100 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7918 (mm-30) REVERT: p 11 GLU cc_start: 0.7419 (tp30) cc_final: 0.7048 (tm-30) REVERT: p 38 LEU cc_start: 0.8174 (mm) cc_final: 0.7714 (tp) REVERT: p 42 TRP cc_start: 0.8453 (t60) cc_final: 0.8193 (t60) REVERT: p 98 ASP cc_start: 0.7483 (m-30) cc_final: 0.7073 (m-30) REVERT: p 170 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7255 (mtt180) outliers start: 137 outliers final: 107 residues processed: 1068 average time/residue: 0.6066 time to fit residues: 1096.2314 Evaluate side-chains 1081 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 962 time to evaluate : 5.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 409 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 437 HIS Chi-restraints excluded: chain G residue 455 SER Chi-restraints excluded: chain G residue 521 MET Chi-restraints excluded: chain G residue 544 VAL Chi-restraints excluded: chain G residue 587 VAL Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 109 TYR Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain P residue 275 PHE Chi-restraints excluded: chain P residue 341 ASN Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 52 ILE Chi-restraints excluded: chain T residue 56 ASP Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain W residue 119 ASP Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 86 ASP Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain d residue 108 THR Chi-restraints excluded: chain e residue 49 THR Chi-restraints excluded: chain e residue 102 GLU Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 31 GLU Chi-restraints excluded: chain f residue 50 ASN Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 30 MET Chi-restraints excluded: chain h residue 32 THR Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 51 ASN Chi-restraints excluded: chain l residue 53 SER Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain l residue 152 VAL Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 85 ASN Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain o residue 32 GLU Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 25 LEU Chi-restraints excluded: chain p residue 170 ARG Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain r residue 109 GLN Chi-restraints excluded: chain s residue 30 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 667 optimal weight: 1.9990 chunk 702 optimal weight: 4.9990 chunk 641 optimal weight: 0.8980 chunk 683 optimal weight: 0.0010 chunk 411 optimal weight: 1.9990 chunk 297 optimal weight: 0.8980 chunk 536 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 617 optimal weight: 4.9990 chunk 646 optimal weight: 0.8980 chunk 681 optimal weight: 2.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 HIS ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 125 HIS ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 10 ASN m 85 ASN r 72 GLN s 59 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 65326 Z= 0.555 Angle : 1.578 50.753 88506 Z= 1.028 Chirality : 0.316 6.398 9707 Planarity : 0.004 0.069 11070 Dihedral : 9.209 171.834 9485 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.85 % Allowed : 14.77 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % 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: 1.34 (0.10), residues: 7698 helix: 1.82 (0.08), residues: 4247 sheet: -0.21 (0.27), residues: 363 loop : -0.23 (0.11), residues: 3088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 85 HIS 0.005 0.001 HIS R 68 PHE 0.026 0.001 PHE N 292 TYR 0.030 0.001 TYR F 43 ARG 0.009 0.000 ARG E 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 994 time to evaluate : 5.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8413 (tp40) cc_final: 0.7906 (tp40) REVERT: A 85 SER cc_start: 0.8895 (m) cc_final: 0.8563 (p) REVERT: B 126 MET cc_start: 0.8351 (ptm) cc_final: 0.8085 (ttp) REVERT: C 113 GLU cc_start: 0.6361 (mp0) cc_final: 0.6131 (mp0) REVERT: D 105 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.6459 (mtt-85) REVERT: E 15 ASN cc_start: 0.8690 (t0) cc_final: 0.8146 (t0) REVERT: E 18 ASP cc_start: 0.7136 (m-30) cc_final: 0.6708 (m-30) REVERT: E 112 ASP cc_start: 0.7745 (t0) cc_final: 0.7517 (t0) REVERT: E 187 ARG cc_start: 0.6925 (mtt90) cc_final: 0.6566 (mtt90) REVERT: F 212 ASP cc_start: 0.7919 (t0) cc_final: 0.7534 (t0) REVERT: F 248 GLU cc_start: 0.7163 (mp0) cc_final: 0.6450 (mt-10) REVERT: F 279 LEU cc_start: 0.8403 (tt) cc_final: 0.8139 (mt) REVERT: F 324 GLN cc_start: 0.8339 (mm110) cc_final: 0.8018 (mp10) REVERT: F 409 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8301 (m-30) REVERT: F 430 MET cc_start: 0.7901 (mtt) cc_final: 0.7668 (mtt) REVERT: G 135 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.6890 (ptt90) REVERT: G 418 ARG cc_start: 0.7131 (tpp-160) cc_final: 0.6569 (mtm110) REVERT: G 439 PHE cc_start: 0.7270 (t80) cc_final: 0.6824 (t80) REVERT: G 592 LEU cc_start: 0.6582 (mt) cc_final: 0.6073 (mt) REVERT: G 684 MET cc_start: 0.7196 (mmt) cc_final: 0.6829 (mmt) REVERT: H 181 MET cc_start: 0.8867 (mtm) cc_final: 0.8652 (mtm) REVERT: H 277 TYR cc_start: 0.8584 (m-80) cc_final: 0.7991 (m-80) REVERT: J 130 ASP cc_start: 0.8444 (m-30) cc_final: 0.8085 (m-30) REVERT: J 152 MET cc_start: 0.8817 (ttm) cc_final: 0.8442 (tpp) REVERT: K 91 GLN cc_start: 0.8369 (mp10) cc_final: 0.8148 (mp10) REVERT: L 124 PHE cc_start: 0.7313 (t80) cc_final: 0.6898 (t80) REVERT: L 140 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8529 (tt) REVERT: L 247 LEU cc_start: 0.8449 (mp) cc_final: 0.8172 (mt) REVERT: L 340 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7117 (m-80) REVERT: L 352 ASP cc_start: 0.7399 (t0) cc_final: 0.7063 (t0) REVERT: L 397 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7264 (mt-10) REVERT: M 168 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: M 255 LYS cc_start: 0.7390 (mtmt) cc_final: 0.7164 (tmtt) REVERT: M 310 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7755 (ttp) REVERT: N 323 ASN cc_start: 0.7625 (m-40) cc_final: 0.7420 (p0) REVERT: O 2 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6989 (ttp80) REVERT: O 65 ASP cc_start: 0.7548 (t0) cc_final: 0.7282 (t0) REVERT: P 57 MET cc_start: 0.8589 (mmt) cc_final: 0.8304 (mmp) REVERT: P 248 MET cc_start: 0.8095 (mmt) cc_final: 0.7677 (mmm) REVERT: P 263 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.7323 (t80) REVERT: P 275 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: R 92 LYS cc_start: 0.8295 (ttmm) cc_final: 0.7388 (tttp) REVERT: T 47 GLN cc_start: 0.7069 (tm-30) cc_final: 0.6600 (tm-30) REVERT: T 71 MET cc_start: 0.7025 (mmm) cc_final: 0.6423 (mtm) REVERT: W 36 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7372 (mt-10) REVERT: W 126 MET cc_start: 0.6222 (ptm) cc_final: 0.5704 (ptt) REVERT: Y 12 GLU cc_start: 0.6274 (mm-30) cc_final: 0.5899 (mt-10) REVERT: Y 48 ASP cc_start: 0.7274 (m-30) cc_final: 0.6744 (p0) REVERT: Z 9 MET cc_start: 0.8427 (mmm) cc_final: 0.8141 (mmm) REVERT: a 43 TYR cc_start: 0.8475 (t80) cc_final: 0.8176 (t80) REVERT: b 81 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7921 (tttm) REVERT: d 2 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8254 (mtm) REVERT: e 75 MET cc_start: 0.8729 (mmm) cc_final: 0.8306 (mmm) REVERT: e 102 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7291 (pp20) REVERT: f 13 ILE cc_start: 0.8890 (tp) cc_final: 0.8539 (tp) REVERT: f 28 LYS cc_start: 0.6975 (mmpt) cc_final: 0.6524 (mmmm) REVERT: f 31 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6803 (mt-10) REVERT: f 34 THR cc_start: 0.8229 (m) cc_final: 0.7969 (m) REVERT: g 56 MET cc_start: 0.7865 (tmm) cc_final: 0.7458 (tmm) REVERT: g 112 ASP cc_start: 0.8965 (t70) cc_final: 0.8612 (t70) REVERT: h 106 LYS cc_start: 0.8344 (mttm) cc_final: 0.7996 (mttt) REVERT: i 111 GLU cc_start: 0.7977 (mp0) cc_final: 0.7598 (mp0) REVERT: l 7 MET cc_start: 0.8418 (mtt) cc_final: 0.8069 (mtt) REVERT: l 93 THR cc_start: 0.8723 (m) cc_final: 0.8217 (p) REVERT: l 100 MET cc_start: 0.8406 (mtm) cc_final: 0.8063 (mtm) REVERT: l 102 LYS cc_start: 0.8116 (mttm) cc_final: 0.7806 (mtmm) REVERT: m 4 LYS cc_start: 0.7707 (ttmt) cc_final: 0.6675 (ttpp) REVERT: m 27 GLU cc_start: 0.8164 (mp0) cc_final: 0.7804 (tm-30) REVERT: m 111 LYS cc_start: 0.7792 (ttpp) cc_final: 0.6857 (ttmt) REVERT: m 123 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7022 (mtmm) REVERT: n 54 LYS cc_start: 0.8450 (mmmt) cc_final: 0.7878 (mmtp) REVERT: n 57 MET cc_start: 0.7816 (mpp) cc_final: 0.7591 (mmm) REVERT: n 65 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7477 (mt-10) REVERT: o 17 ASP cc_start: 0.8346 (t0) cc_final: 0.7835 (t0) REVERT: o 100 GLU cc_start: 0.8241 (mm-30) cc_final: 0.8007 (mm-30) REVERT: p 11 GLU cc_start: 0.7476 (tp30) cc_final: 0.7074 (tm-30) REVERT: p 42 TRP cc_start: 0.8411 (t60) cc_final: 0.8145 (t60) REVERT: p 98 ASP cc_start: 0.7455 (m-30) cc_final: 0.7181 (m-30) outliers start: 126 outliers final: 98 residues processed: 1069 average time/residue: 0.6462 time to fit residues: 1171.4139 Evaluate side-chains 1079 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 967 time to evaluate : 5.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain F residue 409 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 437 HIS Chi-restraints excluded: chain G residue 455 SER Chi-restraints excluded: chain G residue 521 MET Chi-restraints excluded: chain G residue 544 VAL Chi-restraints excluded: chain G residue 587 VAL Chi-restraints excluded: chain H residue 5 ASN Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 109 TYR Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 577 THR Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 310 MET Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 2 ARG Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain P residue 275 PHE Chi-restraints excluded: chain P residue 341 ASN Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 52 ILE Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain W residue 119 ASP Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 86 ASP Chi-restraints excluded: chain Z residue 140 THR Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 MET Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain d residue 108 THR Chi-restraints excluded: chain e residue 49 THR Chi-restraints excluded: chain e residue 102 GLU Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 31 GLU Chi-restraints excluded: chain f residue 50 ASN Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 30 MET Chi-restraints excluded: chain h residue 32 THR Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 51 ASN Chi-restraints excluded: chain l residue 53 SER Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain l residue 152 VAL Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 85 ASN Chi-restraints excluded: chain m residue 119 LYS Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 25 LEU Chi-restraints excluded: chain r residue 109 GLN Chi-restraints excluded: chain s residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 448 optimal weight: 6.9990 chunk 722 optimal weight: 6.9990 chunk 441 optimal weight: 0.0970 chunk 342 optimal weight: 5.9990 chunk 502 optimal weight: 8.9990 chunk 758 optimal weight: 5.9990 chunk 697 optimal weight: 0.0670 chunk 603 optimal weight: 0.0970 chunk 62 optimal weight: 3.9990 chunk 466 optimal weight: 0.9990 chunk 370 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN F 148 ASN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 ASN ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 273 ASN ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 108 GLN b 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 65326 Z= 0.554 Angle : 1.577 50.733 88506 Z= 1.028 Chirality : 0.315 6.391 9707 Planarity : 0.004 0.071 11070 Dihedral : 9.062 171.298 9485 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.82 % Allowed : 14.91 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % 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: 1.39 (0.10), residues: 7698 helix: 1.85 (0.08), residues: 4246 sheet: -0.13 (0.27), residues: 371 loop : -0.20 (0.11), residues: 3081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 65 HIS 0.005 0.001 HIS R 68 PHE 0.026 0.001 PHE N 292 TYR 0.030 0.001 TYR F 43 ARG 0.009 0.000 ARG E 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 997 time to evaluate : 5.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8402 (tp40) cc_final: 0.7883 (tp40) REVERT: A 85 SER cc_start: 0.8890 (m) cc_final: 0.8551 (p) REVERT: B 126 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8113 (ttt) REVERT: C 113 GLU cc_start: 0.6362 (mp0) cc_final: 0.6136 (mp0) REVERT: D 105 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.6421 (mtt-85) REVERT: E 15 ASN cc_start: 0.8631 (t0) cc_final: 0.8240 (t0) REVERT: E 112 ASP cc_start: 0.7746 (t0) cc_final: 0.7520 (t0) REVERT: F 212 ASP cc_start: 0.7970 (t0) cc_final: 0.7595 (t0) REVERT: F 248 GLU cc_start: 0.7132 (mp0) cc_final: 0.6422 (mt-10) REVERT: F 279 LEU cc_start: 0.8379 (tt) cc_final: 0.8152 (mt) REVERT: F 324 GLN cc_start: 0.8345 (mm110) cc_final: 0.8020 (mp10) REVERT: F 409 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: F 430 MET cc_start: 0.7887 (mtt) cc_final: 0.7674 (mtt) REVERT: G 135 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.6955 (ptt90) REVERT: G 418 ARG cc_start: 0.7118 (tpp-160) cc_final: 0.6567 (mtm110) REVERT: G 439 PHE cc_start: 0.7342 (t80) cc_final: 0.6820 (t80) REVERT: G 592 LEU cc_start: 0.6520 (mt) cc_final: 0.6035 (mt) REVERT: H 277 TYR cc_start: 0.8499 (m-80) cc_final: 0.8004 (m-80) REVERT: H 302 MET cc_start: 0.8417 (ttm) cc_final: 0.8028 (mmm) REVERT: J 130 ASP cc_start: 0.8446 (m-30) cc_final: 0.8093 (m-30) REVERT: J 152 MET cc_start: 0.8782 (ttm) cc_final: 0.8432 (tpp) REVERT: K 91 GLN cc_start: 0.8405 (mp10) cc_final: 0.8186 (mp10) REVERT: L 124 PHE cc_start: 0.7316 (t80) cc_final: 0.6943 (t80) REVERT: L 140 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8535 (tt) REVERT: L 170 GLN cc_start: 0.8412 (tt0) cc_final: 0.8026 (tt0) REVERT: L 247 LEU cc_start: 0.8433 (mp) cc_final: 0.8172 (mt) REVERT: L 340 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7114 (m-80) REVERT: L 352 ASP cc_start: 0.7400 (t0) cc_final: 0.7063 (t0) REVERT: L 397 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7241 (mt-10) REVERT: M 168 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: M 255 LYS cc_start: 0.7378 (mtmt) cc_final: 0.7156 (tmtt) REVERT: O 2 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6990 (ttp80) REVERT: O 65 ASP cc_start: 0.7542 (t0) cc_final: 0.7278 (t0) REVERT: P 57 MET cc_start: 0.8589 (mmt) cc_final: 0.8312 (mmp) REVERT: P 248 MET cc_start: 0.8102 (mmt) cc_final: 0.7677 (mmm) REVERT: P 263 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7402 (t80) REVERT: P 275 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: R 92 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7378 (tttp) REVERT: S 30 GLN cc_start: 0.6931 (tp-100) cc_final: 0.6525 (tp40) REVERT: S 82 SER cc_start: 0.7929 (m) cc_final: 0.7508 (t) REVERT: T 47 GLN cc_start: 0.7052 (tm-30) cc_final: 0.6606 (tm-30) REVERT: T 71 MET cc_start: 0.7054 (mmm) cc_final: 0.6488 (mtm) REVERT: V 109 ASN cc_start: 0.8343 (m110) cc_final: 0.8141 (m-40) REVERT: W 126 MET cc_start: 0.6209 (ptm) cc_final: 0.5700 (ptt) REVERT: Y 12 GLU cc_start: 0.6237 (mm-30) cc_final: 0.5894 (mt-10) REVERT: Y 48 ASP cc_start: 0.7264 (m-30) cc_final: 0.6744 (p0) REVERT: Z 9 MET cc_start: 0.8389 (mmm) cc_final: 0.8120 (mmm) REVERT: a 43 TYR cc_start: 0.8518 (t80) cc_final: 0.8208 (t80) REVERT: b 81 LYS cc_start: 0.8353 (ttmt) cc_final: 0.7928 (tttm) REVERT: d 2 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8248 (mtm) REVERT: e 75 MET cc_start: 0.8757 (mmm) cc_final: 0.8271 (mmm) REVERT: e 102 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7286 (pp20) REVERT: f 13 ILE cc_start: 0.8883 (tp) cc_final: 0.8537 (tp) REVERT: f 28 LYS cc_start: 0.6975 (mmpt) cc_final: 0.6522 (mmmm) REVERT: f 31 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: f 34 THR cc_start: 0.8215 (m) cc_final: 0.7954 (m) REVERT: g 56 MET cc_start: 0.7873 (tmm) cc_final: 0.7470 (tmm) REVERT: g 112 ASP cc_start: 0.8964 (t70) cc_final: 0.8607 (t70) REVERT: h 106 LYS cc_start: 0.8330 (mttm) cc_final: 0.7991 (mttt) REVERT: i 111 GLU cc_start: 0.7985 (mp0) cc_final: 0.7566 (mp0) REVERT: l 7 MET cc_start: 0.8410 (mtt) cc_final: 0.8060 (mtt) REVERT: l 17 GLU cc_start: 0.7969 (mp0) cc_final: 0.7754 (mp0) REVERT: l 93 THR cc_start: 0.8719 (m) cc_final: 0.8218 (p) REVERT: l 100 MET cc_start: 0.8395 (mtm) cc_final: 0.8029 (mtm) REVERT: l 102 LYS cc_start: 0.8104 (mttm) cc_final: 0.7801 (mtmm) REVERT: m 4 LYS cc_start: 0.7644 (ttmt) cc_final: 0.6592 (ttpp) REVERT: m 27 GLU cc_start: 0.8146 (mp0) cc_final: 0.7761 (tm-30) REVERT: m 111 LYS cc_start: 0.7792 (ttpp) cc_final: 0.6853 (ttmt) REVERT: m 123 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7023 (mtmm) REVERT: n 54 LYS cc_start: 0.8372 (mmmt) cc_final: 0.7808 (mmtp) REVERT: n 57 MET cc_start: 0.7813 (mpp) cc_final: 0.7582 (mmm) REVERT: n 65 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7477 (mt-10) REVERT: o 17 ASP cc_start: 0.8334 (t0) cc_final: 0.7820 (t0) REVERT: o 100 GLU cc_start: 0.8219 (mm-30) cc_final: 0.8013 (mm-30) REVERT: p 11 GLU cc_start: 0.7478 (tp30) cc_final: 0.7112 (tm-30) REVERT: p 42 TRP cc_start: 0.8414 (t60) cc_final: 0.8151 (t60) REVERT: p 98 ASP cc_start: 0.7460 (m-30) cc_final: 0.7255 (m-30) outliers start: 124 outliers final: 93 residues processed: 1072 average time/residue: 0.6172 time to fit residues: 1118.1305 Evaluate side-chains 1076 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 969 time to evaluate : 5.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain F residue 409 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 437 HIS Chi-restraints excluded: chain G residue 455 SER Chi-restraints excluded: chain G residue 521 MET Chi-restraints excluded: chain G residue 544 VAL Chi-restraints excluded: chain G residue 587 VAL Chi-restraints excluded: chain H residue 5 ASN Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 109 TYR Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 163 ASP Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 2 ARG Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 263 VAL Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain P residue 275 PHE Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 52 ILE Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain W residue 119 ASP Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 86 ASP Chi-restraints excluded: chain Y residue 114 MET Chi-restraints excluded: chain b residue 14 LYS Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 MET Chi-restraints excluded: chain d residue 87 ASP Chi-restraints excluded: chain d residue 108 THR Chi-restraints excluded: chain e residue 49 THR Chi-restraints excluded: chain e residue 102 GLU Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 25 LEU Chi-restraints excluded: chain f residue 31 GLU Chi-restraints excluded: chain f residue 50 ASN Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 30 MET Chi-restraints excluded: chain h residue 32 THR Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain l residue 3 MET Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 51 ASN Chi-restraints excluded: chain l residue 53 SER Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain l residue 152 VAL Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 119 LYS Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain r residue 109 GLN Chi-restraints excluded: chain s residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 479 optimal weight: 3.9990 chunk 643 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 556 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 604 optimal weight: 5.9990 chunk 253 optimal weight: 0.1980 chunk 620 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 108 GLN b 10 ASN ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.082533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.065239 restraints weight = 100227.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.065895 restraints weight = 70442.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.066094 restraints weight = 56811.293| |-----------------------------------------------------------------------------| r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 65326 Z= 0.566 Angle : 1.583 50.745 88506 Z= 1.030 Chirality : 0.316 6.406 9707 Planarity : 0.004 0.072 11070 Dihedral : 9.068 171.727 9485 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.81 % Allowed : 15.05 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % 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: 1.36 (0.10), residues: 7698 helix: 1.82 (0.08), residues: 4238 sheet: -0.19 (0.27), residues: 369 loop : -0.20 (0.11), residues: 3091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 85 HIS 0.006 0.001 HIS X 76 PHE 0.026 0.001 PHE L 124 TYR 0.028 0.001 TYR F 43 ARG 0.009 0.000 ARG E 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15889.75 seconds wall clock time: 279 minutes 45.91 seconds (16785.91 seconds total)